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

Justin A. Lemkul jalemkul at vt.edu
Mon Jun 21 15:02:06 CEST 2010

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 parameters?
> 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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