AMBER Archive (2004)

Subject: Re: AMBER: Fe parameter

From: Wu Lei (wulei_at_biophy.nju.edu.cn)
Date: Mon Jul 12 2004 - 02:51:18 CDT


There is no Fe ion parameters in library but i think you can build a Fe unit in leap and bond it to the involved residues.

The tutorial html contains detailed similar steps.

----- Original Message -----
From: "hj zou" <hjzou_at_iris3.simm.ac.cn>
To: <amber_at_scripps.edu>
Sent: Monday, July 12, 2004 3:00 PM
Subject: AMBER: Fe parameter

> Dear amber usersúČ
> I run into a problem while I set up my simulation .There is a iron ion which forms several coordinate bonds with residues of protein.Then,where can I find the parameters of Fe?I have got the parameters of heme.I'm not sure whether that can be used on my system .
> On the other hand,as the purpose of simulation is to optimize the structure modeled from another protein,I have run the simulation without iron ion while I used the "nmropt" to restrain the distance between the residues which form coordinate bonds with iron ion.Can anyone tell me whether it is reasonable or not?
> Any suggestions are highly appreciated!
> Have fun
>
>
>
>
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