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16:35, 22 April 2026 Brendan talk contribs created page Tutorial:kturn tut (Page created)
18:55, 10 April 2026 Pren talk contribs created page File:TinkerMeeting 2025.jpg
18:55, 10 April 2026 Pren talk contribs uploaded File:TinkerMeeting 2025.jpg
18:52, 10 April 2026 Pren talk contribs created page Tinkermeeting:tinkermeeting2025 (Tinker 2025) Tag: Visual edit
20:29, 8 April 2026 Pren talk contribs created page Tinkersctipts (Created page with "# <code>/home/pren/bin/density.sh some.xyz</code> is a shell script to compute density for a Tinker xyz file. The second line of the file needs to be the box dimension # Convert from tinker xyz to PDB or cif (if more than 99,999 atoms). Let me if you need to add more functionality or have problems <code>python ~/bin/tinker2pdb.py --water-type 349 --format cif popcbi221.xyz</code> <code>python ~/bin/tinker2pdb.py -h</code> # In tinker "arcedit" is the command for conver...") Tag: Visual edit
17:43, 20 January 2026 User account Pradip talk contribs was created by Admin talk contribs and password was sent by email
16:29, 17 December 2025 User account Rusen talk contribs was created by Admin talk contribs and password was sent by email
16:28, 17 December 2025 User account Brendan talk contribs was created by Admin talk contribs and password was sent by email
18:53, 25 September 2025 Pren talk contribs created page File:REM2023.pdf
18:53, 25 September 2025 Pren talk contribs uploaded File:REM2023.pdf
23:40, 21 April 2025 Eew947 talk contribs created page Software:links (Created page with "Moved http://biomolmd.org/tinkergpu/index.php/Tinkergpu:Software-list#Arguslab")
23:39, 21 April 2025 Eew947 talk contribs created page Research:Svn documentation (Created page with "Subversion is a source control program much like cvs or rcs. It works by keeping track of a main copy of a codebase known as the repository. One checks out a working copy into thier own working directory or codebase. As changes are made to different files in the codebase they are first updated from the repository so that any conflicts can be resolve between conflicting code that some one else may have committed during the time that the changes were made. Next they co...")
23:38, 21 April 2025 Eew947 talk contribs created page Research:Programming (Created page with "=Links= *[http://www.intel.com/software/products/compilers/flin/docs/main_for Intel Fortran Compiler Documentation] *[http://www.unix.org.ua/orelly/perl/index.htm Perl Reference] **Also available here: /home/golubkov/Documents/Books/perl_books/index.htm *SVN Documentation *Program Profiling *Neighborlist Tests")
23:38, 21 April 2025 Eew947 talk contribs created page Software:Development (Created page with "=Links= * Programming * Corase-grain program subversion * compiler option: add this to F77Flag to intel 9.0 ifort to deal with large arrays (over 2GB static memory) -i-dynamic -mcmodel=large intel math library: LINKFLAGS = -lsvml -Vaxlib -static-libcxa -pg")
23:37, 21 April 2025 Eew947 talk contribs created page Software:CGMD (Created page with "==CG code== The latest code (containing bond, angle, torsion, neighbor list, and 1-2 scaling) is located on bme-earth subersion repository. It can be checked out with: =>svn checkout svn+ssh://bme-earth/subversion/tinker-bat Use this syntax even if you are on bme-earth, so the directory is set up properly for when you update and commit from other machines. I also have a working directory in /home/golubkov/tinker-bat that I try to keep up-to-day with the compiled execut...")
23:37, 21 April 2025 Eew947 talk contribs created page Software:GB Param (Created page with "==Pavel== crsparam.f int tinker-bat ==Bradley== http://biomol.bme.utexas.edu/wiki/index.php/Research:Dna#GAY-BERNE_PARAMETERIZATION /home/others/hamiltonba/dev/crs-param-cpp/trunk Brad has prgroams to generating all atom dimer configurations at various distances, and at each distance the molecule is rotated about the symmetry axis to get a Boltzmann average all-atom energy for that distance. /home/other/hamiltonab/nuc/vdw2 He has one script for each configuration,...")
