On Jul 3, 2014, at 7:16 AM, Krisztina Feher <feher_krisztina.yahoo.com> 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
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Thu Jul 03 2014 - 09:30:02 PDT
