[gmx-users] building C-Ter residues : automated

[Mark Abraham]

lorna mendonca wrote:
> Hi all,
> 
> I have a bunch of 200 pdb structures with missing C terminal residues ,
> namely OC1 and OC2 due to which I am unable to build a topology file .
> I would appreciate if anyone knows of a tool or program which is capable of
> automatically adding these residues in a batch mode rather than manually
> adding these residues using pymol or swisspdviewer etc.

A correctly formatted C-terminal database for the right forcefield 
should be capable of building those two atoms - see section 5.6.3 of the 
manual. Then you can script pdb2gmx to build these atoms and 
incidentally produce topologies. The advice here 
http://oldwiki.gromacs.org/index.php/Making_Commands_Non-Interactive may 
help.

Mark