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19:52, 10 August 2022 Eew947 talk contribs created page File:BFE Energy-vs-RC.png
19:52, 10 August 2022 Eew947 talk contribs uploaded File:BFE Energy-vs-RC.png
13:31, 9 August 2022 Eew947 talk contribs created page 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
14:34, 4 August 2022 Admin talk contribs created page Ammm:chgcorr (Created page with "Corrections in free energy calculations when the simulation box/ligand has a net charge Pengyu Ren Hydration free energy HFE is the free energy of solute transfer from gas to solution. Experimentally only salt property can be determined reliably and single ion HFE requires additional procedure to decompose. Thus there has been a great deal of controversy on what is experimental HFE (see discussion in (1)). Experimental hydration free energy may contain two corrections...")
14:07, 4 August 2022 Liuchw talk contribs created page File:2022 AMM-AMOEBA+ Part I.pdf
14:07, 4 August 2022 Liuchw talk contribs uploaded File:2022 AMM-AMOEBA+ Part I.pdf
18:23, 3 August 2022 Xy3866 talk contribs created page File:Image.png
18:23, 3 August 2022 Xy3866 talk contribs uploaded File:Image.png
16:16, 25 July 2022 Liuchw talk contribs created page File:SAPT.jpg
16:16, 25 July 2022 Liuchw talk contribs uploaded File:SAPT.jpg
22:15, 19 July 2022 Admin talk contribs created page Tutorial:tools (Created page with " Convert PDB to xyz Features: * It does not change atom order so good for post-MD processing. so it is a one-to-one mapping * It supports other fragments (user needs provide) besides amoebabio18. This is good for, such as, chemical modified residues * Link: https://github.com/leucinw/TIPTOP/blob/main/IP_PDB2txyz.py")
18:44, 30 June 2022 Pren talk contribs created page File:Ironporphyrin.png
18:44, 30 June 2022 Pren talk contribs uploaded File:Ironporphyrin.png
17:50, 26 May 2022 Bdw2 talk contribs created page File:Poltype2.pdf
17:50, 26 May 2022 Bdw2 talk contribs uploaded File:Poltype2.pdf
17:49, 26 May 2022 Bdw2 talk contribs created page Ammm:Poltype 2 (Created page with "Testing")
17:41, 26 May 2022 User account Bdw2 talk contribs was created by Admin talk contribs and password was sent by email
14:33, 22 May 2022 User account Xy3866 talk contribs was created by Admin talk contribs and password was sent by email
14:31, 22 May 2022 User account Cda923 talk contribs was created by Admin talk contribs and password was sent by email
14:43, 12 May 2022 User account Bdw2292 talk contribs was created by Admin talk contribs and password was sent by email
14:43, 12 May 2022 User account Kz4686 talk contribs was created by Admin talk contribs and password was sent by email
14:42, 12 May 2022 User account Jtg2769 talk contribs was created by Admin talk contribs and password was sent by email
14:41, 12 May 2022 User account Eew947 talk contribs was created by Admin talk contribs and password was sent by email
14:39, 12 May 2022 Admin talk contribs created page Biowiki:Tutorials-rna (Created page with " <big>Software and example files can be downloaded here: http://biomol.bme.utexas.edu/~davbell/RNACG</big> = Mapping to RACER coarse-grained coordinates starting from PDB crystal structure = Example: 1AL5 Example key file: Parameters /home/user/RNA_CG.prm DEBYE-HUCKEL openmp-threads 1 dielectric 25 debye-length 10 vdwtype LJ-LP #Canonical Hydrogen bonds #G-C CGHBOND 3 6 5 8 4 7 2.0 2.9 6.0 CGHBOND 6 5 3 4 7 8 2.0 2.9 6.0 #A...")
14:39, 12 May 2022 Admin talk contribs created page Biowiki:Development-rna (Created page with " = Download and Install = == Download (2017) == This page is for coarse-grained RNA model '''<big>RACER</big>''' that we have developed to model and simulate RNA molecules and predict RNA structures. The simulation program is based on Tinker (in Fortran), and is available free of charge from [http://biomol.bme.utexas.edu/~rnacg/RNACG http://biomol.bme.utexas.edu/~rnacg/RNACG] or a compressed tarball without *.x and *.o file (compilation is needed) [http://biomo...")
