Software:labsoft
Also see Tutorial
https://biomolmd.org/mw/index.php/Tutroial:alltut
3D molecule builder
Free software for building and modifying chemical structure in 3D
Avogadro
* can build polypeptide, nucleic acids using Insert function * cheap structural optimization & energy minimization using GAFF, MMFF, UFF etc
iqmol
* Can build using common chemical groups and fragments * Geometry optimizaiton using Qchem server (or our own server on water.bme.utexas.edu)
Arguslab
- Has built-in semi-empirical and simple force field optimization.
- Nive building function (polypeptides are easy)
- No longer supported. Sometimes crashes.
ACD labs
Academic version: http://www.acdlabs.com/resources/freeware/chemsketch/
ForceBalance
Installation files: ~pren/forcebalance-installation/
to Update: svn update
run on node100 and beyond to install:
source ~pren/.cshrc.force python setup.py install --prefix=/home/pren/forcebalance
replace the last PATH to your desired path (or just use mine) Won't work on bme-nova or water (too old).
Check python: python -c 'import sys; print sys.path'
How did I compile python 2.7 (not able to do yum on old nodes): python 2.7
Tutorial and example how to fit liquid and gas-phase dimer energy is in /Users/pren/Dropbox/RESEARCH/AMOEBA/AMOEBA-halogen/leeping/CondensedPhase_Update_03-07
pymol
Linux
Try this first: /opt/software/CHEM/pymol2016/pymol Official installation guide
http://www.pymolwiki.org/index.php/TOPTOC
64 bit on Centos 6.6
/opt/software/CHEM/pymol64/pymol/pymol
Can be run on biomol, bme-venus, bme-pluto, bme-neptune and bme-saturn.
http://www.pymolwiki.org/index.php/User:Tlinnet/Linux_Install
replace the fist wget:
wget http://download.fedoraproject.org/pub/epel/6/i386/epel-release-6-8.noarch.rpm
http://www.tecmint.com/how-to-enable-epel-repository-for-rhel-centos-6-5/
After install all the rpms, don't need to installpymol.sh, just run
/opt/software/CHEM/pymol64/pymol/pymol
Run this before pymol if need MPEG support
/opt/software/CHEM/pymol64/pymol/pymolMPEG.sh
pymol prebuild
Download from here: http://biomol.bme.utexas.edu/~pren/courses/bme346-soft/
http://biomol.bme.utexas.edu/~pren/courses/bme346-soft/archive/ (linux)
These educational version has no Ray tracing ability
pymol on windows (with Ray Tracing)
http://tubiana.me/how-to-install-and-compile-pymol-windows-linux-mac/
From this site: http://www.pymolwiki.org/index.php/Windows_Install
Download the 4 files (*.whl) below from http://www.lfd.uci.edu/~gohlke/pythonlibs/#pymol
Open a CMD windows as admin, cd Downloads\ and run the following (if you install 64 bit pythin, you may need download 64 bits for below as well)
C:\Users\macbook12\Downloads>C:\Python27\python.exe pip-8.1.2-py2.py3-none-any.whl/pip install pip-8.1.2-py2.py3-none-any.whl C:\Users\macbook12\Downloads>C:\Python27\python.exe pip-8.1.2-py2.py3-none-any.whl/pip install "numpy-1.11.1+mkl-cp27-cp27m-win32.whl" C:\Users\macbook12\Downloads>C:\Python27\python.exe pip-8.1.2-py2.py3-none-any.whl/pip install Pmw-2.0.1-py2-none-any.whl C:\Users\macbook12\Downloads>C:\Python27\python.exe pip-8.1.2-py2.py3-none-any.whl/pip install pymol-1.7.6.0-cp27-none-win32.whl
Create a folder from command line (this allows you to write output etc in your own folder)
mkdir %HOMEPATH%\pymol
Make a shortcut to C:\pthyon29\scripts\pymol (right click) and move it to above folder.
Right click the shortcut and select “properties”, change the “starts in” filed to %HOMEPATH%\pymol You can rename the shortcut to mypymol.cmd or anything you like.
Math
Matlab
Matlab is available on water (linux) and bme-black (windows)
Chemistry
pubchem
Here you can download the 3D structure quickly of known compounds. Or smile string, 2d structure etc. http://pubchem.ncbi.nlm.nih.gov
logP
You can enter the smile string and it predicts the logP. It'll be useful to screen for bioavailability. It is a quick empirical prediction. You can get the smile string from pubchem or babel.
http://www.molinspiration.com/services/logp.html http://www.molinspiration.com/cgi-bin/properties --
add H to proteins based on predicted pKa
To add H to proteins based on predicted pKa
1. Use PROPKA and PDB2PQR to add hydrogens to your x-ray structure:
PDB2PQR: http://pdb2pqr.sourceforge.net/ http://www.poissonboltzmann.org/ PROPKA: http://propka.ki.ku.dk/
2. H++ http://biophysics.cs.vt.edu/index.php
Openeye
We have academic license for a suite of software from openeye forsimilarity search, docking, molecular conformation generation (2d to 3d conversion) etc.
2016-2018
REHL 6 version, including fastroc on GPU
/opt/software/CHEM/openeye2016/openeye/
Source /opt/software/CHEM/openeye2016/openeye/bashrc
See /opt/software/CHEM/openeye2016/openeye/readme for fastroc on GPU example.
2013 edition
You can only run the new openeye software on RHEL5 or centos5, which means water.bme.utexas.edu or bme-nova. The license file is in /opt/openeye/license/ which expires in Aug 2013.
Set up bashrc:
export OE_LICENSE=/opt/openeye/license/oe_license.txt export OE_DIR=/opt/openeye/RHEL5/openeye/ export PATH=/opt/openeye/RHEL5/openeye/bin:$PATH
That should be it...Try type "rocs"
tutorial
ROCS and eon
similarity search
old version
How do I install the license file (/opt/openeye/license)? Place the license file named oe_license.txt in the OpenEye directory and define the environme nt variable OE_LICENSE to point to the location of the license file.
On windows the envir var can be set up for $OE_DIR (see below). The oe_license.txt should be located under the $OE_DIR. On WinXP/Vista/Windows7, use Start->Settings->Control Panel->System->Advanced->Environment Va riables
- How do I install my license file oe_license.txt on linux?
License files should be defined by environment variable $OE_LICENSE. It is recommended that t hese files be located at OE_DIR=/usr/local/openeye/etc/oe_license.txt. License files can also
be used if named oe_license.txt and either (1) present in the current working directory or (
2) present in the directory defined by environment variable $OE_DIR. However, these methods a re not as reliable and not generally recommended.
/usr/local/openeye/ $OE_DIR /usr/local/openeye/etc/oe_license.txt $OE_LICENSE
NIH online tool
- Convert molecular name to structure using URL
- Convert smile to PDB etc, 2d to 3D using Corina.
openbabel
Latest openbabel 3.1 is installed cluster wide:
/opt/software/openbabel311/bin/obabel
Add to your path in bashrc or cshrc and you can use this "obabel" in any node or WS.
A great chemoinformatics tool, for converting files from one format to another and now generate 3D structure for molecule. Available on linux, window and Mac osx.
