[gmx-users] segment fault when using editconf

Justin Lemkul jalemkul at vt.edu
Thu Dec 5 14:28:19 CET 2013

On 12/5/13 5:38 AM, sunyeping wrote:
> Dear gromcas users, I have a receptor-ligand complex pdb file, and I want to
> use editconf to generate the receptor pdb file and the ligand pdb file. I use
> the following commands:editconf -f _comp0.pdb -o _receptor0.pdb -n
> index.ndxeditconf -f _comp0.pdb -o _ligand0.pdb -n index.ndxThe first command
> seems to work and I get the receptor pdb file. However, the second command
> doesn't work. It gives a "segment fault" information and generate a empty pdb
> file. Could anyone tell me what cause this error?

The most likely cause is a malformatted .pdb or .ndx file.



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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