AMBER Archive (2009)

Subject: Re: [AMBER] GB and Atom Type

From: Sally Pias (sallypias_at_gmail.com)
Date: Wed Nov 18 2009 - 23:11:27 CST

There is a database of "contributed parameters" linked from the Amber
website, which provides parameters for some residues not included in
the standard Amber force fields. You will find the heme group listed
there:
http://www.pharmacy.manchester.ac.uk/bryce/amber#cof

I hope this helps.

Sally Pias

On Wed, Nov 18, 2009 at 1:58 AM, Alexander Seifert
<alexander.seifert_at_itb.uni-stuttgart.de> wrote:
> Dear all,
>
>
>
> I am trying to run an implicit solvent MD simulation on a protein that
> contains a heme iron taking into account the hydrophobic effect of the
> protein surface. I read a request on the AMBER mailing list concerning
> missing parameters (http://archive.ambermd.org/200401/0083.html) and David's
> reply (http://archive.ambermd.org/200401/0089.html). I have the same problem
> with the missing heme parameters and to be honest I don't really get how the
> parameters are defined in the mdread.f file or what the values stand for.
> Does anyone has suggestions how I get the missing iron parameters or is
> there a way to exclude the heme from the hydrophobic effect calculation,
> since it is located in the interior of the protein and therefore shouldn't
> have any effect on the protein's surface interactions.  I appreciate your
> efforts.
>
>
>
> Best regards,
>
>
>
> Alexander
>
>
>
>
>
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