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
Received on Sat Oct 02 2021 - 05:30:02 PDT
