[gmx-users] how to apply distance restrains between a residue and an ion
jalemkul at vt.edu
Tue Sep 1 23:27:46 CEST 2015
On 9/1/15 2:54 PM, Victor Ma wrote:
> hello all
> I need to apply a distance restraint between a sodium and a residue. I read
> the manual, etc, which seems to suggest adding something like below to the
> .itp file.
> [ distance_restraints ]
> ; ai aj type index type’ low up1 up2 fac
> 10 16 1 0 1 0.0 0.3 0.4 1.0
> 10 28 1 1 1 0.0 0.3 0.4 1.0
> But my protein and ions are in two separate itp file. So how do I do it?
> Also I have multiple sodiums, but in the SOD.itp file, there is only one line
> [ moleculetype ]
> ; name nrexcl
> SOD 1
> [ atoms ]
> ; nr type resnr residu atom cgnr charge mass
> 1 SOD 1 SOD SOD 1 1.000 22.9898
> ; qtot 1.000
> So how do I get the atom number for the specific sodium I want to restraint?
Either you need to use the pull code (simple harmonic restraint) or if you need
the flat-bottom nature of the distance restraints, you need to place the
[distance_restraints] directive under an [intermolecular_interactions] directive
and use global atom numbers. This feature is only available in version 5.1.
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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