Re: [AMBER] neighbours around an atom

From: Jason Swails <>
Date: Thu, 3 Jul 2014 09:21:57 -0700

On Jul 3, 2014, at 7:16 AM, Krisztina Feher <> wrote:

> 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
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Received on Thu Jul 03 2014 - 09:30:02 PDT
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