Hi,
On Sat, Jul 5, 2014 at 8:18 AM, Krisztina Fehér <Krisztina.Feher.ugent.be>
wrote:
>
> :4.SG<:5.0&.C
>
This mask seems valid. Did you receive an error message when you used it?
-Dan
>
> which did not work and would like to know why. Is there a limitation
> in the use of the logical operators?
>
> Thank you,
> Krisztina
>
>
>
>
>
>
>
>
> Quoting Daniel Roe <daniel.r.roe.gmail.com>:
>
> > 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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> > http://lists.ambermd.org/mailman/listinfo/amber
>
>
>
>
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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 Sat Jul 05 2014 - 08:00:03 PDT
