[gmx-users] grompp does not find atomtype

[Justin Lemkul]

On 6/30/14, 5:12 AM, Dawid das wrote:
> O'right, I'ill do that but I have also noticed visually something strange.
> The thing is that for my new residue there is no bond shown between two
> atoms although the distance between them is correct and usual for C-S
> single bond.
> I used vmd and opened *.gro file. May that be a problem?
>

No.  VMD's impression of what a bond is is irrelevant.

http://www.gromacs.org/Downloads/Related_Software/Visualization_Software#Topology_bonds_vs_Rendered_bonds

-Justin

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

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

==================================================