AMBER Archive (2005)

Subject: AMBER: about salt bridges

From: xueping (xueping22_at_yahoo.com)
Date: Fri Aug 05 2005 - 01:34:18 CDT

Dear all,

I am doing simulation at high temperature for
thermophilic protein. I was thinking to look into the
analysis of the salt bridges, But i do not know
how...Is there a way that i can monitor the formation
and disruption of salt bridges throughout the MD
simulations? (like hbond analysis in ptraj) and is it
possible for me to get the solvation free energy for
charge side chains, and also the total electrostatic
contribution to the free energy change upon the
formation of a salt bridge. I notice that Delphi is
able to do that, but is this possible for amber
analysis package to do this?

Please give me some advices and idea, I really
appreciate that. Thank you so much!

Thanks

Regards
xueping

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