Hi,
Cpptraj can do something like what you ask via the "mask" command. For
example, given the input:
parm prmtop
trajin mdcrd.nc
mask (:195<:3.0)&:WAT maskout mask.out
cpptraj will print out all atoms within 3.0 angstroms of residue 195
that are also WAT residues. The output will look something like:
#Frame AtomNum Atom ResNum Res MolNum
1 8838 O 1865 WAT 1598
1 8839 H1 1865 WAT 1598
1 8840 H2 1865 WAT 1598
1 14235 O 3664 WAT 3397
1 14236 H1 3664 WAT 3397
1 14237 H2 3664 WAT 3397
...
You could change the mask to "(:195<:3.0)&!(:WAT)" to select all
non-WAT residues. See the cpptraj mask syntax (7.2.2.1) and mask
command syntax (7.2.2.6) for more details. Let me know if you have any
more questions.
-Dan
On Wed, Jun 8, 2011 at 8:40 AM, Guenegou, Guillaume [ORDFR]
<GGUENEGO.its.jnj.com> wrote:
> Dear all,
>
> Is there a way to detect protein residues within a sphere (e.g. 5
> angstrom radius) around a given residue of this protein?
> I am working with Amber11 and AmberTools1.5.
>
> I guess it was possible with Carnal, but it is no longer used in those
> versions.
>
> Regards,
> G.GUENEGOU
>
> _______________________________________________
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> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Wed Jun 08 2011 - 06:30:02 PDT
