Thank you very much for implementing the distance-based atom selection from
the center of mass.
I have a question regarding the selections of atoms. Does the current
implementation select the whole residues or a subset of the residues from
the center of mass of the reference residue? If it selects the whole
residue how one can select a subset of atoms using distance-based atom
selection from the center of mass.
Thank you.
With best regards,
Umesh Roy
On Tue, Oct 5, 2021 at 7:34 PM Daniel Roe <daniel.r.roe.gmail.com> wrote:
> Hi,
>
> This has been implemented in the GitHub version of cpptraj as of
> version 6.0.1. The residue center distance operator is ';', so '<:'
> means 'residues within' and '>:' means 'residues outside of'. Hope it
> helps,
>
> -Dan
>
> On Sat, Oct 2, 2021 at 9:10 AM Daniel Roe <daniel.r.roe.gmail.com> wrote:
> >
> > Hi,
> >
> > This is a good feature idea. I've opened up an issue on the cpptraj
> > GitHub site and hopefully will implement it soon:
> > https://github.com/Amber-MD/cpptraj/issues/917
> >
> > -Dan
> >
> > On Sat, Oct 2, 2021 at 8:02 AM Umesh Roy <umesh24crp.gmail.com> wrote:
> > >
> > > Dear All!
> > > I want to select a group of atoms within a particular distance
> from
> > > the center of mass of a residue. I have used following distance-based
> > > criteria:
> > >
> > > parm protein.prmtop
> > > trajin product.nc 1 1
> > > autoimage
> > > reference ../product.nc 1 1
> > >
> > > #CASE-I
> > > mask (:19<:6.57)&:WAT maskout Res19WATER1.dat
> > >
> > > #CASE-II
> > > mask (:19<.6.57)&:WAT maskout Res19WATER2.dat
> > >
> > >
> > > In the first case, the "mask" selects the whole residue named :WAT if
> any
> > > atom of a :WAT lies within the specified cutoff distance, whereas in
> the
> > > 2nd case it selects the atoms, not the whole residue, that lies within
> the
> > > specified cutoff distance.
> > >
> > >
> > > The distance is calculated from any atom of the reference residue to
> the
> > > target residue/atom(s), if I'm not mistaken. How can I select the
> group of
> > > atoms using distance-based criteria from the center of mass of a
> particular
> > > residue?
> > >
> > >
> > > Any suggestions from the community would be highly appreciated.
> > >
> > >
> > > Thank you.
> > >
> > >
> > > With regards,
> > >
> > > Dr. Umesh Roy
> > >
> > > SCIS,JNU
> > > New Delhi, INDIA
> > > _______________________________________________
> > > AMBER mailing list
> > > AMBER.ambermd.org
> > > http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Mon Oct 11 2021 - 03:00:02 PDT