Now support 2d to 3d conversion
-rwxr-xr-x. 1 root root 43920 Dec 20 15:50 obabel -rwxr-xr-x. 1 root root 30224 Dec 20 15:50 obconformer -rwxr-xr-x. 1 root root 34752 Dec 20 15:50 obenergy -rwxr-xr-x. 1 root root 39600 Dec 20 15:50 obfit -rwxr-xr-x. 1 root root 39408 Dec 20 15:50 obfitall -rwxr-xr-x. 1 root root 35432 Dec 20 15:50 obgen -rwxr-xr-x. 1 root root 34416 Dec 20 15:50 obgrep -rwxr-xr-x. 1 root root 35736 Dec 20 15:50 obminimize -rwxr-xr-x. 1 root root 43896 Dec 20 15:50 obmm -rwxr-xr-x. 1 root root 40776 Dec 20 15:50 obprobe -rwxr-xr-x. 1 root root 39832 Dec 20 15:50 obprop -rwxr-xr-x. 1 root root 39576 Dec 20 15:50 obrotamer -rwxr-xr-x. 1 root root 34024 Dec 20 15:50 obrotate -rwxr-xr-x. 1 root root 81104 Dec 20 15:50 obspectrophore -rwxr-xr-x. 1 root root 29264 Dec 20 15:50 obsym -rwxr-xr-x. 1 root root 30072 Dec 20 15:50 obtautomer -rwxr-xr-x. 1 root root 29480 Dec 20 15:50 obthermo -rwxr-xr-x. 1 root root 29184 Dec 20 15:50 roundtrip -rwxr-xr-x. 1 root root 29704 Dec 20 15:50 test_inchiwrite -rwxr-xr-x. 1 root root 975472 Dec 20 15:50 test_runner
See here for detailed description: http://openbabel.org/wiki/Guides
obabel -L formats list all formats supported (including read Gaussian fchk and output so you can convert other format such as pdb for visualization).
The installation source files are in /opt/openbabel-2.2.0/ or /opt/software/CHEM/openbabel/
Computational Chemistry
Tips about setting memory disk etc
QM jobs are usually highly demanding of CPU, memory and disk. It is important to set the limit properly in the input file.
In Gaussian for example, you can do so by
%NProc=8 or %CPU=8 (in Gaussain 16) %Mem=15000MB %Chk=ccb.chk #MP2/aug-cc-pvtz Density=MP2 MaxDisk=150GB
Gaussian 16 manual (some keywords changed) https://gaussian.com/running/?tabid=6 & https://gaussian.com/link0/
These limits should be less than what is available/free on the specific node. You can find out these information on Linux by using these commands:
nproc #number of threads (2x no of cores) free -g # memory usage df -h # disk space usage (look for /scratch)
You should not use more than 8-12 threads for each QM job due to the poor parallel salability.
"df -h" to check available scratch disk space. Your MaxDisk should be much less than (e.g. 50%; even less if there other jobs running on the same node) available since others may need the scratch disk too. DO NOT STRESS the node or it will slow down everyone. If your QM job crashes, you will need manually clean the /scratch disk (you could use a script to run jobs/clean afterwards).
"free -g" output changed from centos 6 to 7.
[pren@node41 ~]$ free -g
total used free shared buffers cached
Mem: 31 14 16 0 0 11
-/+ buffers/cache: 2 28
Swap: 15 1717986918 15
Above is Centos 6 (3 rows)ouput. the "-/+buff" number under free (28 GB) is what's available
[pren@node64 ~]$ free -g
total used free shared buff/cache available
Mem: 31 10 4 0 16 20
Swap: 15 0 15
Above is centos 7 (two rows). The "20" GB under "available" is the number (or less) you should use for %mem
Gaussian
Gaussian 16
Latest as of 2019
To use the latest Gaussian: “g16 myjob.com” (basically replace g09 with g16).
But first you need to create and source this file (if csh):
setenv g16root "/opt/software/Gaussian16/bin/avx" setenv GAUSS_SCRDIR "/scratch" source $g16root/g16/bsd/g16.login
If bash:
g16root="/opt/software/Gaussian16/bin/avx" GAUSS_SCRDIR="/scratch" export g16root GAUSS_SCRDIR . $g16root/g16/bsd/g16.profile
Gaussian 16 tutorial
Input syntax: case-insensitive, free-format (sensitive to blank lines). Space, comma and tab can be used as a delimiter. All keywords and options may be shortened to their shortest unique abbreviation. Keyword and options:
keyword = option keyword(option) keyword=(option1, option2, …) keyword(option1, option2, …)
%rwf=/scratch/Gau-water/,60GB %chk=water.chk ! Link 0 section. Output and resource specification %mem=8GB %nproc=8 # MP2/6-31G(d) ! Route section. End with a blank line water energy ! Title section. End with a blank line 0 1 ! Molecule specification. End with a blank line O -0.464 0.177 0.0 H -0.464 1.137 0.0 H 0.441 -0.143 0.0
Output files: *.out or *.log (energy, coordinates, frequencies, ...). *.chk (electron density and other information; can be read by other programs)
The energy can be found in the output file in the format
SCF Done: E(RB3LYP) = ### A.U. after ## cycles
A successfully finished job ends with the line
Normal termination of Gaussian XXX
Types of computation: sp (default, single point calculation), opt (geometry optimization), freq (frequency), polar (polarizability)
Computational methods (in general order of increasing accuracy and cost): HF, DFT methods (B3LYP, wB97XD), MP2, CCSD(T). For transition metal ions, restricted open-shell wavefunctions may be needed. Preface the keywork by RO, e.g. ROHF. Implicit solvation (SCRF).
Basis sets:
6-31G, 6-31+G(d), 6-311++G(2d,2p) ...
def2TZVPP, def2QZVPP, ...
cc-pVTZ, aug-cc-pVQZ, aug-cc-pV5Z, ...
Gen (user-specified basis set. Useful for hybrid basis sets and for some transition metals)
Basis set extrapolation. The energy typically decreases with increasing size of the basis set. Assuming a simple relationship between the energy and the size of basis set, such as E(n) = E(CBS) + K/n or E(n) = E(CBS) + exp(-A*n), one can do extrapolation to obtain E(CBS). n is the number of zetas in cc-pV*Z basis set. Of course, the larger basis sets are used as input, the better the interpolation results are. (https://doi.org/10.1021/acs.jctc.5b00267)
Single point calculation
The interaction energy between fragments. Counterpoise correction (basis-set superposition error).
# B3LYP/6-31G(d) Counterpoise=2 Counterpoise on water dimer 0,1 0,1 0,1 O(Fragment=1) 0.00 0.00 0.00 H(Fragment=1) 0.49 0.76 -0.29 H(Fragment=1) 0.49 -0.76 -0.29 O(Fragment=2) 0.00 0.00 2.98 H(Fragment=2) -0.91 0.00 3.24 H(Fragment=2) -0.01 0.00 2.03
Geometry optimization Optimization with restraint on cartesian coordinate (X), bond (B), angle (A) or dihedral (D).
%chk=Asp-090-000.chk %nproc=12 %mem=50GB # opt=ModRedundant freq b3lyp/6-31g(d) scrf=pcm nosymm ! Geometry optimization with redundant internal coordinate, followed by frequency calculation Ace-Asp-NMe -1 1 C -0.051237 0.026635 -0.000187 C -0.047739 -0.050718 1.518390 O 1.019569 -0.121175 2.135311 H -1.074728 0.094187 -0.430415 H 0.437648 -0.877255 -0.425686 H 0.518496 0.921014 -0.335147 N -1.258811 -0.011713 2.130962 C -1.492666 -0.118061 3.568820 C -1.021236 -1.406075 4.262506 H -2.112694 -0.008704 1.555853 O -0.872499 -1.416891 5.492335 H -0.814136 0.646375 4.025748 C -2.942279 0.313077 3.948700 C -4.058922 -0.713527 3.975701 O -3.832849 -1.916173 3.694369 O -5.221538 -0.313729 4.245555 H -2.888069 0.717014 4.990238 H -3.258114 1.180766 3.321244 N -0.758839 -2.493440 3.494647 C -0.287386 -3.768629 3.978826 H -0.964272 -2.486848 2.487606 H 0.203785 -4.348693 3.168012 H -1.127920 -4.384617 4.365829 H 0.452648 -3.653697 4.800493 D 7 8 13 14 F ! This Dihedral angle is fixed during optimization D 8 13 14 15 F D 2 7 8 9 F D 7 8 9 19 F
If the restraint is specified correctly, you will see the output
! D9 D(3,2,7,8) -6.5623 estimate D2E/DX2 ! ! D10 D(3,2,7,10) -171.5371 estimate D2E/DX2 ! ! D11 D(2,7,8,9) -60.0011 Frozen ! ! D12 D(2,7,8,12) 51.2325 estimate D2E/DX2 ! ! D13 D(2,7,8,13) 165.3165 estimate D2E/DX2 !
