[gmx-developers] Problem with creating a topolgy from PDB file

Justin Lemkul jalemkul at vt.edu
Tue Mar 31 17:49:55 CEST 2015

Please do not post usage questions on the developers' list.  I am CC'ing this 
over to gmx-users; please continue any discussion there.

On 3/31/15 11:36 AM, Asmaa El khodary wrote:
> Hi,
> I'm a new user of gromacs and I follow some tutorials to run a simulation of
> lysozyme using OPLS-AA/L force field . The problem is: when I type the command
> *pdb2gmx -f 1LYD.pdb -water tip3p *in the terminal and choose the force field ,I
> get this error
> Program pdb2gmx, VERSION 5.0.4
> Source code file:
> /home/asmaa/Downloads/gromacs-5.0.4/src/gromacs/fileio/futil.cpp, line: 545
> File input/output error:
> 1LYD.pdb

An I/O error means the file isn't in your working directory (or, less likely, 
the file isn't readable to you).  List your files to verify.



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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