[gmx-users] question

[Justin Lemkul]

On 5/13/15 9:15 AM, Andrew Bostick wrote:
> Dear Justin,
>
> For 2 new entries in aminoacids.rtp file, I deleted OE2 atom of GLU
> residue and HZ2 and HZ3 atoms of LYS residue. Is it true? I compared
> CYS and CYS2 residues in aminoacids.rtp file, in both case all atoms
> exist (unlike my case). But there are difference in charges and charge
> groups. How to set charges and charge groups in my case (for Gly2 and
> Lys2)?
>

Based on a peptide bond.

>
> You mentioned to special bond distance matrix. Which file contains special
> bond distance matrix, after pdb2gmx?
>

It's printed in the terminal output.

-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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