The coordinates in each iteration start with the line "Standard orientation" or "Input orientation" depending on the setting.
Standard orientation:
---------------------------------------------------------------------
Center Atomic Atomic Coordinates (Angstroms)
Number Number Type X Y Z
---------------------------------------------------------------------
1 6 0 -3.158798 -1.400996 -1.145889
2 6 0 -2.360207 -0.768947 -0.008899
3 8 0 -2.910645 -0.063771 0.836128
Convergence criteria. Sometimes it's ok that the Force convergence is met but the displacement convergence is not.
Item Value Threshold Converged? Maximum Force 0.000028 0.000450 YES RMS Force 0.000005 0.000300 YES Maximum Displacement 0.001759 0.001800 YES RMS Displacement 0.000433 0.001200 YES
Check frequencies to make sure minimum energy point is reached. If there is (large) negative frequency, it means the maximum point on a concave curve.
Harmonic frequencies (cm**-1), IR intensities (KM/Mole), Raman scattering
activities (A**4/AMU), depolarization ratios for plane and unpolarized
incident light, reduced masses (AMU), force constants (mDyne/A),
and normal coordinates:
1 2 3
A A A
Frequencies -- -29.6237 28.3840 40.0446
Red. masses -- 9.3990 5.7633 3.4850
Frc consts -- 0.0049 0.0027 0.0033
IR Inten -- 5.0560 10.5798 1.2347
Atom AN X Y Z X Y Z X Y Z
1 6 -0.10 0.00 0.09 -0.15 0.14 0.03 -0.11 -0.06 0.09
2 6 -0.04 0.03 0.03 -0.07 0.05 0.02 -0.06 -0.04 0.04
3 8 0.02 0.12 -0.01 0.00 0.06 0.06 -0.04 -0.11 0.11
4 1 -0.18 -0.12 0.18 -0.24 0.08 0.03 -0.02 0.16 -0.14
Gaussian 09
The csh source file is ~pren/.g09gh
This version can use multiple CPU cores. See ~pren/QuantumMechanics/gaussian-test/ for examples.
If you source it and see permission error, this is because the files in /opt/g09gh/... are only readable/executable by users in "users" group. Change the group and passwd files accordingly (by admin). Log out and log back in!
Change the source file to bash if you are using bash.
Below is obsolete.....(as of Aug 2015)
If you see an error about out of space but you are sure you are, try this (as root): echo 0 > /proc/sys/kernel/randomize_va_space
Before we have g03 compiled using pgi 32 bit. As a results we can not use more than 2G memory, but we can use multiprocessors on the same node. To use this version, you need these lines in your .cshrc or in a separate file and source before you run.
setenv PGI /usr/pgi setenv g03root /opt source $g03root/g03/bsd/g03.login.pgi setenv GAUSS_SCRDIR /scratch
We now have the 64-bit intel compiled version. We can use as much as memory you like with it, BUT NO MULTIPROCESSOR. Still this single cpu version will be faster than the previous version using multiprocessors.
source /opt/intel/cce/10.1.011/bin/iccvars.csh source /opt/intel/fce/10.1.011/bin/ifortvars.csh setenv g03root /opt/gaussian source $g03root/g03/bsd/g03.login setenv GAUSS_SCRDIR /scratch
The intel version is not necessarily faster since you can’t use multiple processor as the old PGI version.
You can only use the intel version of Gaussian on bme-sun and cluster nodes, which have fedora 7 OS. It does not work on nodes 16-18 , however, since they have AMD processors. Source ~pren/.g03.intel and you can start using g03.
If you upgraded your OS on your workstation, you can’t use the old PGI version of g03 on your workstation. But you should be able to continue to use it on our cluster. Your previous .cshrc should continue to work. You may also try source ~pren/.g03.pgi
You can take a look at the two files .g03* to see the difference.
Each software is compiled for specific OS environment so you should expect many things will be broken when you mess with your workstation.
Also you probably can’t switch from one to another without logging out your shell, which resets your environmental variables.
You need to set maxdisk=1000MW (example) in the gaussian input (if you have an error of memory allocation, try not specify %chk in your input, and delete all the temp files before you restart) You need a directory /scratch. This may not be created on new workstation yet You need /usr/pgi to use the pgi 32 bit version Remember to clean /scratch aftewards but watch out that you don't delete files belong to others
On fedroa 10, we need glibc 386 library to run PGI (/lib/ld-linux.so.2). cd /opt/fedora-iso/fc10-rpms rpm -Uvh glibc-2.9-3.* glibc-*-2.9-3.x86_64.rpm ALso need /usr/pgi and /scratch
Psi4
(Last update: Sept. 18, 2019 by Chengwen)
Psi4 is a Python/C++, Open source, quantum software package that can be run as
- An executable on command line
- Python module in python script
To run on command line, log in to one of the nodes with big memory/disk
node35, node36, node37, node38, node51, node52, node54, node56, node59, node70, node83
Then source this file and you are ready to run psi4 jobs
source /home/liuchw/.bashrc.psi4conda
A tutorial on the input files and how to run psi4 can be found here: https://leucinw.github.io/home/tutorial/2019/08/02/tut-psi4.html
jmol
can view Gaussian and many other format; make small molecules.
/opt/software/CHEM/jmol-13.2.3/jmol.sh
Avogadro
Installed on bme-earth (2/2014). "ssh -X bme-earth" and the "avogadro".
Avogadro is a free, open source, cross-platform molecular editor designed for flexible use in computational chemistry, molecular modeling, bioinformatics, materials science, and related areas. Packages are available for Mac OSX, Windows and Linux, as well as source code provided under the GNU GPL.
Can built peptides etc.
To download: http://avogadro.openmolecules.net/wiki/Get_Avogadro
Gabedit
Read and visualize Gaussian, Gamess, Mopac, molpro... file (first structure and last structure in optimization). Runs on Linux!
/opt/software/CHEM/Gabedit/gabedit
To visualize (gaussian optimized) structure, click on menu "Geometry" and then "draw" right click on black window and select read ....
MS Windows
FreeCommander: Free file manager. Alternative to total commander. Dual panels. Capable of synchronization and compare directories. Download: http://www.freecommander.com/
Visualization:
Facio
2/2007 Jenny
There is a new visulization software Facio available, which is publicly available at no charge. You can download it for your windows machine from the website. Although Facio is a native application of Windows environment, it can work on Linux with the help of WINE, which we have already. To download the software for your WINDOWS machine and know more about the software, please visit this website:
http://www1.bbiq.jp/zzzfelis/Facio.html
To use facio on your workstation without vmware or remote access, please place the following alias in your .cshrc file
alias facio "/opt/cxoffice/bin/wine /opt/software/Facio1081/Facio.exe"
It is an OpenGL-based graphics program for molecular modeling and visualization of quantum chemical calculations(GAUSSIAN and GAMESS), so it is easy to write the GAUSSIAN input file, view the output for optimized Geometry or load checkpoint file etc. It can also load TINKER xyz,PDB...format files. I am also attaching the manual on this email for your reference.
