[gmx-users] question

[Justin Lemkul]

On 5/13/15 8:50 AM, Andrew Bostick wrote:
> Dear Justin
>
> Thanks for your attention.
>
> I viewed coordination file, distance between these atoms are greater
> than distance
> criterion in specbond.dat file. you are right. I will correct this distance.
>
> Is my manner true (1 new entry in specbond.dat file and 2 new entries in
> aminoacids.rtp file)? If I correct this distance, will my problem resolve?
>

Yes.  See previous posts in the archive on this exact approach and consider the 
fact that it's the exact mechanism as in the case of disulfides.

-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 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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