Hi,
On Fri, Jul 4, 2014 at 3:48 AM, Krisztina Fehér <Krisztina.Feher.ugent.be>
wrote:
> circle. I wonder if I could rather use the distance action command. I
> tried this:
>
> distance 4CB :4.CB :*.C out 4CBtoCO.dist noimage
>
> but it averages all distances into one distance:
>
It's actually the distance between the the first atom and the center of
mass of the atoms selected by ':*.C' (note that the :* is not necessary as
.C implies :*).
You can generate the input you need relatively easily via a script. Cpptraj
has several command-line flags which allow you to access the mask parser in
various ways. For example you could use something like (in bash):
for ATOM in `cpptraj -p topology.parm7 -ms '.C'` ; do
if [[ $ATOM != "Selected=" ]] ; then
echo "distance 4CB_$ATOM :4.CB .$ATOM out 4CBtoCO.dist noimage" >>
cpptraj.in
fi
done
Hope this helps,
-Dan
> Frame 4CB
> 1 8.6029
> 2 8.9513
> 3 8.9097
> 4 8.6357
> 5 8.4419
> 6 8.7178
> ....
>
> Is there some way to force cpptraj to iterate over the atoms in the mask?
>
>
> Thanks,
> Krisztina
>
>
>
>
>
>
>
>
> > Dear All,
> >
> > I would like to qualitatively understand which other atoms could
> > potentially affect the 13C chemical shift of :4.CG via anisotropic
> > shielding effects. For this reason I am looking for an analysis
> > command, which would enable me to list all atoms within a certain
> > threshold around a particular atom (let's say :4.CG) during the
> > trajectory. I am searching for something similar to
> > Action/modfiy/around/atoms withing 5A function in Pymol, just
> > applied to a whole trajectory. I was trying the contact command in
> > ccptraj, but it generated either contacts from all atoms to all atoms:
> >
> > contacts first out contact.out distance 5
> >
> >
> > or certain atoms to certain atoms:
> >
> > contacts first out contacts.out distance 5 @CG
> >
> > while I would like to have :4.CG to all atoms (or maybe only to
> > carbonyl or nitrogen groups).
>
> Perhaps a mask that selects based on a distance criteria will work?
>
> Something like "(:4.CG<@5.0)" will select all atoms within 5 angstroms
> of the CG atom of residue 4. Replacing @5.0 with :5.0 will select all
> residues within 5 Angstroms of the CG atom of residue 4.
>
> You can use the "mask" command in cpptraj to write a list of atoms
> that satisfy the criteria. In general, masks are evaluated once at
> the beginning (on the reference structure or first frame), but I think
> the "mask" command is different in this regard and evaluates the mask
> for every frame. Dan can correct me if I'm wrong here.
>
> Hope this helps,
> Jason
>
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
>
> ----- End forwarded message -----
>
>
>
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--
-------------------------
Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 201
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 Fri Jul 04 2014 - 11:30:02 PDT
