[AMBER] neighbours around an atom

From: Krisztina Feher <feher_krisztina.yahoo.com>
Date: Thu, 3 Jul 2014 07:16:14 -0700

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).

Thank you in advance,
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Received on Thu Jul 03 2014 - 07:30:02 PDT
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