[gmx-users] Updated CHARMM36 force field files available
guillaume.chevrot at gmail.com
Mon Nov 17 12:04:51 CET 2014
thanks for the new version of the charmm36 force field.
I have a question concerning the file merged.hdb.
I noticed that ADP has disappeared from this file. As consequence,
pdb2gmx now (it was not the case with previous release charmm36-mar2014)
WARNING: atom H4' is missing in residue ADP ....
Is there a good reason to have made this modification?
I also noticed that there is no entry in merged.hdb for TP2 (the
On 11/06/2014 01:57 AM, Justin Lemkul wrote:
> I upload a new version of the GROMACS port for the CHARMM36 force
> field today. You can find the files at:
> We have steadily been adding to these files since the last release in
> March. Most fixes are trivial nomenclature adjustments and changes
> related to a few bugs that were propagated in files found in
> charmm27.ff that were subsequently fixed. All were things that would
> have been obvious because they would have triggered fatal errors when
> running pdb2gmx.
> New in this version of the force field are:
> 1. Changed nucleic acid nomenclature (H5' and H5'') for ease of
> interfacing with CHARMM-GUI
> 2. New atom type for Mg2+ to use parameters from
> dx.doi.org/10.1021/ct3000734, see MG entry in ions.itp for the
> "define" keyword
> 3. Addition of phosphorylated amino acids (mono- and dianionic forms
> of Ser, Thr, and Tyr)
> 4. Addition of bacterial lipids
> 5. Addition of S-adenosyl methionine
> Happy simulating!
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