[gmx-users] error in creat topology

shahrbanoo karbalaee shahrbanoo at gmail.com
Tue Sep 23 15:04:44 CEST 2008

Dear justin
I want to creat topology file tfe by ffopls.I get pdb file tfe and add
atoms and bond  tfe atoms to ffoplsrtp file in top file gromacs.so in
hdd  I add hydrogen atoms.when I do pdb2gmx -f tfe.pdb.I get this
Opening library file /usr/local/gromacs/share/gromacs/top/ffoplsaa.rtp
Residue 56
Sorting it all out...
Opening library file /usr/local/gromacs/share/gromacs/top/ffoplsaa.hdb
Opening library file /usr/local/gromacs/share/gromacs/top/ffoplsaa-n.tdb
Opening library file /usr/local/gromacs/share/gromacs/top/ffoplsaa-c.tdb

Back Off! I just backed up topol.top to ./#topol.top.8#
Processing chain 1 (9 atoms, 1 residues)
There are 0 donors and 0 acceptors
There are 0 hydrogen bonds

Program pdb2gmx, VERSION 3.3.2
Source code file: resall.c, line: 436

Fatal error:
Residue 'TFE' not found in residue topology database

thank you foe your advise.

More information about the gromacs.org_gmx-users mailing list