[gmx-users] PTM force field

[Jianqing Xu]

Thanks Justin,

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!

Best regards,

Jianqing

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 :
>> http://selene.princeton.edu/FFPTM/
>> http://vienna-ptm.univie.ac.at/
>>
>> PTM-GROMOS can be downloaded and used in GROMACS without problems.
>> However,
>> 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
>> is
>> 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
> decade.
>
> -Justin
>
> --
> ==================================================
>
> 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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