AMBER Archive (2009)

Subject: Re: [AMBER] Iron 2+ parameters

From: FyD (fyd_at_q4md-forcefieldtools.org)
Date: Mon Feb 16 2009 - 12:25:45 CST

Dear Hrvoje Brkić,

> Does ayone know parameters of Fe2+ ion coordinated with 2 histidines,
> glutamine, and aspecting coordination with water. I need .lib file, and
> .frcmod file, or instructions how to make them.

You first need to characterize the ligands of your Fe2+ ion, then,
simplify these ligands. Optimize the complex previously defined by
quantum mechanics, compute the MEP and perfom the fit using the RESP
program. All this can be automatically done using the R.E.D. program.
In this case, you need to prepare a P2N input file (for your complex)
for R.E.D. using Ante_R.E.D.

I am aware these explanations are a little short, but you could
clearly follow this plan. To start, I could help you to prepare a P2N
input file for your complex if you wish. You should be able to use it
in R.E.D. Server soon... Through R.E.D. Server we will provide
specific and general help to users.

regards, Francois

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