23:36, 21 April 2025 Eew947 talk contribs created page Research:Ions (Created page with "=Zinc= ==literature== Modeling of Zinc is one of our focuses so we need better understanding of the zinc-protein interactions. I have collect some papers in /opt/reprints/ion-proteins/ZN-pro and …/ZN-MMP In Zn-pro: The zinc-finger.pdf has discussion of various CCCC, CCHC, CCHH complexation with Zn. It suggests that two of the C (cys) lose protons and the total charge of the Zn[CCCC] would be 0. However zn-cystine-expt-solv-lim.pdf suggests that all 4 Cys should l...")
23:36, 21 April 2025 Eew947 talk contribs created page Research:Proteomics (Created page with "= Introduction = The Need: It is universally recognized that early detection of cancer and coronary artery disease leads to dramatically improved health outcomes. Yet, there is great scarcity, of minimally invasive, economically feasible approaches to early detection. The ability to obtain early warning information from proteins and other molecules in blood or other biological fluids would represent an epochal advance. However, this approach is extraordinarily difficult...")
23:35, 21 April 2025 Eew947 talk contribs created page Research:Peptide (Created page with "* Howto REMD * extract peptide from gromacs * Sai's log ")
23:35, 21 April 2025 Eew947 talk contribs created page Research:Coarsegrain (Created page with "=RNA Statistical Potential with psudoatoms = * Pseudo atom based statistical potential (Zhen and Bell) *Research:RNA Statistical Potentials * RNA project 2006 and prior =GB EMP based model = ==GBEMP== *CG project log *coarse_grain_parameter_document *Deriving molecular multipoles consistent with inertial frame *Research...")
23:34, 21 April 2025 Eew947 talk contribs created page Research:amber prog tips (Created page with "== VALENCE == opbend is included in angle energy ''' in amoeba_interface.f: ''' call AM_BONDS_eval(crd,frc,ene(1),vir_tensor) call AM_UREYB_eval(crd,frc,ene(2),vir_tensor) call AM_REG_ANGLES_eval(crd,frc,ene(3),vir_tensor) call AM_TRIG_ANGLES_eval(crd,frc,ene(4),vir_tensor) call AM_OPBEND_ANGLES_eval(crd,frc,ene(5),vir_tensor) call AM_TORSIONS_eval(crd,frc,ene(6),vir_tensor) ...")
23:33, 21 April 2025 Eew947 talk contribs created page Research:amber modification (Created page with "=== nint in sande needs to be replaced by dinit in pmemmd === === Modifying Sander (amber 8 by Darden, in house) to accept coupling parameter (Chona) === Note: The instructions here refer to the source directory in lela.tacc.utexas.edu. Except for changing <AMBER_TOP>, these instructions should be platform-independent. *'''''Go to <AMBER_TOP>/SRC/sander. The sander source files are in ~chona/amoeba/amber06a7l5_p/SRC/sander, so <AMBER_TOP>=~chona/amo...")
23:33, 21 April 2025 Eew947 talk contribs created page Research:condor cluster (Created page with "== Running on the Condor cluster == * An example working directory is in ~chona/amoeba/softcore_vdw3 on lela.tacc.utexas.edu. * Prior to submitting the job, make sure that the dynamic libraries can be found by the dynamic linker. This can be done by redefining the environment library LD_LIBRARY_PATH. In bash, lela% export LD_LIBRARY_PATH=.:$LD_LIBRARY_PATH will prepend the current directory to the list of paths searched by ld or ld.so. Then run ldd lela% ldd sander...")
23:32, 21 April 2025 Eew947 talk contribs created page Research:build instructions sander (Created page with "== New build instructions for Sander == * A better optimized BLAS library is available [http://www.tacc.utexas.edu/resources/software/#blas here] for free download. This has been built in bme-earth under ~chona/GotoBLAS. * Intel has optimized LAPACK routines as part of MKL. On bme-earth, this is installed in ~chona/intel/mkl/8.1/lib/em64t/. * Edit the <AMBER_TOP>/SRC/sander/Makefile to point to the MKL LAPACK and GotoBLAS libraries. The build rule for the sander* targets...")
