Thanks to both of you for your suggestions. :)
On 24 March 2011 21:29, Chris Chris <alpharecept.yahoo.com> wrote:
> 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 <sketchfoot.gmail.com>
> To: amber.ambermd.org
> Sent: Thu, March 24, 2011 3:01:36 PM
> Subject: [AMBER] deleting protein atoms from prmtop topology files using
> rdparm
>
> 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
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Received on Fri Mar 25 2011 - 04:00:02 PDT
