AMBER Archive (2009)

Subject: [AMBER] question about ptraj hydrogen bond analysis

From: monica bhattacharee (monahawk217_at_gmail.com)
Date: Wed Feb 18 2009 - 13:45:17 CST

Hi I am trying to do a hydrogen bond analysis using ptraj. I want to track
if specific atoms are making hydrogen bond contacts during the trajectories.
However I notice that the ptraj script I am using reads in the donors and
the acceptors and then returns any hydrogen bonds that they make. I want the
first donor and first acceptor listed to specify a hydrogen bond, second
donor and second acceptor to track another hbond, etc. Is there any way to
do this?

Thanks

Monica



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