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

From: Chris Chris <>
Date: Thu, 24 Mar 2011 14:29:25 -0700 (PDT)

It's always easiest to work with PDB files rather than topology files. When
working with PDB files where you want to get rid of waters, learn how to use the
'sed' command in unix if you already don't know how. For example, one can delete
all of the waters in a file by using

sed '/WAT/,d$'
this will delete all the waters in your pdb fike, provided all of your protein
and/or nucleic acid data is included before the waters. My work demands that I
extensively edit PDB files and find such commands to be great time savers. Now
you can go into leap and make your new .top and .crd files.

From: g t <>
Sent: Thu, March 24, 2011 3:01:36 PM
Subject: [AMBER] deleting protein atoms from prmtop topology files using rdparm


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,
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Received on Thu Mar 24 2011 - 14:30:02 PDT
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