14:38, 12 May 2022 Admin talk contribs created page Software:labsoft (Created page with "=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 op...")
14:37, 12 May 2022 Admin talk contribs created page Tutroial:alltut (Created page with " = Modeling books in dropbox = [https://www.dropbox.com/sh/g3myhes5y1rd6sv/AAAW2FsReOuamNvVWHjqzEA9a?dl=0 https://www.dropbox.com/sh/g3myhes5y1rd6sv/AAAW2FsReOuamNvVWHjqzEA9a?dl=0] = Running Gaussian QM job in tacc = Stampede each node in the '''Normal''' queue has 16 core and 32GB memory. Each job can run for 2 days. There are additional 16 nodes in the “'''largemem'''” queue, each with 1TB memory and 32 core. Create a submission script for each job. ''Only...")
14:34, 12 May 2022 Admin talk contribs created page Tutorial:amber (Created page with "= MM-PBSA free energy estimation tutorial = <div>Author: Chengwen Liu</div> <div>Latest update: Dec. 6th, 2017</div> == a. Theory preparation == A very good tutorial can be found in [http://ambermd.org/tutorials/advanced/tutorial3/ http://ambermd.org/tutorials/advanced/tutorial3/]. I will suggest you to first read this tutorial so you can get a basic understanding of MM-PB/GBSA. The following steps will guide you to b) set up the complex system, c) run MD simulati...")
14:33, 12 May 2022 Admin talk contribs created page Tutorial:amm (Created page with "'''Advanced Molecular Modeling Methods''' = ''Molecular Mechanics and Force Fields (Ren, 3 lectures)'' = == Molecular Mechanics and General force fields == == Electrostatic:polarizable multipole == == Ewald and vdw long range correction == == AMOEBA+ == = ''Molecular Dynamics'' = == Lagrangian and Hamiltonian (Ren) == == Liouville Equation and Ergodicity == =...")
22:27, 11 May 2022 Admin talk contribs created page File:LabCluster.pdf
22:27, 11 May 2022 Admin talk contribs uploaded File:LabCluster.pdf
22:25, 11 May 2022 Admin talk contribs created page Lab:newuser (Created page with " = How to use lab cluster = == Preparation == If you are new to Linux: [https://ryanstutorials.net/linuxtutorial/ https://ryanstutorials.net/linuxtutorial/] == Lab cluster == === ''login'' === You need an account to login to lab cluster to use various software and perform calcualtions. We can no longer log in remotely using password. SSH key is required. '''''You have to come to the lab to do the below in person. If not, ask admin to do it for you...")
16:14, 10 May 2022 Admin talk contribs created page Ammm:Rigid body MD (Steven 12/2) (Created page with "= <references />Introduction = Image:Gay-Berne.png Recall our primary motivations for coarse-graining: 1. Eliminate high frequency motions (if possible), AND, 2. Eliminate "uninteresting" degrees of freedom (both in translation and in rotation) = Rigid Body Equations of Motion = *'''Linear Momentum:''' 1. Definition Image:Linear mom...")
16:13, 10 May 2022 Admin talk contribs created page Ammm:Coarse grain modeling (Created page with "= Introduction = *The time and length scales accessible by all-atom molecular models are limited. *Common bead-springs coarse-grain models cannot represent anisotropy of proteins such as differentiation of φ and ψ angles. *Brownian dynamics used to study diffusion limited reactions. = A Coarse-Grain Model with Anisotropic vdW and Electrostatic Multipoles = *Energy functions has been developed for rigid bodi...")
16:11, 10 May 2022 Admin talk contribs created page Ammm:Comparative Analysis of RNA And Mfold (Created page with "= Prediction of RNA Secondary Structure With Free-Energy Minimization = 400px 700px == Reasons for Predicting the RNA Secondary Structure == === Simpler problem === * RNA secondary structure has a regular structure. * The secondary structure can be broken up into helices(paired) & loops(unpaired). === Kinetics of RNA Folding === * Secondary structure forms very fast; transcription can be the rate-limiting step....")
