[gmx-users] long-stick molecule solvation

Justin Lemkul jalemkul at vt.edu
Wed Nov 4 13:55:42 CET 2015

On 11/4/15 7:53 AM, xy21hb wrote:
> Hi Justin,
> thanks for your reply. I actually just followed your tutorial on lysozyme.
> I did not set any termini or merge any chains.

Without the exact information I requested, there's nothing anyone can do to help 
you.  Please provide it.  Descriptions of what you did (or what you think you 
did) mean far less than actual input and output from the terminal, especially 
pdb2gmx.  The DD information about bonds suggests something is wrong with the 
topology.  Since pdb2gmx generates the topology, this is where we need to start.



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


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