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

[Justin A. Lemkul]

olaniyi yusuff wrote:
> 
> 
> 
> 
> 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.

If these parameters are already published, the authors of those papers may be 
willing to share them directly by providing a suitable topology.  If you want to 
make your own topology with pdb2gmx, you need to define appropriate .rtp entries 
(see Chapter 5 of the manual).  That would, of course, imply that you have 
parameters already in order to design this .rtp entry.  If you don't have these 
parameters under the given force field, you cannot use pdb2gmx; it is not magic.

> 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.

CHARMM is not yet supported, but will be in a future release (4.1).

-Justin

> 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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-- 
========================================

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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