[gmx-users] Dipole calculation for one residue.

[Justin Lemkul]

On 8/19/14, 1:16 PM, Dawid das wrote:
> I was trying to calculate total dipole moment for one residue of protein
> and I got this error:
>
> Fatal error:
> index[1]=972 does not correspond to the first atom of a molecule
>
> Is it possible at all to calculate dipole for one residue inside  aminoacid
> chain?
>

Not without either (1) changes to the g_dipoles code or (2) a bit of legwork.

In the latter case, you need to generate a topology and .tpr file for the single 
residue of interest, then extract those coordinates from the trajectory using 
trjconv, and then run the analysis to fool g_dipoles into thinking you are 
working with only that molecule.

-Justin

-- 
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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
http://mackerell.umaryland.edu/~jalemkul

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