16:06, 10 May 2022 Admin talk contribs created page Ammm:MM/PBSA with amber: theory and application (Created page with "= Introduction = MM-PBSA method implemented in AMBER is to calculate the binding free energy for the association of two proteins or protein-ligand interation. It represents the postprocessing method to evaluate free energies of binding or to calculate absolute or relative free energies of molecules in solution.The sets of structures are usually collected with molecular dynamics or Monte Carlo methods. The first application of this model in its present form was to study t...")
16:06, 10 May 2022 Admin talk contribs created page Ammm:Flexible Docking with GOLD and GLIDE (Created page with "= Introduction = Many biological processes involve binding of a protein to some target model: * Signaling mechanism between cells * Mechanical operation (e.g. muscle contraction) * Mediation of a catalytic event * ... Drugs can work as competitive inhibitors by binding to proteins more strongly than their natural partners. Laboratory techniques for drug discovery are very time-consuming and expensive, therefore, there is a great deal of interest in developing accurate...") Tag: Visual edit: Switched
16:02, 10 May 2022 Admin talk contribs created page Non equilibrium method and AFM simulation w gromacs (Created page with "== Atomic Force Microscopy == Atomic Force Microscopy (AFM) encompasses a variety of techniques related to the use of an extremely small mechanical probe - the probe tip can have a radius as small as 2 nm - that interacts physically with the sample of interest. In addition, the probe tip can be modified with biomolecules of interest, such as single-stranded DNA, that will interact with other biomolecules on a surface. One measurement an AFM can make is the force require...")
15:59, 10 May 2022 Admin talk contribs created page Ammm:Adaptive umbrella sampling (Created page with "= Multicanonical ensemble = 500px <ref>Ulrich H.E. Hansmann a, Yuko Okamoto, Comparative study of multicanonical and simulated annealing algorithms in the protein folding problem. Physica A 212 (1994) 415-437</ref> Image:Umbrella 22.PNG Image:Umbrella 23.PNG Image:Umbrella 24.PNG = Background of adaptive umbrella sam...")
15:57, 10 May 2022 Admin talk contribs created page Ammm:REMD jenny (Created page with "To enable logging immediately on lonestar, "setenv LOG_BUFS 0". Otherwise the log may be empty when your job dies. Put in brun. == gromacs instruction == http://www.gromacs.org/WIKI-import/REMD Server: http://folding.bmc.uu.se/remd/ paper: http://www.rsc.org/ej/CP/2008/b716554d.pdf '''GROMACS Procedure''' (http://www.gromacs.org/WIKI-import/REMD) The setup of a REMD simulation is actually quite straightforward. The following describes the steps that lead to hav...")
15:57, 10 May 2022 Admin talk contribs created page Ammm:Umbrella sampling and WHAM (Created page with "= Reaction Coordinate = *A reaction coordinate is an abstract one-dimensional coordinate which represents progress along a reaction pathway. **Real coordinate system: bond length, bond angle, torsion **Non geometric parameters: bond order, Hydrogen bonds, RMSD *Reaction coordinates are often plotted against free energy to demonstrate in some schematic form the potential energy profile associated to the...")
15:57, 10 May 2022 Admin talk contribs created page Ammm:Free energy simulations (Created page with "=Free Energy Calculations<ref name="chipot2007">[http://catalog.lib.utexas.edu/record=b5260291~S29 Frenkel, D.; Smit, B., ''Understanding molecular simulation: from algorithms to applications''. Academic: San Diego, Calif. London, 2002.]</ref><ref name="frenkel2002">[http://catalog.lib.utexas.edu/record=b6499358~S29 Chipot, C.; Pohorille, A., ''Free Energy Calculations - Theory and Applications in Chemistry and Biology''. Springer-Verlag: Berlin Heidelberg, 2007; Vol. 86...")
