Another way of doing it is to use the ambmask command:
ambmask -p prmtop -c inpcrd -prnlev [0|1|2|3] -out [format] -find maskstr
where
prmtop : amber topology
inpcrd : amber (restrt) coordinates
prnlev : amount of (debugging) info printed
format : output format: short|pdb|amber
maskstr : mask string expression (put it in quotes
if spaces or special shell chars present)
In this case you have three output formats, so it may (or may not) be more
helpful, depending on your needs.
Ignacio
On Wed, Jun 8, 2011 at 9:07 AM, Daniel Roe <daniel.r.roe.gmail.com> wrote:
> 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 - 07:00:03 PDT
