Top Tweets for #CGenFF
Run CGenFF for Just $1 per Molecule (July Only)
Industry users can now generate topology and parameters for small molecules for just $1 each.
Explore #CGenFF with minimal commitment and maximum flexibility.
https://t.co/jrDZasf1JC
#CompChem #MolecularModeling
Disappointed to learn that #CGenFF for #CHARMM is not free for all academic research BUT only universities. Apparently, all non-profit research institutes need to pay. Thus, claims that it is free for any academic research I find misleading. @alex_mackerell @CharmmGui @silcsbio
Try FFParam. It's based on #CGenFF, allowing for novel molecules to be generated and the needed QM and subsequent MM calculations performed followed by fitting of both nonbond and bonded parameters. https://t.co/FrOpoiOozF 10.1002/jcc.26138
What is your favourite tool for parameterizing molecules for #MolecularDynamics? I use @CharmmGui but is limited at 350 atoms for ligands and doesn't let tweak the already available polymers, sugars etc. I wonder if there's a better option!
PS I need input for #Gromacs
#compchem
Nice extension of the #CHARMM additive FF, including #CGenFF, in combination with the @CharmmGui to study a large heterogeneous system. Did you use the C36 carbohydrate params or CGenFF to model the glycans?
#MolecularModeling and Simulation of the #Peptidoglycan Layer of Gram Positive Bacteria #Staphylococcusaureus #MolecularSimulations
https://t.co/Kimf0egi5R
#vol62 #issue20 #JCIM #compchem
@marcvanderkamp Good performance of EnzyDock is in part thanks to the very good parameters from #CGenFF and #CHARMM and of course the underlying CHARMM simulation machinery
We've just submitted a manuscript on an extension of the #CHARMM additive force field combined with #CGenFF to 333 non-standard amino acids. Collaboration with Alexey Aleksandrov and @CharmmGui That should help with the FF side of things.
What's the state of the art these days for constructing rotamer libraries for nonstandard amino acids? I used to use a method based on https://t.co/RxcXzgKlRh, but it was very hands-on, involving fitting forcefield terms. Anything both accurate and mostly automated?
#CGenFF (https://t.co/N7MA6N2mpc and https://t.co/mLeV8eh5jd) is among the TOP-CITED @JCIM_ACS papers published in the past 60 years! https://t.co/YY64jttrqU
Contact us for academic & commercial licensing of the CGenFF program.
#compchem #drugdiscovery
Assessment of the Fragment #Docking Program #SEED
https://t.co/snZaBKdUBh
@hermanvvlijmen
@amedeocaflisch @hans_silicos_it
#ASAP
Labmates and I visited @alex_mackerell lab on Fri to learn the newly developed FFParam. Through it, I savored the art of FF parametrization. It was a great visit. At dinner table in Maiwand Grill, students had discussions about CHARMM, FF, software develop...
The #CGenFF program produces the required topology and parameter information for ligands instantaneously allowing for high-throughput applications on 10's or 100's of thousands of compounds or more.
The CGenFF program provides ligand topology and parameter files in CHARMM (stream file) format and in GROMACS-friendly formats, letting you more easily use your MD engine of choice.
#GROMACS #compchem #MolecularDynamics
The latest updates to the CGenFF program (version 2.3.0) include improved support for tetrazoles, oxetanones, protonated amines, and alkynes by explicit paramaterization of select molecules of these types, and improved halogen-protein interactions.
https://t.co/DzjrHwoUCs
Improved Modeling of Halogenated #LigandโProtein Interactions Using the #Drude Polarizable and CHARMM Additive Empirical Force Fields
https://t.co/tJrnCuQ2TE
@alex_mackerell
#Current_Issue #Computational_chemistry
12 low-micromolar inhibitors for JMJD3 jumonji demethylase by a novel multi-step protocol for in silico screening. @JCIM_ACS @jcim_papers
https://t.co/WTaczSS2HZ
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