User contributions for Eew947

23:4023:40, 21 April 2025 diff hist +78 N Software:links Created page with "Moved http://biomolmd.org/tinkergpu/index.php/Tinkergpu:Software-list#Arguslab" current
23:3923:39, 21 April 2025 diff hist +935 N 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..." current
23:3823:38, 21 April 2025 diff hist +397 N 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" current
23:3823:38, 21 April 2025 diff hist +290 N 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" current
23:3723:37, 21 April 2025 diff hist +1,263 N 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..." current
23:3723:37, 21 April 2025 diff hist +7,222 N 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,..." current
23:3623:36, 21 April 2025 diff hist +9,473 N 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..." current
23:3623:36, 21 April 2025 diff hist +1,410 N 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..." current
23:3523:35, 21 April 2025 diff hist +139 N Research:Peptide Created page with "* Howto REMD * extract peptide from gromacs * Sai's log " current
23:3523:35, 21 April 2025 diff hist +2,510 N 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..." current
23:3423:34, 21 April 2025 diff hist +7,398 N 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) ..." current
23:3323:33, 21 April 2025 diff hist +38,201 N 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..." current
23:3323:33, 21 April 2025 diff hist +3,448 N 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..." current
23:3223:32, 21 April 2025 diff hist +1,094 N 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..." current
23:3223:32, 21 April 2025 diff hist +3,646 N 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..." current
23:3123:31, 21 April 2025 diff hist +3,362 N 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..." current
23:3023:30, 21 April 2025 diff hist +3,203 N Research:pmemd tacc Created page with "'''Install PMEMD on ranger (or lonestar)''' === Configure === <span style="font..." current
23:3023:30, 21 April 2025 diff hist +2,143 N 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..." current
23:2923:29, 21 April 2025 diff hist +7,743 N 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..." current
23:2923:29, 21 April 2025 diff hist +2,258 N 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/..." current
23:2823:28, 21 April 2025 diff hist +434 N 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" current
23:2823:28, 21 April 2025 diff hist 0 Research:AMOEBA →AMOEBA force field current Tag: Visual edit
23:2723:27, 21 April 2025 diff hist +2,860 N 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..." current
23:2623:26, 21 April 2025 diff hist +3,318 N 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..." current Tag: Visual edit: Switched
23:2623:26, 21 April 2025 diff hist +1 Research:AMOEBA →AMOEBA force field Tag: Visual edit
23:2523:25, 21 April 2025 diff hist +1 Research:AMOEBA →What is next Tag: Visual edit
23:2223:22, 21 April 2025 diff hist −382 Research:Discussion No edit summary current Tag: Visual edit: Switched
23:2123:21, 21 April 2025 diff hist +3,178 N Research:Discussion added page Tag: Visual edit
23:2023:20, 21 April 2025 diff hist +2 Research:amoeba force field →Amoeba: Fixed broken links. The EF hand page was blank on the old biomol so I left it broken here instead of creating blank page. Maybe then it will be a reminder to actually put something current Tag: Visual edit
23:1623:16, 21 April 2025 diff hist +510 N Research:amoeba force field Copied, haven't checked
23:1523:15, 21 April 2025 diff hist +1,225 N Talk:Logs:parameterization Copied, haven't checked current
23:1423:14, 21 April 2025 diff hist +11,710 N Research: AMOEBA Ligand Par Copied, haven't checked current
23:1323:13, 21 April 2025 diff hist +11,733 N Research:AMOEBA Amber Free Copied, haven't checked current
23:1223:12, 21 April 2025 diff hist +812 N 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..." current
23:1223:12, 21 April 2025 diff hist +22,247 N 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-..." current
23:1123:11, 21 April 2025 diff hist +510 N Research:AMOEBA Force Field Copied, haven't checked current
23:1123:11, 21 April 2025 diff hist +8,918 N Logs:parameterization Copied, haven't checked current
23:1023:10, 21 April 2025 diff hist +1,826 N Research:Typer Copied, haven't checked current
23:0923:09, 21 April 2025 diff hist +1,648 N Research:AMOEBA Copied, haven't checked
23:0823:08, 21 April 2025 diff hist +19,524 N Research:DrugDesign Copied, haven't checked current
23:0723:07, 21 April 2025 diff hist +311 N 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== ..." current
23:0723:07, 21 April 2025 diff hist +2,521 N Research:AMOEBA NA Copied, haven't checked current
23:0623:06, 21 April 2025 diff hist +510 N 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..." current
23:0523:05, 21 April 2025 diff hist +17,247 N Research ex:OpenMM Copied, have not edited. Already see some old links I will have to take care of. current
23:0323:03, 21 April 2025 diff hist +53,132 N 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..." current
23:0223:02, 21 April 2025 diff hist +19,090 N Research ex:Tinker OLD Old version of Tinker tut page with some defunct stuff. Wanted to have it somewhere so it wasn't lost current
22:5622:56, 21 April 2025 diff hist +621 N Course:blogs Created page with "== standard formation entropy== *For pure element molecules, the standard formation of free energy and enthalpy are set to 0 (since we only care about relative). *For entropy, however, we use 0K as the reference, so that the absolute entropy of any substance can be measured from Cp vs. T: S(T)=S(0)+integral (Cp/T). *For example, H2 (g)'s standard state absolute entropy (relative to 0K) is 130.6 J/mol K. The standard formation entropy (130.6-130.6) is still 0. The stand..." current
22:5522:55, 21 April 2025 diff hist +5,521 N Course:ABS created Course:ABS page. Need to check that files, links, etc are working current
22:5422:54, 21 April 2025 diff hist +220 N Course: CompMethod Need to check that courses are somewhere so they can be accessed. All I did to edit here was add the page and change biomole.bme.utexas.edu to biomolmd.org. Don't know if that actually exists current
22:5122:51, 21 April 2025 diff hist +613 N Research ex:AMOEBA param added research ex: AMOEBA param current Tag: Visual edit

User contributions for Eew947

21 April 2025

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