Dear justin I guess I did right.I add in my topoly file tfe in part of dehedrals " gd_24".(from your edit in dmso topolgy last another mail)and I could minimize. what do you think this adding ?.any way thank you for every thing.now about my peptide I have this error .(in c terminal peptide is amidated) and in this force field ffG53a5,I tried to edit this error (refine pdb file and ...). but didnot.(the 14 residue is phe) 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 ------------------------------------------------------- -- 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