[AMBER] debug energy into individual atoms

From: Jorgen Simonsen <jorgen589.gmail.com>
Date: Sun, 1 Apr 2012 23:16:39 +0200

Hi all,

I am simulating a protein which contains a lot of cysteine residues -
after ~ 20 ns of simulation two sulfur atoms are getting very close
1.72 as their mean value with minimum distance of 1.21. All the
cysteines in the protein are modeled as CYM with a negative charge so
I would image that they would be repulsed. My question is if it is
possible to somehow deduced the force contributions using ambertools
or something like that too find gradient/force that are so big that
they are able to push these atoms together (being real or an artifact)
?

Thanks in advance

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Received on Sun Apr 01 2012 - 14:30:04 PDT
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