Dear Jason and Dan,
Thank you for the suggestion. I tried this:
contacts ref mut1_2w_dynV.pdb out contacts.out distance 5 :4.CB<.5.0
which gave 471 native contacts.
And this:
contacts ref mut1_2w_dynV.pdb out contacts.out distance 5 :4.CB<:5.0
which gave 1079 native contacts.
What I need is only small subset of this, ca. 30 distances. These
commands seem to calculate contacts between ALL atoms in that 5A
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:
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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Received on Fri Jul 04 2014 - 03:00:02 PDT
