Thanks for the shell script, Dan.
One more question: can you combine a distance-based criterion with an
atom name selection? So, is it possible to select e.g. carbonyl atoms
within 5A distance from :4.SG? I tried to join these two selections
with "&":
.C&:4.SG<:5.0
and
:4.SG<:5.0&@C
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 -----
>>
>>
>>
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>
>
>
> --
> -------------------------
> 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)
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Sat Jul 05 2014 - 07:30:02 PDT
