[gmx-users] RE: Re: Gromos Parameters for Heme bound Oxygen

[Erik Marklund]

Hi,

There are HEME entry in the ffG43a1-files that come with gromacs. Wether 
it's oxy- deoxy- or other heme I do not know. At some point I used them 
for a myoglobin simulation, but I don't remember the details.

/Erik

olaniyi yusuff skrev:
>
>
>
>
> Hi,
> Thanks for the your reply. I quite know that there is need for 
> expertise to be able to derive parameters, that's why i want to know 
> if anyone already have the gromos parameters for the oxy- and 
> carbomonoxy- heme.
> The references i've seen so far for related works in my literature 
> search used the charmm force field parameters and amber but again i 
> had problems when i try to use amber, pdb2gmx complain of not finding 
> residue heme in the topology file.
> The question now is can i use charmm force field parameters in gromacs 
> and how do i go about incorporating charmm ff into gromacs.
> Please i need a guide because i'm relatively new in simulation work, i 
> am from experimental background.
> thanks. 
>
> > Message: 5
> > Date: Tue, 27 Oct 2009 13:36:49 -0400
> > From: "Justin A. Lemkul" <jalemkul at vt.edu>
> > Subject: Re: [gmx-users] Gromos Parameters for Heme bound Oxygen
> > To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> > Message-ID: <4AE72FB1.5020602 at vt.edu>
> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed
> >
> >
> >
> > Olaniyi Yusuff wrote:
> > > Dear gmx users,
> > > I would like to know if any one has parameters for oxygen or
> > > carbonmonoxide bound to the heme in hemoglobin.
> > > I am running MD simulations on hemoglobin using the gromos force 
> field
> > > G43a1 in gromacs, i had no problem when i used the pdb structure for
> > > pure hemoglobin, but when i try to convert the pdb structure files 
> for
> > > the liganded hemoglobin (both oxy- and carbonmonoxy- ), there was
> > > complain of my oxy and carbomonoxy residue unknown i.e not defined in
> > > the .rtp file.
> > > so i would like to know if there is anyone with parameters for these
> > > kind of heme in gromacs or better still another reference of force 
> field
> > > with parameters for them that can be use in gromacs.
> > >
> >
> > If it has been published, then perhaps the authors of that 
> particular study will
> > share them with you. If not, then realize what you are trying to do is
> > certainly an expert topic, one that is not addressed easily:
> >
> > 
> http://www.gromacs.org/Documentation/How-tos/Parameterization#Exotic_Species
> >
> > -Justin
> >
> > > Thanks
>
>
>
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-- 
-----------------------------------------------
Erik Marklund, PhD student
Laboratory of Molecular Biophysics,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,    75124 Uppsala, Sweden
phone:    +46 18 471 4537        fax: +46 18 511 755
erikm at xray.bmc.uu.se    http://xray.bmc.uu.se/molbiophys