Jchem and Marvin
http://www.chemaxon.com/products.html visualization, pka, logP, logD, 2D to 3D, fragmentation and many other usages.
- Windows: Version 5.3 installed on bme-mercury OBSOLETE
- Linux: Version 5.2 (11/2009)
To access, put “/opt/software/CHEM/ChemAxon5.2/JChem/bin” in your path, and add the following environmental variable in your .cshrc file
setenv CHEMAXON_LICENSE_URL /opt/software/CHEM/chemaxon/license.cxl
You can then use ChemAxon software For example type "mview /opt/database/known_drug/cmc20021_he.mol2"
I have installed a very useful Jchem package (http://www.chemaxon.com/products.html)
To access, put “/opt/software/CHEM/ChemAxon/JChem/bin” in your path, and add the following environmental variable in your .cshrc file
setenv CHEMAXON_LICENSE_URL /opt/software/CHEM/chemaxon/license.cxl
Now you can use the executables in bin on your worksrtation: mview can let you view a database of small molecules, for example:
“mview /opt/database/kinase-biogen/ligands_4pengyu.sdf” You can clean up and convert 2d structure to 3d structure using Edit/clean/3d …
Msapce let you viz PDB structure of proteins. Msketch let you draw a new molecule
Mview read gaussian output file.
To install on your windows/linux computer, you can use the installation file in /opt/software/CHEM/chemaxon/ (note chemaxon and ChemAxon are two different directories). Copy the license.cxl into /User/yourusername/chemaxon (to make the new folder chemaxon yourself) for vista. For XP, create the same directory in user directory and copy the license file.
vmd
Since vmd186 is not functioning correctly on Linux workstation, you may want to use vmd 1.8.5 (type plain vmd) for now. To use the rmsd plot function, create a file .vmdrc in your home directory with the following content:
lappend auto_path {/usr/local/lib/vmd/plugins/noarch/tcl/rmsdtt} vmd_install_extension rmsdtt rmsdtt_tk_cb "WMC PhysBio/RMSDTT" menu main on
For admin: To install vmd, cd into /opt/vmdxxx/, run “configure LINUXAMD64 OPENGL”, and the cd ./src and “make install”.
Simulation: GROMACS
Installation (updated 8/20/2014)
Installed under /opt/, can run on all nodes.
- /opt/gromacs-4.5.3-mpi/bin
- /opt/gromacs-4.5.3-intel/bin (need source ~pren/.cshrc.f13)
- /opt/gromacs-4.5.4/bin
Add /opt/gromacs-4.5.3-mpi/bin to your path (cshrc or bashrc) to use the executables.
In gromacs-4.5.3-mpi/bin mdrun_mpi is that one does mpi parallel simualtions, mdrun is serial.
- General Instruction: http://ccmst.gatech.edu/wiki/index.php?title=GROMACS *
- On nova fftw (3.2.4) was built by mike in /opt/fftw, copied to in /usr/local on NOVA
- On nodes fftw (3.2.4) was installed through yum, in /usr/lib64 (single, double, long double)
- How mike compiled /opt/gromacs-4.5.4: /home/schnied/Software/gromacs-4.5.4/config.log
- Here is how I compiled gromacs-4.5.3-mpi on NOVA (fftw is in /opt/fftw)
- Use intel compiler 10: source /opt/intel/fce/10.0.023/bin/ifortvars.csh; source /opt/intel/cce/10.0.023/bin/iccvars.csh
- cd /home/pren/gromacs/gromacs-4.5.3
- make clean
- ./configure --enable-mpi --program-suffix=_mpi --enable-float --with-fft=fftw3 CPPFLAGS=-I/opt/fftw3/include LDFLAGS=-L/opt/fftw3/lib --prefix=/home/pren/gromacs/gromacs-4.5.3
- Note the enable-float (single precision) was used for fftw so it should be used for gromacs to be consistent
- make -j 6; make install
- I then copied everything to /opt/gromacs-4.5.3-mpi
- How to compile gromacs-4.5.3-intel using intel compiler (v13) and mkl (2013) fftw on NOVA
- reference: http://www.hpcadvisorycouncil.com/pdf/GROMACS_Best_Practices.pdf
- make clean
- source ~/.cshrc.f13
- ./configure --enable-mpi --with-fft=mkl CC=icc F77=ifort CXX=icpc --program-suffix=_mpi --prefix=/home/pren/gromacs/gromacs-4.5.3
- make -j 4
- make install
- copy to /opt/gromacs-4.5.3-intel
- To run mdrun_mpi etc on nodes, source ~pren/.cshrc,f13
- If you run mdrun_mpi and see error related fftw3f library not found, that is because fftw library is not installed in /usr/lib64 (yum install fftw* should solve this)
Check Gromacs WIKI following the link below
http://wiki.gromacs.org/index.php/Main_Page
Quick Guide
~/gromacs/parallel/bin/pdb2gmx -f prozn.pdb -o prozn -ff oplsaa -p prozn.top -ter ~/gromacs/parallel/bin/editconf -f prozn.gro -o proznw.gro -d 0.8 -bt octahedron cp prozn.top proznwat.top ~/gromacs/parallel/bin/genbox -cp proznw.gro -cs spc216 -o proznwat.gro -p proznwat.top
// any constraints, rstarin put right behind the itp in top file.
~/gromacs/parallel/bin/grompp -v -f em -c proznwat.gro -o em -p proznwat.top ~/gromacs/parallel/bin/mdrun -v -s em.tpr -o em.trj -c after_em -g emlog
mpdboot -n 4 -f ./mpd.hosts --ncpus=2
~/gromacs/parallel/bin/grompp -v -f md -o md -c after_em -p proznwat.top -shuffle -np 8
- in case refined with short no-constraint md
~/gromacs/parallel/bin/grompp -v -f md -o md -c after_md0 -p proznwat.top -shuffle -np 8
restart from the last frame (or given time, see grompp): ~/gromacs/parallel/bin/grompp -v -f md -o md -c after_md.gro -t md.trj -p proznwat.top -shuffle -np 2
mpirun -n 2 mdrun_mpi -v -e md -s md.tpr -o md.trj -c after_md.gro -g md.log > & md.job &
- mpirun -n 2 ~pren/gromacs/parallel/bin/mdrun_mpi -v -e md -s md.tpr -o md.trj -c after_md.gro -g md.log > & md.job &
trjconv -f md.trj -o movie.pdb -n now.ndx -s md -b 1 -e 100 -skip 1
make_ndx -f after_md.gro -o now.ndx
1 | 12 | 13 | 14
make index to creat new index
a 1-10 //a group of atoms from 1-10
name 17 pep // rename group 17
1 & ! pep // a group with all protein atoms except 1-10 (pep)
Running mpi
If you see an error related to "libmpich.so.1.2:" not found, add the mpich2 lib path
setenv LD_LIBRARY_PATH "/opt/mpich2-fc13-p26/lib/:/opt/software/CHEM/openbabel-2.3.0/lib:"{$ATLAS}
Benchmarks
Here are some observations for Kinase system (38772 atoms) using our own cluster from node18 to node30.
Using 8 , the speed is 2.54 ns/day. Using 12 , the speed is 3.14 ns/day. Using 15 , the speed is 3.38 ns/day. The scaling become worse beyond 20, the speed is lower than 1ns/day.
