[gmx-users] pdb2gmx-4.5 treats DNA as protein (and fails)

[Maiki]

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
-------------------------------------------------------