AMBER Archive (2004)

Subject: Re: AMBER: Fe parameter

From: scopio (
Date: Mon Jul 12 2004 - 09:18:52 CDT

Dear Zou:

I think you can try to find if there have literatures published Fe
parameters of your system. If you are lucky to find them, try to build
frcmod with the help of antechamber.

Good Luck!


hj zou wrote:

>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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