[AMBER] Problem cpptraj Bridging H-Bond analysis

From: Beuerle, Matthias <m.beuerle14.imperial.ac.uk>
Date: Mon, 20 Jul 2015 13:52:22 +0000

Hello everyone,

I have a problem using the hbond function of cpptraj. I try to analyze hydrogen bonds bridged by water molecules of my system. My cpptraj script is working and the results look correct in principle, however the lifetime of some solute-solvent and solute-solvent-solute interactions in the avgout and bridgeout files are bigger than one (in terms of fractions of the whole simulation length), which obviously can not be true. Solute-Solute H-Bond lifetimes are fine. I read that one of the latest bug fixes aimed at problems with lifetime of solute-solvent H-Bond however updating to the latest version did not help. My system is a protein DNA complex meaning I have 3 separate solute molecules. Anyone has a similar problem and or solution? Help would be very much appreciated!

Best regards,
AMBER mailing list
Received on Mon Jul 20 2015 - 07:00:03 PDT
Custom Search