[gmx-users] No automatic terminus detection

[Mark Abraham]

On 8/12/2011 9:40 PM, Matthias Ernst wrote:
> 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.

OK, but the valences still have to be satisifed. It's up to you to 
decide how.

>
> 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?

pdb2gmx can only put pieces together that are defined in the forcefield 
.rtp and .tdb. It knows that termini have to be different from mid-chain 
residues. Either it needs to find a named capping residue in the 
coordinate file that matches the .rtp, or the -ter mechanism needs to be 
used to generate a terminus from the .tdb on a normal residue in the 
.rtp identified from the coordinate file.

Mark