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
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