[gmx-users] name problem

Justin Lemkul jalemkul at vt.edu
Tue Jan 14 18:47:39 CET 2014

On 1/14/14, 12:37 PM, Albert wrote:
> Hello:
> I found a problem of lipids name when I use editconf each time. My lipids name
> are: POPC and POPG. When I run command:
> editconf -f em.gro -o em.pdb
> the name of my lipids for both POPC and POPG are "POP". I am just wondering how
> can we solve this problem by exporting the full name of lipids?

editconf only writes 3 characters for PDB residue names, per standard format. 
The same is true with other Gromacs programs like trjconv.  Either stick with 
.gro format, which permits 4 characters, or write a script to post-process the 



Justin A. Lemkul, Ph.D.
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


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