[gmx-users] pdb2gmx error

Mark Abraham Mark.Abraham at anu.edu.au
Tue Mar 18 01:26:01 CET 2008

Gadzikano Munyuki wrote:
> Hi, i am new to gromacs want to do dynamics on a cyclic polypeptide. The peptide contains a residue that is not standard.I however have included this residue in the ffaoplsaa.rtp file as well as the aminoacids.dat file. When i run  pdb2gmx its giving me a fatal error and its saying the residue is not in the residue topology  database.
> What could be the problem?

Mis-spelling ffoplsaa.rtp?

Beyond that, we have no chance of guessing your problem with this 
information. Please give your command lines, the actual error message 
from pdb2gmx, the contents of your insertion into the .rtp file, the 
file location of that .rtp, and the value of environment variable GMXLIB.


More information about the gromacs.org_gmx-users mailing list