Ravi
Ran Cao has pointed to the AMBER archive suggestion provided by Dr. Yong
Duan from UC Davis in response to my earlier question.
http://archive.ambermd.org/200608/0085.html
I am using GAFF parameters for ligands and lipids and AMBER ff03 parameters
for my GPCR protein, and that seems to be allowed as they do not conflict
with each other. CHARMm mailing list might also be a good place to ask that.
Best
Akshay
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Akshay Patny
PhD Candidate (5th Yr.), Computational Chemistry
Department of Medicinal Chemistry, School of Pharmacy
The University of Mississippi
805 College Hill Rd, # 9, Oxford, MS 38655
E-mail: akshay17.olemiss.edu
Phone (O): (662)-915-1286,(M): (662)-801-5496
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-----Original Message-----
From: owner-amber.scripps.edu [mailto:owner-amber.scripps.edu] On Behalf Of
Ravinder Abrol
Sent: Wednesday, December 20, 2006 1:09 AM
To: amber.scripps.edu
Subject: AMBER: mixing GAFF and CHARMM
Hi All,
We are looking at protein-ligand complexes embedded in lipids and I am
curious to find out
if someone has experience using GAFF parameters for ligands and CHARMM
parameters
for the rest of the system (protein and lipids). Can GAFF (being a
generalized FF) be mixed with
CHARMM in this way to carry out MD simulations? Thanks.
Ravi
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Received on Sun Dec 24 2006 - 06:07:10 PST
