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

[Maiki]

So, anybody knows why it does that or how to deal with nucleic acids?
I only saw one similar question asked recently (with different error)
which was also left without answer.

Maiki wrote:
> 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
> -------------------------------------------------------
>
>