Hi, I'm trying to convert protein-DNA complex using pdb2gmx with gromos53a6.ff
$ pdb2gmx -f del.pdb -o del.gro -p del.top -i del.itp -n del.ndx -ignh In gromacs version 4.5-beta2 the result is: Processing chain 3 'C' (516 atoms, 25 residues) There are 0 donors and 0 acceptors There are 0 hydrogen bonds Identified residue DT1 as a starting terminus. Identified residue DA25 as a ending terminus. 8 out of 8 lines of specbond.dat converted successfully Warning: 'DT' not found in residue topology database, trying to use 'DTHY' Start terminus: NH3+ Warning: 'DA' not found in residue topology database, trying to use 'DADE' End terminus: COO- Warning: 'DT' not found in residue topology database, trying to use 'DTHY' Warning: 'DA' not found in residue topology database, trying to use 'DADE' Warning: 'DG' not found in residue topology database, trying to use 'DGUA' (...) Warning: 'DA' not found in residue topology database, trying to use 'DADE' ------------------------------------------------------- Program pdb2gmx, VERSION 4.5-beta2 Source code file: pdb2top.c, line: 922 Fatal error: atom N not found in buiding block 1DT while combining tdb and rtp For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors ------------------------------------------------------- -- 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
