Dear justin Hi, In my simulation with ff53a5 when I do this command pdb2gmx -f name.pdb -ter -ignh -water spce .I find this error .C-terminus: None Now there are 14 residues with 138 atoms Making bonds... Opening library file /usr/local/gromacs/share/gromacs/top/aminoacids.dat Number of bonds was 142, now 139 Generating angles, dihedrals and pairs... Before cleaning: 210 pairs
------------------------------------------------------- Program pdb2gmx, VERSION 3.3.2 Source code file: pgutil.c, line: 87 Fatal error: Atom H not found in residue 14 while adding improper how can resolve this problem? best regards -- sh-karbalaee _______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