23:32, 21 April 2025 Eew947 talk contribs created page Research:compile amber (Created page with "= sander of amber pre 9 or DARDEN-AMOBEA version = The original source is in /home/pren/DARDEN_amber An example compiled on pluto: /home/pren/AMOEBA/amber-range-soft source ~/.cshrc.f10 cd sander make sander Modified (by socar) source in /home/oscar/data2-oscar/amber_mod_org/ See here for detailed modification http://biomol.bme.utexas.edu/wiki/index.php/Research:Amber_modification README file in the directory explain the process. Esstially cd S...")
23:31, 21 April 2025 Eew947 talk contribs created page Research:remd tutorial (Created page with "'''Example system: (ala)5 peptide in water''' *'''Get coordinate file and parameter/topology file in Amber format.''' /home/yues/amoebapro/helix/ala5-prot/wt6 A quick guide can be seen in http://water.bme.utexas.edu/wiki/index.php/Software:amber#A_Quick_Guide *<span style...")
23:30, 21 April 2025 Eew947 talk contribs created page Research:pmemd tacc (Created page with "'''Install PMEMD on ranger (or lonestar)''' === Configure === <span style="font...")
23:30, 21 April 2025 Eew947 talk contribs created page Research:amber tips pr (Created page with "= Ren's example for running sander and pmemd = == Executables == Oscar's mod sander in /home/oscar/data2-oscar mod pmemd in /home/oscar/pmemd/src example mdin and run script files in /home/pren/AMOEBA/solvation/compare/ == A Quick Guide == TO run sander: xyzpdb ele.xyz analyze box30 PC > ele.analout /opt/amber/bin/amoeba_parm -name ele -title "water" > ele.amoeba_parm.out /opt/amber/bin/sander -i ele.mdin -c ele.in...")
23:29, 21 April 2025 Eew947 talk contribs created page Research:amber tips (Created page with "=Renumber xyz/pdb file= If you want to renumber xyz file, e.g. delete a molecule from the old xyz, you can manually remove the lines for these atoms. However, you cannot manually modify the pdb in the same way by deleting the ATOM and CONNECT entries. It will cause trouble running amber later on. (Well, no error msg would be printed out, but it stops right before the first step). The correct way is to convert xyz to pdb with xyzpdb command. =FEP-vdw= During the FEP, yo...")
23:29, 21 April 2025 Eew947 talk contribs created page Research:GK FEP BAR (Created page with "= Simulation process and the parameters = The execuable for GK/Bar simulaton is located at: /users/jzhen/tinker5.1-gk-param/source4/ With RESPA multi-step implement (from Tinker6): /users/jzhen/tinker5.1-gk-param/source4-respa/ Relative binding free energy calculation: two states bound state: protein-ligand in GK solvent free state: ligand only in GK solvent In each state, we scale ele first, and then vdW. A example of prameter and key file can be seen at: /users/...")
23:28, 21 April 2025 Eew947 talk contribs created page Research:amoeba dev protocol (Created page with " *optimization performed at level of MP2/6-31G*; DMA MP2/6-311G**; ESP MP2/Aug-cc-pvtz *gdmain file format: Title MoleculeMP2sp gdmain File ./311gss-2d2p/c5_311gss.fchk density MP2 Angstrom AU Multipoles SWITCH 0 Limit 2 Punch ./311gss-2d2p/c5_311gss.punch Radius H 0.65 Start Finish *For Alanine Dipeptide, 7 gas phase conformers are used to fit the multipoles. c5, c7a, c7e, alpha_l, alpha_p, beta2, alpha_r")
23:27, 21 April 2025 Eew947 talk contribs created page Research:AMOEBA HFE (Created page with "= The script does the automation -- hfe_setup.pl= You can find the script here /work/oscar/bin = Files you need = (1) xyz file of the ligand (2) amoeba parameter file (3) xyz file of water box (4) AMBER input file template =Procedures= == Set-ups == (1) After you run hfe_setup.pl, a prompt pops up "Enter the xyz file name of the ligand" Make sure you have that file in your current directory and type in the file name. The script will figure out how many atoms...")
