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

Omololu Akin-Ojo prayerz4users at yahoo.com
Mon Jun 21 14:58:31 CEST 2010


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? ***

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)?

Any help will be appreciated.



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