[gmx-users] Going from OPLS-AA dihedrals to CHARMM22 dihedrals.
jalemkul at vt.edu
Wed Jul 16 13:55:12 CEST 2014
On 7/16/14, 6:51 AM, Dawid das wrote:
> Dear Justin,
> In this case may I use Ryckaert-Bellemans dihedral (func. type 3) for one
> part of the new residue and proper dihedral (multiple) (func. type 9) for
> the rest? Is this "mixing" allowed?
No. Force fields are self-consistent entities; even what may seem like a minor
change can have major implications. CHARMM uses periodic dihedrals, so hacking
in some R-B dihedrals that exist in another force field makes no sense at all.
> 2014-07-16 1:34 GMT+01:00 Justin Lemkul <jalemkul at vt.edu>:
>> On 7/15/14, 1:29 PM, Dawid das wrote:
>>> Dear Gromacs experts,
>>> I have following issue. I need torsional parameters from this publication:
>>> D. V. Dmitrienko et al., Biochemistry (Moscow), 2006, Vol. 71, No. 10,
>>> where OPLS-AA FF has been used but I need to adapt them for CHARMM22 FF.
>>> Now the thing is that there are two different torsional energy expression
>>> used in those FFs.
>>> How can I go from one to another?
>>> To be precise I want to adapt parameters from the above mentioned
>>> publication to expression for torsional potential from this publication:
>>> N. Reuter et al., J. Phys. Chem. B, 2002, Vol. 106, 6310-6321
>>> Any help will be appreciated.
>> It's not wise to try to hack parameters developed for one force field into
>> another. Dihedrals are especially dangerous, because their validity is
>> also dependent upon the nonbonded interactions of atoms 1 and 4 in the
>> interaction; differences in charges and LJ parameters between OPLS-AA and
>> CHARMM will make the dihedral non-transferable.
>> Justin A. Lemkul, Ph.D.
>> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>> Department of Pharmaceutical Sciences
>> School of Pharmacy
>> Health Sciences Facility II, Room 601
>> University of Maryland, Baltimore
>> 20 Penn St.
>> Baltimore, MD 21201
>> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
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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 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201
jalemkul at outerbanks.umaryland.edu | (410) 706-7441
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