[AMBER] Fwd: neighbours around an atom

From: Krisztina Fehér <Krisztina.Feher.UGent.be>
Date: Fri, 04 Jul 2014 11:48:08 +0200

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?


> 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 M. Swails
Rutgers University
Postdoctoral Researcher
----- End forwarded message -----
AMBER mailing list
Received on Fri Jul 04 2014 - 03:00:02 PDT
Custom Search