[gmx-users] how to apply distance restrains between a residue and an ion

[Justin Lemkul]

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

-- 
==================================================

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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