Home

anténa Krejčí Číst cgenff server políček autorita Profese

Large scale relative protein ligand binding affinities using  non-equilibrium alchemy - Chemical Science (RSC Publishing)  DOI:10.1039/C9SC03754C
Large scale relative protein ligand binding affinities using non-equilibrium alchemy - Chemical Science (RSC Publishing) DOI:10.1039/C9SC03754C

Frontiers | Computational Characterizations of the Interactions Between the  Pontacyl Violet 6R and Exoribonuclease as a Potential Drug Target Against  SARS-CoV-2 | Chemistry
Frontiers | Computational Characterizations of the Interactions Between the Pontacyl Violet 6R and Exoribonuclease as a Potential Drug Target Against SARS-CoV-2 | Chemistry

How to overcome the error: "CGenFF versions are not equivalent!" in running  Gromacs?
How to overcome the error: "CGenFF versions are not equivalent!" in running Gromacs?

FStorm Render | Hi guys, really need you help | Facebook
FStorm Render | Hi guys, really need you help | Facebook

Simultaneous molecular docking of different ligands to His6-tagged  organophosphorus hydrolase as an effective tool for assessing their effect  on the enzyme [PeerJ]
Simultaneous molecular docking of different ligands to His6-tagged organophosphorus hydrolase as an effective tool for assessing their effect on the enzyme [PeerJ]

Precise force-field-based calculations of octanol-water partition  coefficients for the SAMPL7 molecules | SpringerLink
Precise force-field-based calculations of octanol-water partition coefficients for the SAMPL7 molecules | SpringerLink

A scaffolded approach to unearth potential antibacterial components from  epicarp of Malaysian Nephelium lappaceum L. | Scientific Reports
A scaffolded approach to unearth potential antibacterial components from epicarp of Malaysian Nephelium lappaceum L. | Scientific Reports

In silico characterization and homology modeling of cytosolic APX gene  predicts novel glycine residue modulating waterlogging stress response in  pigeon pea [PeerJ]
In silico characterization and homology modeling of cytosolic APX gene predicts novel glycine residue modulating waterlogging stress response in pigeon pea [PeerJ]

parameters for pyridoxal-5'-phosphate (PLP)-serine - CHARMM forums
parameters for pyridoxal-5'-phosphate (PLP)-serine - CHARMM forums

Precise force-field-based calculations of octanol-water partition  coefficients for the SAMPL7 molecules | SpringerLink
Precise force-field-based calculations of octanol-water partition coefficients for the SAMPL7 molecules | SpringerLink

Molecules | Free Full-Text | Drug Repurposing for Influenza Virus  Polymerase Acidic (PA) Endonuclease Inhibitor | HTML
Molecules | Free Full-Text | Drug Repurposing for Influenza Virus Polymerase Acidic (PA) Endonuclease Inhibitor | HTML

Evaluation of nine condensed-phase force fields of the GROMOS, CHARMM,  OPLS, AMBER, and OpenFF families against experimental cross-solvation free  ener ... - Physical Chemistry Chemical Physics (RSC Publishing)  DOI:10.1039/D1CP00215E
Evaluation of nine condensed-phase force fields of the GROMOS, CHARMM, OPLS, AMBER, and OpenFF families against experimental cross-solvation free ener ... - Physical Chemistry Chemical Physics (RSC Publishing) DOI:10.1039/D1CP00215E

Additive CHARMM force field for naturally occurring modified  ribonucleotides - Xu - 2016 - Journal of Computational Chemistry - Wiley  Online Library
Additive CHARMM force field for naturally occurring modified ribonucleotides - Xu - 2016 - Journal of Computational Chemistry - Wiley Online Library

RESNAME error while using cgenff python script - User discussions - GROMACS  forums
RESNAME error while using cgenff python script - User discussions - GROMACS forums

CHARMM force field parameters for 2′-hydroxybiphenyl-2-sulfinate,  2-hydroxybiphenyl, and related analogs - ScienceDirect
CHARMM force field parameters for 2′-hydroxybiphenyl-2-sulfinate, 2-hydroxybiphenyl, and related analogs - ScienceDirect

GitHub - jandom/paramchem: Python scrapper for paramche/cgenff server,  small molecule parametrization
GitHub - jandom/paramchem: Python scrapper for paramche/cgenff server, small molecule parametrization

Prediction of octanol-water partition coefficients for the SAMPL6-[Formula:  see text] molecules using molecular dynamics simulations with OPLS-AA,  AMBER and CHARMM force fields. - Abstract - Europe PMC
Prediction of octanol-water partition coefficients for the SAMPL6-[Formula: see text] molecules using molecular dynamics simulations with OPLS-AA, AMBER and CHARMM force fields. - Abstract - Europe PMC

Tutorial: MD Simulation of a Protein-Ligand Complex using GROMACS —  Bioinformatics Review
Tutorial: MD Simulation of a Protein-Ligand Complex using GROMACS — Bioinformatics Review

Protein-Ligand Simulation Using GROMACS - 作业部落 Cmd Markdown 编辑阅读器
Protein-Ligand Simulation Using GROMACS - 作业部落 Cmd Markdown 编辑阅读器

Prediction of octanol-water partition coefficients for the SAMPL6-[Formula:  see text] molecules using molecular dynamics simulations with OPLS-AA,  AMBER and CHARMM force fields. - Abstract - Europe PMC
Prediction of octanol-water partition coefficients for the SAMPL6-[Formula: see text] molecules using molecular dynamics simulations with OPLS-AA, AMBER and CHARMM force fields. - Abstract - Europe PMC

How to overcome the error: "CGenFF versions are not equivalent!" in running  Gromacs?
How to overcome the error: "CGenFF versions are not equivalent!" in running Gromacs?

FFParam: Standalone package for CHARMM additive and Drude polarizable force  field parametrization of small molecules - Kumar - 2020 - Journal of  Computational Chemistry - Wiley Online Library
FFParam: Standalone package for CHARMM additive and Drude polarizable force field parametrization of small molecules - Kumar - 2020 - Journal of Computational Chemistry - Wiley Online Library

Molecules | Free Full-Text | Comparing Dimerization Free Energies and  Binding Modes of Small Aromatic Molecules with Different Force Fields | HTML
Molecules | Free Full-Text | Comparing Dimerization Free Energies and Binding Modes of Small Aromatic Molecules with Different Force Fields | HTML

Problem while generating JZ4 Topology with CGenFF - User discussions -  GROMACS forums
Problem while generating JZ4 Topology with CGenFF - User discussions - GROMACS forums

CGenFF Server Ligand Penalties - User discussions - GROMACS forums
CGenFF Server Ligand Penalties - User discussions - GROMACS forums