Main public logs

Combined display of all available logs of biowiki. You can narrow down the view by selecting a log type, the username (case-sensitive), or the affected page (also case-sensitive).

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...")
23:02, 21 April 2025 Eew947 talk contribs created page Research ex:Tinker OLD (Old version of Tinker tut page with some defunct stuff. Wanted to have it somewhere so it wasn't lost)
22:56, 21 April 2025 Eew947 talk contribs created page 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...")
22:55, 21 April 2025 Eew947 talk contribs created page Course:ABS (created Course:ABS page. Need to check that files, links, etc are working)
22:54, 21 April 2025 Eew947 talk contribs created page 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)
22:51, 21 April 2025 Eew947 talk contribs created page Research ex:AMOEBA param (added research ex: AMOEBA param) Tag: Visual edit
22:44, 21 April 2025 Eew947 talk contribs moved page Courses: to Category:Courses
22:44, 21 April 2025 Eew947 talk contribs created page Courses: (Created blank page) Tag: Visual edit
22:42, 21 April 2025 Eew947 talk contribs created page CompBiomol (added CompBiomol Course page, need to add Course group category) Tag: Visual edit
22:40, 21 April 2025 Eew947 talk contribs created page Computing Resources & Admin (added computing resources and admin page because I don't think we had it. Have not edited it or anything) Tag: Visual edit
17:37, 22 November 2024 User account Zh6674 talk contribs was created by Admin talk contribs and password was sent by email
15:42, 18 November 2024 Admin talk contribs created page Tinkermeeting:tinkermeeting2022 (Created page with "2022 Maryland ######################################################################### ATTENDEE LIST FOR TINKER DEVELOPER WORKSHOP, JUNE 2-4 2022, NIH, BETHESDA ######################################################################### Charlles Abreu abreu@eq.ufrj.br U Rio de Janeiro Olivier Adjoua passi.adjoua@sorbonne-universite.fr Sorbonne, Paris Cole Allen coleallen@utexas.edu UTexas Austin Feli...")
18:08, 7 November 2024 User account Mayar talk contribs was created by Admin talk contribs
15:08, 16 June 2024 Pren talk contribs created page File:Program.pdf (Tinker 2024 program)
15:08, 16 June 2024 Pren talk contribs uploaded File:Program.pdf (Tinker 2024 program)
15:03, 16 June 2024 Pren talk contribs created page File:2023-Tinker-Workshop.jpg
15:03, 16 June 2024 Pren talk contribs uploaded File:2023-Tinker-Workshop.jpg
15:00, 16 June 2024 Pren talk contribs created page Tinkermeeting:tinkermeeting2023 (Created page with "######################################################################### ATTENDEE LIST FOR TINKER DEVELOPER WORKSHOP, JUNE 15-17 2023, SAINT LOUIS ######################################################################### Cole Allen coleallen@utexas.edu UT Austin Felix Aviat felixaviat@gmail.com NIH NHLBI Bernie Brooks brb@nhlbi.nih.com NIH NHLBI Dave Cerutti david.cerutti@psivan...")
14:41, 7 June 2024 Pren talk contribs created page Tinkermeeting:tinkermeeting2024 (Created page with "https://molecolab.dcci.unipi.it/program-tinker.html thumb")
14:41, 7 June 2024 Pren talk contribs created page File:Tinker2024 Group Picture.jpg
14:41, 7 June 2024 Pren talk contribs uploaded File:Tinker2024 Group Picture.jpg
13:49, 16 April 2024 Admin talk contribs created page Tutorial:amoeba FF (Created page with "See page under Tutorials")
16:18, 6 February 2024 Admin talk contribs created page File:Tinker2018group.jpg
16:18, 6 February 2024 Admin talk contribs uploaded File:Tinker2018group.jpg
16:16, 30 January 2024 Admin talk contribs created page Poltype:Poltype (Link) Tag: Visual edit
20:24, 16 November 2023 Admin talk contribs created page Software:forcebalance (Created page with "= '''Background''' == ForceBalance is an automatic force field parametrization tool developed by Lee-Ping Wang et al. It allows one to use both quantum chemical data and experimental observables of the liquid phase. It has been applied to parameterize a bunch of water models and organic molecules. The following examples are some of them. <code>'''<cite>J. Phys...")
20:19, 16 November 2023 Admin talk contribs created page Biowiki:Forcebalance (Created page with "Test")
20:51, 15 November 2023 User account Mm227274 talk contribs was created by Admin talk contribs and password was sent by email
22:41, 23 October 2022 Admin talk contribs created page File:Milestoning.pdf
22:41, 23 October 2022 Admin talk contribs uploaded File:Milestoning.pdf

Main public logs

Navigation menu

Search