[gmx-users] Lipid-protein tuturial by Lemkul

seunghwan lee seung43210 at yahoo.com
Fri Oct 16 15:53:07 CEST 2009


I am new to Gromacs and going through some tutorials. I am working on 
lipid-protein tutorial given by Justin Lemkul and I am stuck with the 
very first step. When I execute pdb2gmx to generate .top file and .pdb 
without hydrogen,

pdb2gmx -f KALP-15_princ.pdb -o KALP-15_processed.gro -ignh -ter -water spc

I got the following message:

Program pdb2gmx, VERSION 4.0.4
Source code file: pgutil.c, line: 87

Fatal error:
Atom H not found in residue 17 while adding improper


I made the correction to ffG53a6.rtp file as suggested by Justin, but 
apparently I am still having a problem with -NH2 residue (#17). Is there 
any other corrections I need to do in order to make this work?

Thanks for your help!!
Seunghwan Lee


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