Dear Daniel,
Thank you so much for your response. This helps me out a lot. Also,
congratulations on your second child!
Regarding the distance-based stripping, I have been referencing a specific
frame of interest to use for the strip command. Is there a way to perform
this kind of stripping where the masks are updated each frame? This is more
out of curiosity so no rush as I am sure you are quite occupied with
catching up on all other CPPTRAJ related emails.
Sincerely,
*An T. Ta *
Department of Chemistry | Ph.D. Candidate
Coolbaugh Hall | Room 118
Golden, CO 80401
On Fri, Sep 4, 2020 at 11:55 AM Daniel Roe <daniel.r.roe.gmail.com> wrote:
> 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
> >
> > _______________________________________________
> >
> > AMBER mailing list
> >
> > AMBER.ambermd.org
> >
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
> >
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Fri Sep 04 2020 - 13:00:02 PDT
