AMBER Archive (2003)

Subject: AMBER: following salt and waterbridges during a simulation

From: Karsten Suhre (Karsten.Suhre_at_igs.cnrs-mrs.fr)
Date: Tue Sep 30 2003 - 01:33:31 CDT

Dear all,

for a Amber simulation (i.e. in crd format) I would like to obtain the
fraction of time every individual residue is linked by a salt bridge, a water
bridge or a hydrogen bond with any other residue in the same protein.

This can of course be done using carnal and ptraj, but I am looking for some
kind of "standard" tool or script for this sort of analysis (possible based
on carnal or ptraj), in particular something that could be cited in an
article saying "... bonds were detected using program X with parameters as in
.....".

Thank you very much for your suggestions,

Kind regards, Karsten Suhre.

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