GPU nodes
hostnames
gpu nodes
run "bash"
Source /usr/local/bash/bashrc.amber or /usr/local/bash/bashrc.openmm before use. If has error (esp amber), please try different /opt/software/bash/bashrc.amber.*
installation
We already has Canopy version pythin2.7 but If need to install python: http://toomuchdata.com/2014/02/16/how-to-install-python-on-centos/
- Centos 6.5
node2xxx mount -t nfs 10.0.0.200:/opt /opt mkdir ~/.ssh cp -r /opt/system-setup/rootssh2013/* ~/.ssh restorceon -R ~/.ssh node-setup.sh
- yum update
reboot
- install nvidia graphics driver: /opt/nvidia/NVIDIA-Linux-x86_64-343.22.run
reboot
- Install both nvidia cuda toolkit:
updated:7.5 is latest for OpenMM /opt/nvidia/cuda_6.5.14_linux_64.run (say No to nvidia driver) /opt/nvidia/cuda_6.0.37_linux_64.run (say yes to obsolte/uncompatible and No to nvidia driver)
- Install gdk_ in /opt/nvidia (2016 August: this is now necessary for new stuff Jay put in for detecting GPU automatically)
- mkdir /usr/local/bash
ln -s /opt/software/bash/.bashrc.amber bashrc.amber (newer CPU) ln -s /opt/software/bash/.bashrc.amber.earth bashrc.amber (older CPU)
Run bash; source /opt/software/bash/.bashrc.amber.earth; cd /opt/software/amber14-gpu-earth/test/cuda/dhfr/; ./Run.dhfr.ntb2_ntt1.my
(If you are using different source, go to the corresponsing amber dir)
If this bombs, have to make a copy of the amber-14-gpu, and recompile for that CPU (see amber-GPU below)
Install openMM - Don't have to, just need to link openmm to usr/local/openmm, SEE BELOW
source /opt/software/bash/.bashrc.openmm /opt/software/OpenMM6.1-Linux64/install.sh (this install precompiled opemm into /usr/local and /opt/software/python27
OpenMM-GPU setup
- Yum update your cents 6.5 and reboot
- Install nvidia driver in /opt/nvidia/NVIDIA-Linux-x86_64-343.22.run
- Install nvidia toolkit (opt/nvidia/cuda_6.5xxx cuda_6.0 for openMM6.1 on node201-207) to /usr/loca/ and skip the driver installation (already done above)
Cuda 6.5 required for gtx970 on node210.
- install python 2.7 from Canopy into /opt/software/python27/ (python27-780 for GTX780, openmm6.1 on node201-207)
~pren/canopy-1.4.1-rh5-64.sh this step is already done, no need to repeat for new computers
- Do one of the following (1-3, 2 or 3 is the latest)
- test
- Notes: OpenMM python: /opt/software/python27/appdata/canopy-1.4.1.1975.rh5-x86_64/lib/python2.7/site-packages/simtk/openmm/app
/home/pren/forcebalancev2/lib/python2.7/site-packages/forcebalance/openmmio.py
AMBER-GPU
Run AMBER-GPU
September 2017
node70 to 100
source /home/pren/amber-git/amber17/bashrc.amber16
Install AMBER-GPU
September 2017 --Chengwen
Compile Amber18-gpu for new gpu nodes (node70 to 100)
1. Install cuda7.0 from /opt/nvidia/ (Caution: do NOT install graphic driver)(root)
2. Copy amber file from /home/pren/amber-git:
cp -r /home/pren/amber-git/amber /home/liuchw/
3. Set environmental variables:
source /opt/intel/composer_xe_2013.2.146/bin/compilervars.sh intel64
export AMBERHOME=/home/liuchw/amber
export PATH=$PATH:/usr/local/cuda-7.0/bin
export LD_LIBRARY_PATH=/usr/local/cuda-7.0/lib64:${LD_LIBRARY_PATH}
export LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:$AMBERHOME/lib
export PATH=$PATH:/opt/mpich2-1.4.1p1/bin/mpicc/
export CUDA_HOME=/usr/local/cuda-7.0
export DO_PARALLEL='mpirun -np 1'
4. Configure and install
cd $AMBERHOME ./configure -cuda -mpi -noX11 intel make install
5. Copy the compiled whole directory to /opt/software/ (root)
cp -r amber /opt/software/amber18-gpu
6. Change $AMBERHOME to /opt/software/amber18-gpu
Install CPU version
See /home/pren/amber-git/readme for installation notes
Serial version: /home/pren/amber-git/amber17/ambercpu Parallel version: /home/pren/amber-git/amber17/ambercpu-mpi
Before running jobs (e.g. mmpbsa.py) source bashrc.ambercpu or bashrc.ambercpumpi
September 2014
compiled Amber14-gpu from /home/pren/amber12-2013/
First, install CUDA software AND drivers from NVIDIA website. You should be able to confirm CUDA is installed by running the test /usr/local/bin/deviceQuery or nvidia-smi. You need to define the following environment variables. AMBERHOME and CUDA_HOME need to be defined. Also, the library_path needs to be defined for amber and mpich2. Make sure that a compatible version of python is defined as well. Example:
source /opt/intel/composer_xe_2013.2.146/bin/compilervars.sh intel64
export PATH=$PATH:/usr/local/cuda-6.5/bin
export LD_LIBRARY_PATH=/usr/local/cuda-6.5/lib64:$LD_LIBRARY_PATH
export AMBERHOME=/opt/software/amber14-gpu
export LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:$AMBERHOME/lib
export LD_LIBRARY_PATH=/opt/mpich2-1.4.1p1/lib/:$LD_LIBRARY_PATH
alias python=/usr/bin/env\ python2.6
export PYTHONPATH=/usr/bin/python2.6
export PATH=/opt/mpich2-1.4.1p1/bin/mpicc/:/opt/mpich2-1.4.1p1/bin:$PATH
export CUDA_HOME=/usr/local/cuda-6.5
Second, compile AMBER by the following:
./configure -mpi -cuda intel make install export DO_PARALLEL='mpirun -np 2' make test #(or try the executable test/test_amber_cuda_parallel.sh ; actual cases in test/cuda/)
Run dhfr test: /opt/software/amber16-gpu/test/cuda/dhfr/Run*.my
If you get x11 lib error, yum install *x11* and yum install libXt-devel*. This install pmemd,cuda.mpi in /opt/software/amber14-gpu/bin/
Due to the linking of libraries (intel,nvidia,amber), there will probably be errors. It is easier to compile amber without the flags -mpi and -cuda and then to add those after solving any problems.
2015/6/11 Install on node210, GTX970
cd ~pren/amber-git
Update git: amber.readme.git
git checkout master
git pull
cp amber amber15-gpu (later moved to /op/software/amber16-gpu)
source /opt/software/bash/bashrc.amber.970
./configure -mpi -cuda intel make install
test...
Run AMBER on GPU
1) Log into node201, 202... (2 GTX 780 cards installed). or node 210 3 GTX970 installed
2) nvidia-smi to check which cards are available/busy (by checking the temperature and fan load)
If no card is being used, you can ignore this step. Otherwise you should specify to use the next available card. To select specific GPU card to run, "export CUDA_VISIBLE_DEVICES="0"" ( http://ambermd.org/gpus/#Running for explanation) "0" means the first card, 1 second, 2 the third. ****Also works for OPENMM
3) bash; source /usr/local/bash/bashrc.amber or bashrc.amber.970 (> node210)
4) Run (using 1 card, specify 1 after np option below; use 2 card, specify 2...)
