AMBER Archive (2007)

Subject: Re: AMBER: Antechamber

From: David Mobley (dmobley_at_gmail.com)
Date: Tue Nov 06 2007 - 14:41:17 CST

Hi,

I think the answer to that depends on:
(a) Is the oxidation state right for the system you want to simulate?
(b) There are different types of heme; is this the type that's in the
system you want to simulate?
(c) Whether you are happy with heme parameters that are so old (i.e.,
happy with the derivation procedure, for example).

Best wishes,
David

On 11/6/07, snoze pa <snoze.pa_at_gmail.com> wrote:
> Dear Ilya and David,
> Thanks a lot for your reply.
>
> Ilya, so you i can use those charges directly?
>
> thanks a lot in advance
> s
>
>
> On Nov 6, 2007 11:36 AM, Ilyas Yildirim < yildirim_at_pas.rochester.edu> wrote:
> > If you use antechamber to calculate the charges, they wont be resp
> > charges. For HEME, the parameters are already calculated. Look at the
> > following site:
> >
> > http://pharmacy.man.ac.uk/amber/
> >
> > My rule of thumb is not to calculate something if it is already done. Use
> > the HEME parameters from the above site.
> >
> > Best,
> >
> >
> >
> >
> > On Tue, 6 Nov 2007, snoze pa wrote:
> >
> > > Dear Amber community,
> > > I am working on a heme protein and wondering if I can calculate the
> charges
> > > on HEME using antechamber. If anybody has any prior experience in this
> then
> > > please let me know.
> > > thanks in advance.
> > > s
> > >
> >
> > --
> > Ilyas Yildirim
> >
> ---------------------------------------------------------------
> > = Department of Chemistry - =
> > = University of Rochester - =
> > = Rochester, NY 14627-0216 - Ph.:(585) 275 67 66 (Office) =
> > = http://www.pas.rochester.edu/~yildirim/
> =
> >
> ---------------------------------------------------------------
> >
> >
> >
> >
> >
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>
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