Hi 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 _______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php