Re: [AMBER] strip :WAT command in ptraj

From: Daniel Roe <>
Date: Tue, 11 Jan 2011 16:48:21 -0500


On Tue, Jan 11, 2011 at 3:39 PM, Daniel Scott <> wrote:
> The strip :WAT command in a ptraj job script gets rid of the waters,
> correct?  And if you save this job as:  "ptrajout A6WTnoWAT.mdcrd nobox",
> e.g., can I then use the "A6WTnoWAT.mdcrd file in the job script to
> calculate time correlation functions and other ptraj commands at a much
> faster rate since the waters are gone?

Yes, except you also need to create a topology file that does not
contain any water before you can run ptraj on the stripped trajectory


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Received on Tue Jan 11 2011 - 14:00:02 PST
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