Hi,
The 'mask' action will update a distance-based mask each frame and
report the results or allow you to output PDB/mol2 files of the
selected atoms. The reason this doesnt work for Actions in general is
that once they are set up with a certain number of atoms it's
difficult (and expensive) to change this each input frame, although I
guess technically it could be done. In the meantime check out the
'mask' action.
-Dan
On Fri, Sep 4, 2020 at 3:40 PM An Ta <anta.mymail.mines.edu> wrote:
>
> 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
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Fri Sep 04 2020 - 17:00:03 PDT
