AMBER Archive (2006)

Subject: RE: AMBER: GAFF parameters: DPPC Bilayer

From: Akshay Patny (akshay17_at_olemiss.edu)
Date: Wed Aug 09 2006 - 16:08:00 CDT

Thank you Nitin and Dr. Yong. I will try that.

Akshay Patny

Graduate Research Assistant
Faser Hall 417, Department of Medicinal Chemistry
Research Institute of Pharmaceutical Sciences
University of Mississippi
University, MS 38677
E-mail: akshay17_at_olemiss.edu
Tel: 662-915-1286 (office); Web: www.olemiss.edu

|-----Original Message-----
|From: owner-amber_at_scripps.edu [mailto:owner-amber_at_scripps.edu] On Behalf Of
|Yong Duan
|Sent: Tuesday, August 08, 2006 3:43 PM
|To: amber_at_scripps.edu
|Subject: RE: AMBER: GAFF parameters: DPPC Bilayer
|
|
|Dear Nitin and akshay:
|
|The statement that one should use GAFF for protein, water, if GAFF is used
|for lipid, may not be correct.
|
|Lipids and proteins can have different parameter sets, just as you can use
|"standard" AMBER parameters for proteins and use your favorite parameters
|for lipids (you can even develop your own if you so inclined). In
|particular, GAFF referes to a set of parameters for modeling of general
|organic compounds. This set has not been tuned specifically for proteins
|(or
|peptides), as such there is not much detailed studies on the application of
|GAFF to model proteins. So, you are better off to use "standard" protein
|parameters for proteins and use GAFF for others. Again, there is no
|inherent
|conflict between these sets. It is a matter of accuracy. If you are
|interested in protein dynamics in membrane, you should use the protein
|force
|fields for proteins. As for lipids, you can use others, including GAFF.
|
|Regardless which specific set you choose for the lipid, please make sure
|the
|lipids confirm to experimental observations.
|
|yong
|
|> -----Original Message-----
|> From: owner-amber_at_scripps.edu
|> [mailto:owner-amber_at_scripps.edu] On Behalf Of Nitin Bhardwaj
|> Sent: Tuesday, August 08, 2006 12:59 PM
|> To: amber_at_scripps.edu
|> Subject: Re: AMBER: GAFF parameters: DPPC Bilayer
|>
|>
|> Hi akshay,
|> Yeah its fine to use GAFF parameters for DPPC bilayer. The only
|> thing is in that case you should use GAFF parameters for protein,
|> water and counter-ions in your system.
|>
|> Rgds,
|> Nitin
|
|-----------------------------------------------------------------------
|The AMBER Mail Reflector
|To post, send mail to amber_at_scripps.edu
|To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu

-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu