[gmx-users] Simulation of the Rhodopsin-retinal complex

James Starlight jmsstarlight at gmail.com
Sun Jan 20 21:17:06 CET 2013

Dear Gromacs Users!

I want to simulate sensory rhodopsin which in the ground-state
contains cys-retinal covalently bonded to the polypeptide mainchain of
photoreceptor via Shiff base.  Now I'm looking for reasonable
parameters of that retinal cofactor group for charmm ( 27 or 36 force
field) I'll be very thankfull to anyone who can provide me with such
rtp integrated in the gromacs files.
Recently I've already tried to integrate non-standart residue of the
another protein. That time I've deal with the GFP chromophore wich
should be integrated to the rtp of charmm ff but I forced with the
problems of definition of the contacts of the chromophore with the
rest of the polypeptide of GFP itself. I hope that in case of retinal
situation would be simpler due to only one covalent bond between that
cofactor and photoreceptor. :)

Thanks for help,


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