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

olaniyi yusuff okyusuff at hotmail.com
Thu Oct 29 12:07:59 CET 2009

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.

> 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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