Hi,
First, be aware that distance based masks in general do not update each
frame, with the exception of the ‘mask’ command. Second, the behavior
depends on the type of distance based mask. If it’s atom based (e.g. <@)
then only atoms that satisfy the criterion are chosen. If residue based,
all atoms are chosen if any atom in the residue satisfies the criterion.
Same for molecule based masks.
On Thu, Aug 27, 2020 at 3:50 PM An Ta <anta.mymail.mines.edu> wrote:
> 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.
>
>
>
> Sincerely,
>
> *An T. Ta *
>
> Department of Chemistry | Ph.D. Candidate
>
> Coolbaugh Hall | Room 118
>
> Golden, CO 80401
>
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Received on Fri Sep 04 2020 - 11:00:04 PDT