15:56, 10 May 2022 Admin talk contribs created page Ammm:Nonpolar solvation (Created page with "= '''''Hydrophobicity ''' '' = == '''Hydrophobicity<ref>Chandler, D., "Insight Review: Interfaces and the driving force of hydrophobic assembly” Nature 437, 640-647 (2005).</ref> <ref>Chandler, D., "Two faces of water," Nature 417, 491 (2002). </ref>''' == * The hydrophobic effect - the tendency for oil and water to segregate- is important in diverse phenomena. Oil and wat...")
15:55, 10 May 2022 Admin talk contribs created page Ammm:Molecular surfaces (Created page with "= Introduction = Calculating molecular surfaces is important and useful for structure-based drug design, representing molecules and computing inter-molecular interactions. It is also useful for displaying certain molecular properties on the surface, using color-coded and texture maps. Examples of such properties include atomic charge, electrostatic potential, hydrophobicity, polarizability, etc. = Types of Molecular Surfaces = File:Surfaces.png == Van der Waals S...")
15:54, 10 May 2022 Admin talk contribs created page Ammm:PB (APBS) (Created page with "= What is Poisson-Boltzmann Equation(PBE)? = Electrostatics plays a fundamental role in virtually all processes involving biomolecules in solution. The Poisson–Boltzmann equation is a second order nonlinear partial differential equation. It is one of the most fundamental approaches to treat electrostatic effects in solution. Poisson-Boltzmann equatio...")
15:53, 10 May 2022 Admin talk contribs created page Ammm:Gb gk (Created page with "= '''''Why Implicit Solvent Model? ''' '' = == '''Solvation effect''' == * Solvent effect == '''Explicit vs. Implicit Solvent models''' == {| cellspacing="1" cellpadding="3" border="1" class="wikitable" |+ Table Explicit vs. Implicit Solvent Model |- ! Models ! Explicit Solvent Model ! Implicit Solvent Model |- ! Idea | Re...")
15:52, 10 May 2022 Admin talk contribs created page Ammm:QM/MM (Created page with "= Introduction = == What is QM/MM? == *Hybrid method that QM (Quantum mechanics) and MM (molecular mechanics) calculation schemes *The system is divided into two regions **QM and MM regions **Regions are designed based on compromise in calculation time and accuracy == Why use QM/MM? == *The system is too large to use ''ab initio'' calculations *MM calculations do not give the "correct" answer *Processes involving change in electronic structure...")
15:51, 10 May 2022 Admin talk contribs created page Ammm:Lig ion params (Created page with "= Introduction = == Parameters in AMOEBA == *Water first being parameterized *ions, organic molecules, proteins and nucleic acids (under improvement) == How to get parameters == *Experiment *Ab initio QM *Other force field == Unique parameters in AMOEBA == *Multipole (up to quadrupole) *Polarizability *Damping factor [http://water.bme.utexas.edu/wiki/index.php/ABS:mm_mpole Electrostatic Parameters of AMOEBA] = Metal Ion Parameterization = == Why model m...")
15:50, 10 May 2022 Admin talk contribs created page Ammm:Ff amber ligand parameter (Created page with " = Introduction = [http://ambermd.org/antechamber/antechamber.html Antechamber Online Manual] == Antechamber in Amber == File:Amber_flowchart.png File:hivrt.jpg *Cartesian coordinates for each atom in the system. These usually come from Xray crystallography, NMR spectroscopy, or model-building. They should be in Protein Databank (PDB) or Tripos "mol2" format. The program LEaP provides a platform for carrying out many of these modeling tasks, but users may...")
15:49, 10 May 2022 Admin talk contribs created page Ammm:Ff gau grom prdrug (Created page with "= Introduction = == When do we need to create parameters? == *System size is too large for QM '''and''' *Molecule has not been parameterized for the force field being used '''or''' *Molecular environment or conformation is substantially different == Overview of parameterization: == === Quantum Mechanics (QM) === *Optimized (a.k.a. minimum energy) geometry search *Single point calculation to fit the electrostatic potential *Torsion energy profile to calculate...")

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