Run AMBER GPU (Sep 2017)
GPU version of AMBER was compiled for use on new GPU nodes (node 70 to 90+). Executables are in /opt/software/amber18-gpu. In order to run them, the following environmental variables need to be specified:
#AMBER GPU
source /opt/intel/composer_xe_2013.2.146/bin/compilervars.sh intel64
export AMBERHOME=/opt/software/amber18-gpu
export PATH=$PATH:/usr/local/cuda-7.0/bin
export LD_LIBRARY_PATH=/usr/local/cuda-7.0/lib64:${LD_LIBRARY_PATH}
export LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:$AMBERHOME/lib
export PATH=$PATH:/opt/mpich2-1.4.1p1/bin/mpicc/
export CUDA_HOME=/usr/local/cuda-7.0
export DO_PARALLEL='mpirun -np 1'
Tips to run amber GPU as fast as you can
use single precision floating point SPFP, NOT DPFP write out infrequently (ntpr=1000,ntwx=1000, ntwr=1000) Pressure is expensive to calculate (~15% slower than NVT). Use NPT to estimate density and then use NVT for production run. in NPT, baraostat=2 (Monte Carlo is a little cheaper. Use 4fs (dt=0.004) time step (H mass repartition) if you only care about thermodynamics (kinetics is wrong). More tips can be found here: http://ambermd.org/gpus/#Max_Perf
Using a single card, I was able to get 102ns/day on JAC system (23K atoms) using dt=0.002 (2fs), and 220ns/day using dt=0.004
6) NVT Example: /opt/software/amber14-gpu/test/cuda/jac/Run.jac.my SPFP
see Run.jac.my for options in NVT.
7) NPT example: /opt/software/amber14-gpu/test/cuda/dhfr
see Run.dhfr.ntb2_ntt1.my for NPT options.
Amber 14 manual: http://ambermd.org/doc12/Amber14.pdf
Occasioanlly when you two cards, you may see errors like this. Just rerun
"gpu_allreduce cudaDeviceSynchronize failed an illegal memory access was encountered
4fs timestep
Curves+
Curves+ for analysis of nucleic acid structure
Read both user guide and reference
https://bisi.ibcp.fr/tools/curves_plus/curves-user-guide.html
https://dx.doi.org/10.1093/nar/gkr316
rm r+bdna*.* /Users/RL/Code/Cur+ <<! &inp file=1bna, lis=r+bdna, lib=/Users/RL/Code/standard, &end 2 1 -1 0 0 1:12 24:13 ! # numbers following namelist variables: # [# strands, up to 4] [#nt in strand 1, negative means 3’ to 5’; if 1, then auto-detected] [#nt in strand 2] … # [nt indices in strand 1, 0 means gap, negative means excluding from axis calculation (for flipped base, the other base must be present, otherwise the base pair should be omitted)] # [nt indices in strand 2] # …
To analyze single strand:
/Users/RL/Code/Cur+ <<! &inp file=1bna, lis=r+bdna, lib=/Users/RL/Code/standard, &end 1 -1 0 0 0 24:13 !
or
/Users/RL/Code/Cur+ <<! &inp file=1bna, lis=r+bdna, lib=/Users/RL/Code/standard, &end 2 1 -1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 24:13 !
Trajectory analysis using CANAL
https://bisi.ibcp.fr/tools/curves_plus/canal-user-guide.html
Works with AMBER coordinate format
Requires strict format for Curves+ output. Only supports duplex as of Version 1.3 February 2015. For modified NA, make sure the number of torsions is the same, and five sugar atoms are defined.
To analyze a single strand, add a dummy strand as in the Curves+ example above.
Quick steps to run amber or OpenMM GPU
First, make sure your bashrc has nothing related to mpich, cuda, intel compiler in it. If you need them for specific apps, create a .bashrc.thatapp and source it before running the specific app.
Log into NOVA and then node201, 202, 205, 206, 210, 211, or bme-pluto, saturn or earth
source /usr/local/bash/bashrc.amber or /usr/local/bash/bashrc.openmm
Source the one with xxxx.970 if you are running on 210, 211, earth.
Nvidia-smi to check which device (card) is available. The unused card has a low temperature < 40 C and less memory usage < 30MB.
export CUDA_VISIBLE_DEVICES=“0” to chose card 1 export CUDA_VISIBLE_DEVICES=“0,1” to choose both card 1 and 2 (only amber can use 2 cards in parallel for one simulation; don’t ever use 3)
Then run your amber or open simulation. You can check the examples for amber (only root can actually run this): /opt/software/amber14-gpu/test/cuda/dhfr/Run.dhfr.ntb2_ntt1.my, and you will see the actual pmemd command is
"/opt/software/amber14-gpu-970/bin/pmemd.cuda.MPI”
Everything else is the same as regular amber.
Examples for openmm is in /home/pren/OpenMM/zzz/simulateMTS.py.
More tips to run these fast, such as using 4fs time-step, write files/log as infrequent as possible, avoid pressure control etc can be found here: http://biomol.bme.utexas.edu/wiki/index.php/Software:links#Tips_to_run_amber_GPU_as_fast_as_you_can
Simulaiton analysis with LOOS
LOOS by Alan Gorssfield.
- Work with gromacs, amber, CHARMM and tinker trajectory.
- Compute various properties for you from the trajectory
- Just added native contact fraction calculation upon our request (the first frame define native)
- LOOS document: http://membrane.urmc.rochester.edu/Software/LOOS/Docs/main.html
- Download the loos http://sourceforge.net/projects/loos/
- Download the native contact routine http://biomol.bme.utexas.edu/~pren/down2009/native_contacts.cpp
To use the native_contact.cpp
Here's what you need to do to build it:
1) Download the newest LOOS from loos.sourceforge.net
2) Unpack and build it. If you don't already have them installed, you'll need boost (and boost-devel, if it exists on your distribution), atlas, and scons installed. They should be readily available as packages for most majors linuxes. If I recall correctly, Ubuntu breaks boost into many small packages -- if so, install all of them.
3) Copy native_contacts.cpp into the Tools subdirectory of LOOS.
4) Edit Tools/SConscript, which is actually just a python script. You'll see a series of lines that create a variable called apps. Edit the last one, and append " native_contacts" to it.
5) cd to the main LOOS directory, and say "scons" (or scons -j4 if you've got a 4 core machine). This will build LOOS, and will build native_contacts in the Tools directory.
6) If you want, say "scons install" -- this will create an installed copy, by default in /opt/loos (you can edit this by modifying the custom.py file in the main loos directory.
1) I didn't do a huge amount of checking on it -- I wrote it, ran a couple of quick tests, and sent it along. Don't hesitate to contact me if you're having trouble making sense of it.
2) The way it's written, native_contacts takes a selection (for instance, you could specify the protein, but only include core residues), breaks it into pieces by residue, and computes the contacts between the centers of mass of the residues. So, if you want the whole thing, you'd just select the protein. If you wanted alpha carbons, you'd do something like
segid == "PROT" && name == "CA"
Beta carbons would look very similar. If you wanted to exclude backbone, something like this would work (I haven't tested it)
segid == "PROT" && !(name =~ "^(C|O|CA|N)$"
The above assumes you're using a package that has segid's -- Amber doesn't, so you'd have to specify a range of residue numbers instead, eg
resid >= 3 && resid <=45 && !(name =~ "^(C|O|CA|N)$"
See the LOOS docs, in particular the page about the selection language, for more hints.
- can LOOS directly work on AMBER mdcrd
As for the latter question, yes, it'll work directly on the amber trajectory. If you just run it (say "native_contacts") it'll list the command line arguments it wants. The "system" description should be a pdb file, or an amber parmtop, or a charmm/namd psf. PDB is fine, as long as it has the same atoms (in the same order). That's where LOOS will get the meta-data (atom name, residue name and number, etc). Depending on what format you use, there may or may not be coordinates -- psfs don't have them, for example, and parmtops don't either (although the code will automatically look for an accompanying inpcrd file, which does).
For the next option (trajectory), it takes the name of the trajectory file, which it identifies based on the filename. Amusingly, you can mix and match packages (eg charmm psf with amber mdcrd).