23:26, 21 April 2025 Eew947 talk contribs created page Research:Potential Tutorial (Created page with "=Introduction/Motivation= * GDMA has issues/difficulties with SP calculations of higher basis sets. =What you need= # FCHK file # GDMA output file # Example of input files of para-cresol is available at /home/wuch/work/research/ligand_param/sample/pot/tutorial Image:Cresol.png =Process= *Follow AMOEBA Ligand Param Instructions to get output from GDMA *Generate multipoles in Tinker format (gdout.xyz and gdout...") Tag: Visual edit: Switched
23:21, 21 April 2025 Eew947 talk contribs created page Research:Discussion (added page) Tag: Visual edit
23:16, 21 April 2025 Eew947 talk contribs created page Research:amoeba force field (Copied, haven't checked)
23:15, 21 April 2025 Eew947 talk contribs created page Talk:Logs:parameterization (Copied, haven't checked)
23:14, 21 April 2025 Eew947 talk contribs created page Research: AMOEBA Ligand Par (Copied, haven't checked)
23:13, 21 April 2025 Eew947 talk contribs created page Research:AMOEBA Amber Free (Copied, haven't checked)
23:12, 21 April 2025 Eew947 talk contribs created page Research: AMOEBA Reference Frame (Created page with "1 After we got the moleculeMP2.log file, copy/pasting the new Cartesian coordinates out of the end of moleculeMP2.log into the new .xyz file named moleculeMP2sp.xyz. 600px 2 Then we use one of TINKER's facilities XYZEDIT. It have many interactively selectable options, choose (13) Translate and Rotate to Inertial Frame. At the end of the editing process, a new version of the orginal .xyz file is written as output. In our case, we should have a...")
23:12, 21 April 2025 Eew947 talk contribs created page Research:Amoeba par tut (Created page with "Quantum Calculations From initial structure to TINKER simulation (uses Gaussian03, TINKER, and formatting scripts written by P. Ren and C. King) <P STYLE="margin-...")
23:11, 21 April 2025 Eew947 talk contribs created page Research:AMOEBA Force Field (Copied, haven't checked)
23:11, 21 April 2025 Eew947 talk contribs created page Logs:parameterization (Copied, haven't checked)
23:10, 21 April 2025 Eew947 talk contribs created page Research:Typer (Copied, haven't checked)
23:09, 21 April 2025 Eew947 talk contribs created page Research:AMOEBA (Copied, haven't checked)
23:08, 21 April 2025 Eew947 talk contribs created page Research:DrugDesign (Copied, haven't checked)
23:07, 21 April 2025 Eew947 talk contribs created page Research:Penetration (Created page with "==Multipoles for monomers== From poltype: ~pren/poltype-1.1.3-dev/poltype.py.0.1 -s *.sdf -n 8 -m 6000MB -M 120GB --do-tor-qm-opt --espbasisset=aug-cc-pvtz & Files are in: ... ==SAPT energy for dimer interactions== ===SAPT2+0 methods=== ===SAPT energy data and structures=== ==CP parameter fitting== ...")
23:07, 21 April 2025 Eew947 talk contribs created page Research:AMOEBA NA (Copied, haven't checked)
23:06, 21 April 2025 Eew947 talk contribs created page Research:Reading (Created page with "=General= '''Molecular Modelling''', Principles and Pllications, Andrew Leach '''Computer simulations of liquids''', Allen & Tildesley '''Molecular Simulations''', Frenkel and Smit =Free energy methods= '''Free energy Calculations''', Theory and Applications in Chemistry and bIology, Chipot and Pophorille, Springer =MD books in dropbox = http://biomol.bme.utexas.edu/wiki/index.php/Software:Tutorials#Modeling_books_in_dropbox https://www.dropbox.com/sh/g3myhes5y1r...")
23:05, 21 April 2025 Eew947 talk contribs created page Research ex:OpenMM (Copied, have not edited. Already see some old links I will have to take care of.)
23:03, 21 April 2025 Eew947 talk contribs created page Research ex:AMOEBA in Amber (Created page with "sander and pmemd modification for ligand binding free enery calculations = Important: read me first = '''Now (as of June 2013) you can use the latest tinker (v6) and parameter files to set up the system in TINKER and then convert for amber run.''' *If you have an spherical ion (e.g. Na+, Cl-, Mg++in the system), you may need to modify the analout (see below) to replace multip...")

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