[AMBER] Distanced-based atom selection from the center of mass

From: Umesh Roy <umesh24crp.gmail.com>
Date: Sat, 2 Oct 2021 17:31:20 +0530

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

parm protein.prmtop
trajin product.nc 1 1
reference ../product.nc 1 1

mask (:19<:6.57)&:WAT maskout Res19WATER1.dat

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

Any suggestions from the community would be highly appreciated.

Thank you.

With regards,

Dr. Umesh Roy

New Delhi, INDIA
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Received on Sat Oct 02 2021 - 05:30:02 PDT
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