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 Tue Oct 05 2021 - 07:30:03 PDT
