[gmx-users] amino acid topology

[Justin Lemkul]

On 6/16/17 1:12 PM, suniba shuaib wrote:
> Hello users and experts
> I want to know if I can use gmx x2top for generating topology of a modified
> amino acid linked with a natural peptide sequence?
> or in general topology of a small molecule?
> 

x2top is the wrong tool for this job.  Write an .rtp entry once you have 
parameters from the modified residue.  x2top is good for very generic or 
repeating molecules; if you try to write the .n2t entries for something with 
lots of unique connectivity like an amino acid, you'll be doing a whole lot more 
work that's not necessary.

-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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