[AMBER] deleting protein atoms from prmtop topology files using rdparm

From: g t <sketchfoot.gmail.com>
Date: Thu, 24 Mar 2011 19:01:36 +0000


I have a parm file with a protein complexed to a ligand within a box of
water. I would like to compare the trajectories of the complexed ligand with
that of the uncomplexed ligand. In order to do this I need to strip out the
waters and in the case of the complexed data set, the protein. I can strip
away the waters and protein atoms from the trajectory files easily enough
using ptraj.

However, after stripping away the water atoms (from the topology file) using
rdparm, I do not see a command in rdparm that will allow me to delete the
protein atoms leaving only the ligand. Is there another way to do this, or
can I use a previously created topology file of just the ligand?

Best regards,
AMBER mailing list
Received on Thu Mar 24 2011 - 12:30:03 PDT
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