[gmx-users] Fatal error

Urszula Uciechowska urszula.uciechowska at biotech.ug.edu.pl
Wed May 6 13:56:00 CEST 2015


I am trying to run pdb2gmx by using:

pdb2gmx -f COM-oH.pdb -o COM-oH.gro -p COM-oH.top -ignh -water tip3p -ter

however I am getting a fatal error:

Program pdb2gmx, VERSION 4.5.3
Source code file: pgutil.c, line: 99

Fatal error:
Atom C not found in residue seq.nr. 137 while adding atom

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

"(That makes 100 errors; please try again.)" (TeX)

I have checkec the 137 AA and there is C atom. The system consist of DNA
and 3 protein receptors. I used  6: AMBER99SB-ILDN force field. What is
wrong here?

best regards

University of Gdansk and Medical Univesity of Gdansk
Department of Molecular and Cellular Biology
ul. Kladki 24
80-822 Gdansk

Ta wiadomość została wysłana z serwera Uniwersytetu Gdańskiego

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