Re: [AMBER] Clustering molecule between copies (not between frames)

From: Thomas Cheatham <>
Date: Fri, 30 Jan 2015 08:36:49 -0700 (MST)

> Aha! I think I got it.
> 'closest' command modify coordinate frame *and topology* (not like
> 'strip') so write out the modified topology with 'parmwrite' and use the
> modified topologies to load the produced trajectories right?

...while this will generate smaller trajectories, it will be rather
computationally demanding to generate... A simpler approach if you have
ample disk space is to simply strip out all the peptides except one, for
each peptide, keeping the water and ions. Note that with either the
closest or this option, you will still potentially have artifacts from the
"holes" left over from the missing peptides which will be problematic if
there is close peptide-peptide association... [Note also, that
investigating "dynamics" of water around a cluster is not defined since
there would no longer necessarilly be equal time between frames.]


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Received on Fri Jan 30 2015 - 08:00:05 PST
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