AMBER Archive (2007)

Subject: Re: AMBER: Question

From: David A. Case (case_at_scripps.edu)
Date: Tue Nov 06 2007 - 23:18:33 CST

On Tue, Nov 06, 2007, dykyy wrote:
>
>
> 1. NH of Met-1. It says that amidic proton does not exist for Met1,

The atom names in your pdb file must match those in the library. This
often requires manually editing the pdb file to make sure the names match up.
In many cases, the easiest thing to do is to remove all hydrogen atoms, and
let LEaP (or reduce) add them back.

>
> 2. My previous experience with minimization of metaloproteins using,
> probably Amber 6, was that we simply added the metal ion as a last
> residue (in that case it was a Cu2+ ion). I tried to do the same hear.
> However, it apparently does not work. May be Zn2+ ion is not included in
> the AMBER9 data base?

This is correct. There is a large literature on modeling zinc ions with
molecular mechanics. Try to find a paper that has a zinc site that is
similar to the one you are using.

> Another question. How should I say to AMBER about distances between Zn
> ion and coordinating it cysteines. Just, in AMBER upl file, create 4-8
> constraints about distances between Zn and Sg atoms and angles in
> analogy with normal distance constraints?

You would generally do this with a frcmod file and modified residues, as
described in this tutorial:

   http://www.rosswalker.co.uk/tutorials/amber_workshop/Tutorial_four/

(Ross: shouldn't this tutorial be included in the current main list? I'm
not sure why it has become so hidden....)

...good luck...dac

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