[gmx-users] Help with defining new residue (OXY--HEME)

Omololu Akin-Ojo prayerz4users at yahoo.com
Mon Jun 21 15:56:11 CEST 2010

Thanks, Justin. I appreciate this. I will go with the first option of creating a *.rtp file and manually change the subsequent *.top file to put in the morse potential.

Thanks again.


--- On Mon, 6/21/10, Justin A. Lemkul <jalemkul at vt.edu> wrote:

From: Justin A. Lemkul <jalemkul at vt.edu>
Subject: Re: [gmx-users] Help with defining new residue (OXY--HEME)
To: "Discussion list for GROMACS users" <gmx-users at gromacs.org>
Date: Monday, June 21, 2010, 9:02 AM

Omololu Akin-Ojo wrote:
> Hi,
> I obtained parameters for a Morse potential between Oxygen molecule and Iron in heme (from ab initio calculations).  How can I use this potential with the GROMOS96
> I thought of a couple of options:
> 1) Define a new residue -- OXYHEM using the same parameters for HEME as in ffG43a1.rtp but just adding oxygen--heme interaction.
> (The problem with this is that the bonded interaction in the HEME uses the G96BOND, so, how would I maintain this G96BOND for all the atoms except the oxygen-Fe interaction for which I need to use the Morse potential).
> ** What are the steps needed to do this? ***

You could create an .rtp entry for this species and process it with pdb2gmx.  I don't know how to put a Morse type bond in an .rtp file, but you can easily modify the resulting topology to include the proper term.

> 2. Is it possible to simply create an appropriate *.itp file to use in conjunction with the HEME already defined in the GROMOS96 files (*.atp, *.itp, *.rtp in /usr/local/gromacs/share/gromacs/top)?

Sure, most things
 are possible :)  See the manual, chapter 5.


> Any help will be appreciated.
> Thanks.
> o.

-- ========================================

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080

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