[gmx-users] Updated CHARMM36 force field files available

[Justin Lemkul]

On 11/17/14 6:04 AM, Guillaume Chevrot wrote:
> Dear Justin,
>
> 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) complains:
> WARNING: atom H4' is missing in residue ADP ....
>
> Is there a good reason to have made this modification?
>

It wasn't removed; our released force fields have never had ADP in the .hdb 
file.  The .hdb is written manually, so it doesn't cover everything in the .rtp 
file.

>
> I also noticed that there is no entry in merged.hdb for TP2 (the dianionic
> phosphotyrosine).
>

I will add these for the next release.  For the dianionic species, the .hdb will 
be the same as the unphosphorylated residue, minus the hydroxyl H.  The 
monoanionic are the same, with hydroxyl syntax for the HPO4 atom the same as any 
other hydroxyl.  Let me know if you need help adding these.

-Justin

-- 
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Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

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