[gmx-users] Updated CHARMM36 force field files available

Justin Lemkul jalemkul at vt.edu
Mon Nov 17 22:39:59 CET 2014

On 11/17/14 4:22 PM, Guillaume Chevrot wrote:
> Le 17/11/2014 18:32, Justin Lemkul a écrit :
>> 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.
> OK. So maybe it could also be added in the next release by default? If I can
> help ...

The .hdb for ADP would be the same as ADE, unless you're doing something 
non-physiological with the phosphate protonation states.  Then it's simply 
hydroxyl syntax.

I can certainly add it, but we're still not covering about 90% of the chemical 
space that the .rtp does.  At best, we provide building blocks for the most 
common biopolymers, otherwise it's a never-ending battle for .hdb writing which, 
as I said, manual.  Unless we figure out some very clever way to construct .hdb 
from .rtp, then I can never hope to deliver everything in both files.  Of 
course, if anyone has any brilliant insights on converting CHARMM .rtf to 
GROMACS .hdb using Python (which is what our converter is written in right now), 
I'm all ears...



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


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