Hi James,
I'd recommend following the antechamber tutorial on the amebrmd website: http://ambermd.org/tutorials/basic/tutorial4b/ . It is fairly comprehensive and easy to follow. Additionally if you wanted to generate RESP charges semi-empirically, as well as optimized geometry, for cGMP I would highly recommend using REDS http://q4md-forcefieldtools.org/REDS/ . Sign up for an account to use Guassian09.
Best,
Parker
________________________________________
From: James Starlight [jmsstarlight.gmail.com]
Sent: Monday, April 28, 2014 8:02 AM
To: AMBER Mailing List
Subject: [AMBER] Simulation of protein- cyclic nucleotide complex
Dear Amber Users!
I'd like to perform simulation of the water-soluble protein in complex with
the small ligand where ligand is the cyclic nucleotide guanosine
monophosphate (cGMP). The output trajectory of this simulation will be
further processed by means of
http://scanmail.trustwave.com/?c=129&d=1MPe07wUGAo8aOhatZ8CMsCq5aiGHUg1nTyBAF7YKQ&u=http%3a%2f%2fmmpbsa%2epy analysis. Could you suggest me the
reason amber's param sets for such ligand and protein as well as proper
tutorial for protein-ligand simulation?
Thanks for help,
James
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Received on Mon Apr 28 2014 - 05:30:05 PDT
