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,
Krisztina
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Received on Thu Jul 03 2014 - 07:30:02 PDT
