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.
-Justin
Any help will be appreciated.
Thanks.
o.
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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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