AMBER Archive (2006)

Subject: RE: AMBER: GAFF parameters: DPPC Bilayer

From: Yong Duan (duan_at_ucdavis.edu)
Date: Tue Aug 08 2006 - 15:42:50 CDT

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

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