[gmx-users] gromacs: pdb2gmx error

venkatesh s svenkateshbioinformatics at gmail.com
Sat Feb 25 08:30:42 CET 2012

      i got that error in the step of pdb2gmx what can i do
i read also
can any one tell exact reason and how i handle further
thanking you

All occupancies are one
Opening force field file
Atomtype 1
Reading residue database... (oplsaa)
Opening force field file
Residue 56
Sorting it all out...
Opening force field file
Opening force field file
Opening force field file

Back Off! I just backed up topol.top to ./#topol.top.4#
Processing chain 1 'E' (603 atoms, 20 residues)
Identified residue DG2 as a starting terminus.
Warning: Residue MN1022 in chain has different type (Other) from starting
residue DG2 (DNA).
Identified residue DT20 as a ending terminus.
8 out of 8 lines of specbond.dat converted successfully

Program pdb2gmx, VERSION 4.5.5
Source code file: resall.c, line: 581

Fatal error:
Residue 'DG' not found in residue topology database
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors

II M.Sc Bioinformatics,
Alagappa University,
Tamil Nadu,

Mobile Phone:- 9486494616
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