Hi,
The 'mask' command in CPPTRAJ can be used with a distance-based mask
to generate this information (and/or generate PDBs or mol2 files) like
so:
parm tz2.ortho.parm7
trajin tz2.ortho.nc
mask "(:5 <:3.0)" maskout mask.out maskpdb mask.pdb
The mask in this case specifies all residues within 3.0 Angstroms of
residue 5. The file mask.out will contain information on the
atoms/residues satisfying the selection and a series of PDB files (1
for each frame) named mask.pdb.X will be generated.
Hope this helps,
-Dan
On Tue, Feb 24, 2015 at 12:42 PM, Alessandra Lacetera
<alessandra.lacetera.gmail.com> wrote:
> Hi,
> I was wondering if there is any command in cpptraj/ptraj to visualize which
> residues is near to an atom during the simulation.
> For example, it will be like defining a shell (but not solvent shell) for
> e.g. of 6 Angstroms for an atom (like :LIG.H1) and the output should tell
> us which residues is in that shell during the simulation.
>
> I have checked the manual and I don't think to have seen this kind of thing.
>
> Regards
>
> Alessandra
>
> --
> Alessandra Lacetera
> PhD Student CIB (CSIC)
> Calle Ramiro de Maetzu, 9
> 28040, Madrid - Spain
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--
-------------------------
Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 307
Salt Lake City, UT 84112-5820
http://home.chpc.utah.edu/~cheatham/
(801) 587-9652
(801) 585-6208 (Fax)
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Received on Tue Feb 24 2015 - 12:00:32 PST
