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

Asmaa El khodary asma.moh_990 at aucegypt.edu
Tue Mar 31 17:36:19 CEST 2015

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
 *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:
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors

I thought there's a problem with the pdb file and I tried another 3
different files with different force fields, but each time this error
appears. I checked also line 545 in the mentioned file (futil.cpp) and it
seems to be correct. So, do you have any suggestions to overcome this
Thanks in advance
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