Dear AmberUsers,
I am doing a metal protein simulation. I want to calculate the number of
water molecules present within a distance cutoff of the Zn ion. I guess for
this i should use hbond analysis from ptraj. However, in hbond analysis,
the acceptor mask requires a heavy atom and a hydrogen atom. In my case,
the Zn ion does not have a hydrogen bonded to it and as a result ptraj is
showing error with the mask. How do I specify the details. I have seen a
lot of papers, wherein one calculates the water molecules ard the metal
ion. How are such calculations done??
Should i consider the metal ion as a donor. Would that be wrong.
Any help would be highly appreciated.
Thanks & Regards,
Kanika
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Received on Sat Jan 14 2012 - 00:00:02 PST
