[gmx-users] AMBER99 topology for ADP
jalemkul at vt.edu
Thu Jan 15 18:41:38 CET 2015
On 1/15/15 10:59 AM, Marc Hoemberger wrote:
> I tried converting these so I can use them in GROMASC but I was unable to do so. Specifically I had troubles on how to convert the dihedral and “NONBON" parameters to GROMACS format.
There's probably more on this in the AMBER manual or their mailing list, but
general format stuff is here:
Dihedral parameters are the multiplicity, force constants, etc. The weird part
is if there are any negative values that mean special things in their code. The
NONB section is just Rmin (or Rmin/2, again search their doc) and well depth,
both of which are straightforward to convert to sigma/epsilon.
> -Marc Hoemberger
> On Jan 15, 2015, at 10:39 AM, bipin singh <bipinelmat at gmail.com> wrote:
>> Thanks and Regards,
>> Bipin Singh
>> On Thu, Jan 15, 2015 at 7:48 PM, Marc Hoemberger <hoemberg at brandeis.edu>
>>> Does someone have the topology file of ADP for the AMBER forcefield?
>>> Best regards,
>>> Marc Hoemberger
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Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow
Department of Pharmaceutical Sciences
School of Pharmacy
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University of Maryland, Baltimore
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jalemkul at outerbanks.umaryland.edu | (410) 706-7441
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