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

From: Jason Swails <>
Date: Thu, 24 Mar 2011 13:05:58 -0700


You can only strip out the waters with rdparm. Furthermore, no prmtops
generated with rdparm actually work for running molecular dynamics (only for
visualization and trajectory analysis with ptraj).

Your best bet is to use the "strip" command with ptraj and trajout as a PDB
file. Then you can read that PDB file back into tleap with your original
library files and frcmod files and get your prmtop file.

The upcoming AmberTools release will have a utility that produces an Amber
OFF file and frcmod with all of the information in your prmtop file (every
residue present in your system), which can easily be used to create a new
prmtop file.

Hope this helps,

On Thu, Mar 24, 2011 at 12:01 PM, g t <> wrote:

> Hi,
> 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,
> GT
> _______________________________________________
> AMBER mailing list

Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
AMBER mailing list
Received on Thu Mar 24 2011 - 13:30:03 PDT
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