AMBER Archive (2009)

Subject: Re: [AMBER] carbonic anhydrase (CA) simulation

From: case (case_at_biomaps.rutgers.edu)
Date: Thu Jul 16 2009 - 06:36:17 CDT

On Thu, Jul 16, 2009, vhakkim boy wrote:
>
> I am trying to simulate the CA enzyme for that i have retain the
> active site which is four coordinate Zn(HIS)3H2O (bonded approach: three
> nitrogen atoms of histidine and oxygen atom of water is bonded to
> zinc(II)) and i gave ff parameter for the active site through frcmod file
> but i got the following message
>
> No bond parameter for: Zn -
> can't find angle parameter: NB - Zn -

It looks like you have an atom with a blank atom type, so the program is
telling you that there is no parameter for a bond between a Zn type atom and a
"blank" type atom. You can use the "desc" command in LEaP to find out which
atom this is, and track down the origin from there.

....dac

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