[AMBER] Stripping Protocol in Cpptraj

From: An Ta <anta.mymail.mines.edu>
Date: Thu, 27 Aug 2020 13:50:39 -0600

Dear AMBER colleagues,

I have a question regarding the stripping process used by cpptraj that I
could not find a clear answer too. Regarding the distance-based mask, if a
part of a molecule is not within range of the reference residue, will that
entire molecule be stripped as well? Or is it only molecules that are
completely out of range from the specified distance? From the manual, the
text reads as if the strip function is based on atoms. Would this mean that
the neither case above is true and rather atoms are what will be stripped?
In other words, if part of the residue is out of range of the specified
distance, then part of its structure will be stripped but not the rest?

Thank you for your time and consideration.

*An T. Ta *
Department of Chemistry | Ph.D. Candidate
Coolbaugh Hall | Room 118
Golden, CO 80401
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Received on Thu Aug 27 2020 - 13:00:03 PDT
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