Quantum Mechanics
Psi4
** please see Chengwen's tutorial for using psi4
The latest version of Psi4 has been installed at /users/mh43854/bin/psi4updated. Installation required the latest gcc. To use, you need the following environemental variables( for bash). executable is /users/mh43854/bin/psi4updated/bin/psi4
export PYTHONPATH=/users/mh43854/bin/psi4updated/lib:$PYTHONPATH
export LD_LIBRARY_PATH=/users/mh43854/gcc/lib64:$LD_LIBRARY_PATH
Installation of GCC:
I installed 4.9.4( download info is available at http://www.gnu.org/prep/ftp.html) at ~mh43854/gcc. To add prerequisites to the build, run ./contrib/download_prerequisites. mkdirobjdir. cd into objdir and run /gcc-4.9.4/configure --prefix= /path/to/install/dir/. make and then make install. This will take a long time.
Q-chem 6
Run
Can be used on any nodes. For csh, source the follow (or add to .cshrc)
source /opt/qchem/6.1/qcenv.csh
For bash (add to .bashrc)
source /opt/qchem/6.1/qcenv.sh
Make sure no early version of qchem env sourcing in .cshrc or .bashrc:
Example of input in
/home/pren/QuantumMechanics/qchem/water /home/pren/QuantumMechanics/qchem/
To run jobs (using 8 threads/processors).
qchem -nt 8 water.in water.out &
Important features
Default mem is 12GB. please set your own in input ALMO-EDA second generation for energy decomposition New DFT methods such as wB97M2... https://manual.q-chem.com/6.1/sect_DFTsugg.html User manual and examples: https://manual.q-chem.com/latest/
Install Flexnet
Flexnet came with qchem install already
Need to run this to get host id before emailing qchem for license:
/opt/qchem/6.1/bin/flexnet/lmutil lmhostid
Flexnet on the latest Rocky Linux requires lsb package:
sudo dnf install -y yum-utils sudo dnf config-manager --set-enabled devel sudo dnf update -y (optional) sudo dnf install redhat-lsb-core
Install
The qcaux/license has two license files
qchem.lic qchem_UKVU_demo.lic
Create the qchem.lic following qchem email:
SERVER bme-uranus.bme.utexas.edu 043201278653 USE_SERVER
Edit the 2nd lic file (sent by q-chem)
SERVER bme-nova.bme.utexas.edu b083fee3ba06 58888 VENDOR qchemlm port=58889 OPTIONS=/opt/qchem/etc/qchemlm.opt
Note the 58888 58889 ports are added above and enabled below:
firewall-cmd --zone=internal --add-port=58888-58889/tcp --permanent firewall-cmd --reload
mkdir /opt/qchem/etc/, add qchemlm.opt (may need copy the qchemlm from bin/flexnet here, may not):
GROUP qchemusers pren zj2244 eew947 cda923 liuchw INCLUDE QCHEM GROUP qchemusers
In rc.local, add:
/opt/qchem/6/bin/flexnet/lmgrd -l +/var/log/qchemlm.log -c /opt/qchem/6/qcaux/license/
Q-Chem 5
2023: node34 still can run qchem example job: /home/pren/QuantumMechanics/qchem/water/run "run watera5z"
Need these lines in your source if you use csh (change if you bash)
setenv QCSCRATCH /opt/scratch/qchemscratch setenv QCLOCALSCR /scratch/qchemscratch setenv QCMPI mpich source /opt/qchem/501/qcenv.csh #setenv LD_LIBRARY_PATH /usr/lib64/openmpi-1.10/lib/:$LD_LIBRARY_PATH
2017/7 Qchem 5 is now available on:
node40 node41 node42 node142 node38
Need these lines in your source if you use csh (change if you bash)
setenv QCSCRATCH /opt/scratch/qchemscratch setenv QCLOCALSCR /scratch/qchemscratch setenv QCMPI mpich source /opt/qchem/5/qcenv.csh setenv LD_LIBRARY_PATH /usr/lib64/openmpi-1.10/lib/:$LD_LIBRARY_PATH
Qchem Q-chem 4.1
8/1/2016 See Qchem under tutorial. Qchem (4.2) can be run on the following nodes (all cores):
node50-57, 8 cores each, 7GB memnode35 node36 node37 node38 genome
8/17/2013
License email: license from qchem
Installed the serial and multiple-core version (not MPI yet, available if needed) in /opt/qchem/4.1
To run qchem, see tutorials. Below is the printout after installation. Note that there are few env (crutches) needed to be defined.
To run Q-Chem calculations simply source the setup script below.
[tcsh/csh]
source /opt/qchem/4.1/qcenv.csh
[bash]
. /opt/qchem/4.1/qcenv.sh
You can put the above lines in your shell startup script
~/.cshrc for tcsh/csh or ~/.bashrc for bash.
To get the latest Q-Chem updates please run
/opt/qchem/4.1/qcupdate.sh
To regenerate license data please run
/opt/qchem/4.1/qcinstall.sh --update-lic
Installation files are in /opt/qchem/4.1
To generate licesen for nodes (/opt/qchem/4.1/install-file/lincese_nodes), run
export QC=/opt/qchem/4.1 $QC/bin/license_info <file_for_output> license@q-chem.com
Give the nodes file. Mail the output file to
Q-Chem
Version 4.0 is located in /work/opt/qchem4.0/.
Version 3.2 is located in /opt/qchem-para.
From: Zhen Xia <zhenxia@mail.utexas.edu> Date: Monday, February 27, 2012 1:53 PM To: Daniel Dykstra <dnl.dykstra@gmail.com>, Mike Schneiders <michael.schnieders@gmail.com>, Yue Shi <shiyue8638@gmail.com>, mu xiaojia <muxiaojia2010@gmail.com>, Qiantao Wang <qiantao.wang@gmail.com>, Gaurav Chattree <Gaurav.Chattree@mail.utexas.edu> Cc: Pengyu Ren <pren@mail.utexas.edu> Subject: Q-Chem update to 4.0 version
HI, everyone,
I’m glad to tell you that the Q-Chem software has been updated to 4.0 version. The new features of 4.0 version can be seen at: http://www.q-chem.com/. To use Q-Chem 4.0, please add the following paths to your shell profiles. An example of bash shell is looks like:
#QCHEM #qchem
Please let me know if you have any questions.
Cheers, Zhen
Spartan
Update: Spartan 08 is installed on water.bme.utexas.edu
Bme-nova now has the QM package Spartan 06 (will update to 08 soon). A useful feature is RI-MP2 method, which is much more efficient than canonical MP2 for large molecules. We have 8 license for backend jobs but only one license for GUI. You can start the GUI by typing “spartan” (locally at bme-nova or ssh –X bme-nova from your own workstation).
A manual is available at /opt/software/spartan06.129_26_int9e/Spartan06Manual.pdf.
You can set up and submit jobs using the GUI and then exit (to free the license for others).
ORCA
Free QM package. Run parallel. Compute CD? orca HOWTO
cadpac
http://www-theor.ch.cam.ac.uk/software/cadpac.html
OpenMOPAC
Implement AM1 (stands for Austin Model 1), PM3 and other semiempirical methods (by James Stewart of UT Austin) These methods are also available in G03, GAMESS, etc. How good is SEM multipoles? What is the alternative to Gaussian in derive DMA? http://www.openmopac.net/background.html
AlphaFold3
AlphaFold3 (AF3) requires a GPU card with compute capacity over 8.0 and at least 40 GB display memory to run. Therefore calculations can be conducted on node165 (with 4 RTX A6000). Before deploying AF3, please read the terms and conditions carefully. https://github.com/google-deepmind/alphafold3/blob/main/WEIGHTS_TERMS_OF_USE.md
There are two ways to deploy AF3.
- Follow the official tutorial of af3 https://github.com/google-deepmind/alphafold3/blob/main/docs/installation.md, which requires the root privilege to install and configure Docker.
- Install the model locally as a pacakge. We are introduing this method here.
