User contributions for Eew947

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
22:4422:44, 21 April 2025 diff hist +31 N Courses: Eew947 moved page Courses: to Category:Courses current Tag: New redirect
22:4422:44, 21 April 2025 diff hist 0 m Category:Courses Eew947 moved page Courses: to Category:Courses current
22:4422:44, 21 April 2025 diff hist 0 N Category:Courses Created blank page Tag: Visual edit
22:4222:42, 21 April 2025 diff hist +387 N CompBiomol added CompBiomol Course page, need to add Course group category current Tag: Visual edit
22:4022:40, 21 April 2025 diff hist +40,840 N Computing Resources & Admin added computing resources and admin page because I don't think we had it. Have not edited it or anything current Tag: Visual edit
22:3622:36, 21 April 2025 diff hist +12 Lab:labinfo →Lab policy & resource current Tag: Visual edit
22:3222:32, 21 April 2025 diff hist +86 Lab:labinfo →General Information Tag: Visual edit
22:2722:27, 21 April 2025 diff hist +1,199 Lab:labinfo →Meetings and Conferences Tag: Visual edit
19:5819:58, 21 April 2025 diff hist +86 Lab:labinfo →Vocation and leave Tag: Visual edit

15:5915:59, 11 August 2022 diff hist +459 m Ammm:ProteinLigandBFE No edit summary current Tag: Visual edit
14:5814:58, 11 August 2022 diff hist −38 m Lab:labinfo →Poltype Github Tag: Visual edit
14:5514:55, 11 August 2022 diff hist +545 m Lab:labinfo →Lab Meetings Tag: Visual edit

21:3621:36, 10 August 2022 diff hist +19 m Ammm:ProteinLigandBFE No edit summary Tag: Visual edit
21:3621:36, 10 August 2022 diff hist +10,712 Ammm:ProteinLigandBFE →Why might we care about calculating binding free energy? Tag: Visual edit
21:3421:34, 10 August 2022 diff hist +4 N File:Thermocycle2.png No edit summary current
21:3321:33, 10 August 2022 diff hist +4 N File:Thermocycle1.png No edit summary current
21:2921:29, 10 August 2022 diff hist +4 N File:Kd2.png No edit summary current
21:0221:02, 10 August 2022 diff hist +4 N File:Atequil.png No edit summary current
20:1720:17, 10 August 2022 diff hist +4 N File:Freeenergykd.png No edit summary current
20:1520:15, 10 August 2022 diff hist +4 N File:Kdstuff.png No edit summary current
20:1120:11, 10 August 2022 diff hist +4 N File:Konoff3.png No edit summary current
20:1020:10, 10 August 2022 diff hist +4 N File:Konoff2.png No edit summary current
20:0920:09, 10 August 2022 diff hist +8 N File:Konoff.png No edit summary current
20:0620:06, 10 August 2022 diff hist +72 N File:5maf in17.png No edit summary current
20:0320:03, 10 August 2022 diff hist +30 N File:Lanmodulin.png No edit summary current
20:0120:01, 10 August 2022 diff hist +76 N File:5maf in17 fancylumps2.png No edit summary current
19:5819:58, 10 August 2022 diff hist +9 N File:AMOEBAeqs.png No edit summary current
19:5619:56, 10 August 2022 diff hist +8 N File:Zwanzig EQ.png No edit summary current
19:5419:54, 10 August 2022 diff hist +8 N File:Bfe1.png No edit summary current
19:5219:52, 10 August 2022 diff hist +104 N File:BFE Energy-vs-RC.png No edit summary current
19:4919:49, 10 August 2022 diff hist −105 m Ammm:ProteinLigandBFE →Protein-Ligand Binding Free Energy (Elizabeth E. Wait) Tag: Visual edit: Switched

13:3413:34, 9 August 2022 diff hist +48 Tutorial:amm →Protein-Ligand Binding Free Energy (Elizabeth Wait) 08/2022 Tag: Visual edit
13:3113:31, 9 August 2022 diff hist +497 N Ammm:ProteinLigandBFE Created page with "= Protein-Ligand Binding Free Energy (Elizabeth E. Wait) = == Introduction == Small Difference Between Large Numbers == Why might we care about getting binding free energy == blah == What is binding free energy (what does it actually mean, esp. protein-ligand) == blah == How do we get it == Force Fields Intro AMOEBA is cool BAR - Justin talking about later Restraints Previous Results - Chemical Accuracy == Things to Think About == Entropy Enthalpy Induced Fit..." Tag: Visual edit
13:1913:19, 9 August 2022 diff hist +80 Tutorial:amm →Protein-ligand binding Tag: Visual edit

User contributions for Eew947

21 April 2025

11 August 2022

10 August 2022

9 August 2022

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