[gmx-users] chainsep in pdb2gmx

Justin Lemkul jalemkul at vt.edu
Tue Mar 14 14:29:23 CET 2017

On 3/14/17 8:39 AM, Urszula Uciechowska wrote:
> Dear gmx users,
> I am trying to prepare a protein-dimer DNA complex for MD. The problem is
> that after running pdb2gmx some of the chains are joined. How to use
> chainsep to separate for example chain A and chain B. In my pdb file
> chains are separated by TER flag but it still does not work.

Saying something "does not work" doesn't help anyone diagnose it.  What was your 
exact command line?  Did you get errors, or simply an unexpected outcome?  The 
full screen output can also prove diagnostic for any issues.



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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