[gmx-users] about position restrain
jalemkul at vt.edu
Sat Aug 20 13:12:56 CEST 2016
On 8/19/16 4:14 PM, Albert wrote:
> Hi Justin,
> thanks for the advice.
> The are plenty of paper have discussed that it is necessary to restrain the
> backbone ,or at lease the CA atoms, of a homology models. Otherwise it would
> turn out to be something completely nonsense.
Without context, I can't comment, but I'd stick by my original comments. If you
have to force a protein to stay a certain conformation, what confidence do you
have that that conformation is actually relevant if it otherwise distorts or
changes? Layering assumptions on assumptions is often a bad way to go, but
proceed how you like...
> Probably restrain the secondary structure would be reasonable. May I ask how can
> we do this in Gromacs? Is there any documentation?
Dihedral restraints are described in the print and online manuals, and there are
examples on gromacs.org.
> Thx a lot
> On 08/19/2016 09:32 PM, Justin Lemkul wrote:
>> Why is it necessary to impose any restraint on the backbone in the first
>> place? If you don't have confidence in the homology model and you are
>> enforcing a given structure, then there is little confidence that any observed
>> dimerization is legitimate. You should prove that the structure is
>> reasonable/stable and do a normal simulation without restraints.
>> If, for some reason, you must apply restraints to maintain some secondary
>> structure element(s), then use dihedral restraints, not position restraints.
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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