be very careful with analysis of salt bridges with continuum
models. make sure to read the articles that have been
published about that. It can be very sensitive to choice of
radii (even with PB).
yes, you can use the H-bond analysis tools since the protein
salt bridges involve hydrogen bonding.
xueping wrote:
>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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Received on Fri Aug 05 2005 - 13:53:00 PDT
