[gmx-users] PTM force field
xubest at gmail.com
Thu Dec 18 12:05:25 CET 2014
I do want to manually add the new parameters into the existing Amber force
field in Gromacs.
In the folder of each force field "....../share/gromacs/top/*.ff". There
are many files. Some of them are obvious to modify (e.g. aminoacids.rtp).
Could you please advise a complete file list that I should modify? or a
link of tutorials at somewhere I can read and follow. Thank you very much!
On Thu, Dec 18, 2014 at 10:54 AM, Justin Lemkul <jalemkul at vt.edu> wrote:
> On 12/17/14 4:39 PM, Jianqing Xu wrote:
>> Dear GMX Users,
>> I am trying to simulate a protein with a cysteine sulfenic acid (Cys-SOH).
>> I notice that both AMBER and GROMOS force field should have the parameters
>> for residues having post-translational modifications :
>> PTM-GROMOS can be downloaded and used in GROMACS without problems.
>> looks like the PTM-AMBER force field can only be used in AMBER package, it
>> it correct? For some historical reasons, I am looking for the possibility
>> to consistently use AMBER force field. I was wondering whether PTM-AMBER
>> ready yet for GROMACS?
> If the parameters exist, the only challenge is unit conversion and writing
> them in Gromacs format. Gromacs has supported Amber force fields for a
> 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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