[gmx-users] No automatic terminus detection

[Matthias Ernst]

Hi,

I try to simulate DNA or better parts of a long DNA double-helix. 
Therefore, the system I use is not "correctly" terminated at the ends 
from chemical point of view with OH-groups but rather cut out the longer 
helix. Nevertheless, all residues are named correctly, all atoms needed 
in the residues are present and corresponding parameters exist in the 
Amber-Forcefield which I intent to use.

When I run pdb2gmx, it always tries to recognize start end ending termini:

Identified residue DG1 as a starting terminus.
Identified residue DC34 as a ending terminus.

and then later on, it fails because the P-Atoms are not found in the rtp 
as it searches e.g. in DG5 instead of DG:

Fatal error:
Atom P in residue DG 1 was not found in rtp entry DG5 with 31 atoms
while sorting atoms.

How can I avoid this error? I tried -noter option but this does not help.
Is there a way to just treat the residues as the occur in the pdb-file 
without automatically detection of starting and ending terminus?

Thanks for your help,
Matthias