AF3 is now only supported on linux system, the system we used in this tutorial is Rocky Linux 8.10, with cmake 3.31.1 and gcc 12.4.0. GPU Driver Version: 550.135, cuda 12.6. (AF3 requires cmake >= 3.28 and gcc >= 9.4)
# clone the af3 code
git clone https://github.com/google-deepmind/alphafold3.git ~/opt/alphafold3
cd ~/opt/alphafold3
# af3 is tested based on python 3.11
conda create -n af3 python=3.11
conda activate af3
# Hmmer must be 3.4.0.0 version, do not use conda, which although says 3.4
# on website but will install 3.3
pip install hmmer
pip install -r dev-requirements.txt
# Could add --verbose to check the log if installation fails .
# To my experience, it is most likely to fail because of the
# incorrect version of gcc or cmake. Also check the LD_LIBRARY_PATH
# if any CXX test fails, it probably calls the libraries from another
# software's path for testing.
pip install . --no-deps
build_data
python run_alphafold_test.py # test run
# use jax package to check gpu settings
python
import jax
jax.devices()
>> [CudaDevice(id=0), CudaDevice(id=1), CudaDevice(id=2), CudaDevice(id=3)]
from jax.lib import xla_bridge
xla_bridge.get_backend().platform
>> 'gpu'
# This is used to dowload the database of af3, which is over ~650 GB,
# so it is unnecessary for each member to download it.
# The datebase is already located in /home/zh6674/opt/alphafold3/database
# python fetch_databases.py --download_destination=/If you don't want to create the env from scratch, you can also clone my env by:
conda create --name myaf3 --clone /home/zh6674/opt/miniconda3/envs/af3Then you can run AF3 by such input:
export CUDA_VISIBLE_DEVICES=0
python ~/opt/af3/run_alphafold.py \
--json_path=/your_input_path/af_input.json \
--model_dir=/model \
--db_dir=/home/zh6674/opt/alphafold3/database \
--output_dir=/your_output_path/outputDetails of input.json could be found here. And it should be noticed that AF3 requires every users to submit a form to access their model prameters (--db_dir). So please contact them to get the model parameters for your own use.
Job Scheduling
- http://gridengine.sunsource.net/
- http://www.clusterresources.com/products/torque-resource-manager.php
Docking alternatives:
Rxdock:
https://www.playmolecule.com/AceDock/
Autodock family
Autodock Vina (multiple ligands): https://github.com/ccsb-scripps/AutoDock-Vina
ADFR: https://ccsb.scripps.edu/adfr/
Smina (expt with scoring function): https://sourceforge.net/projects/smina/
Gold Docking
2023
Vince email has a new activation key Download using 771 and this new key: https://www.ccdc.cam.ac.uk/support-and-resources/csdsdownloads/ Installed on uranus /work2/Software, Can use any nodes.
Before use, need to activate using this new key (search GOLD in Slack):
/opt/software/CCDC/CCDC2023/ccdc-utilities/software-activation/bin/ccdc_activator -a -k xxxx
replace /work2/Software by /opt/software/CCDC below Old:
/work2/Software/CCDC2023/ccdc-utilities/software-activation/bin/ccdc_activator -a -k xxxx
Run gui to prepare conf file:
/opt/software/CCDC/CCDC2023/ccdc-software/hermes/bin/gold
Run command line without GUI (may need clean your old GOLD_DIR and LD_LIBRARY_PATH if you set for/used previous GOLD)
/opt/software/CCDC/CCDC2023/ccdc-software/gold/GOLD/bin/gold_auto
Other software, conformer generator, conquest, mercury,....can be found in:
/opt/software/CCDC/CCDC2023/ccdc-software/xxx/bin
Documents for each software
/opt/software/CCDC/CCDC2023/ccdc-software/xxx/docs
In addition to /opt/software/CCDC/CCDC2023/, a copy is backed up to /opt/CCDC/CCDC2023/
2022
2022 GOLD CCDC license and download - installed on bme-uranus. /work2/Software/CCDC2022/
/work2/Software/CCDC2022/Discovery_2022/bin/gold (GUI license expired as of May 2023)
/work2/Software/CCDC2022/Discovery_2022/bin/gold_auto with .conf file?
https://utexas.app.box.com/folder/153544625646 (edited)
Updated license info can be found : Note updated as of 2022 http://legacy.lib.utexas.edu/chem/scifinder/ccdc.html
2020
GOLD Tutorial
Before running GOLD from the command line, it is recommended to follow a tutorial using the graphical interface to gain familarity with how GOLD works.
A tutorial for docking two ligands into a protein while taking flexibility into consideration is located here:
A tutorial for ligand binding pose prediction is located here:
https://www.ccdc.cam.ac.uk/support-and-resources/ccdcresources/GOLD-tutorial-PosePrediction.pdf
Remove old env in your bashrc or cshrc if you have one (so far I don't think we need it for 2020 version)
Activate GOLD the first time you use it:
/opt/CCDC/CCDC2020/CSD_2020/bin/ccdc_activator -k 570769-C9BD90-4986BB-904E59-D56C9B-025394
If you want to use gradphical interface for activating or setting up GOLD job initially (running job requires no GUI), you need a X grapics on your local computer.
Mac has Xquartz. On windows, use mobaxterm that comes with X (or you can install VcXsrv & use it with ubuntu). Make sure you use ssh -Y when logging into a node.
You can check that X is working by typing xeyes and hitting enter. You should get a pair of googly eyes (which may be in another window).
/opt/CCDC/CCDC2020/CSD_2020/bin/ccdc_activator_gui & enter key from above (570769-C9BD90-4986BB-904E59-D56C9B-025394)
Running graphical interface (e.g. to generate gold.conf)
ssh -Y nova
then
/opt/CCDC/CCDC2020/Discovery_2020/bin/gold
Once you set up the job/create the conf file on nova, you can run the job on other nodes (below)
GOLD user guide: https://www.ccdc.cam.ac.uk/support-and-resources/ccdcresources/GOLD_User_Guide.pdf
Running GOLD from the command line (you can use gold.conf above or mannually creat/edit conf)
/opt/CCDC/CCDC2020/Discovery_2020/bingold_auto gold.conf &
2018 update
(installation and activation same as 2016)
setenv GOLD_DIR "/opt/CCDC2018/GoldSuite_2018/GOLD" setenv PVM_ROOT "/opt/CCDC2018/GoldSuite_2018/GOLD/pvm3" setenv PVM_RSH "/usr/bin/ssh" setenv CCDC_CSD_LICENCE_FILE "/opt/CCDC2018/CSD_2018/csd/csd_license.dat" setenv LD_LIBRARY_PATH /opt/CCDC2018/GoldSuite_2018/c_linux-64/lib/:$LD_LIBRARY_PATH
To activate on a node or WS: /opt/CCDC2018/GoldSuite_2018/bin/gold, Enter site 771, Confirmation Code: 1f9986 and email.
After installation, you may run the GUI (hermes) on workstation such as water.bme.utexas.edu
2016
Installation: /opt/CCDC/installation/csds-linux-x64.run Mannual in /op/CCDC
Activate on a node (e.g. node101) by running /"'opt/CCDC/GoldSuite_2016/bin/gold" (using X windows if you do so remotely). Windows will pop up, asking you to enter the site number (771) and purchase number/confirmation code to register online. This confirmation number changes every spring each year (1f9986 for 2018). The code is now available from x-ray lab web site: https://sites.utexas.edu/chem-x-ray/ (right panel)
Once activated, specify the license file: csd_licence.dat /opt/CCDC//CSD_2016/csd/csd_licence.dat
To run:
Notes from Dave Broadwell
You can split the jobs and combine the results by uinsg the script discussed in the link above (Once all the jobs have been launched, a script is generated that may be used to collate all the results once the dockings have completed. )