Re: [AMBER] will AM1-BCC good enough for GAFF lipids?

From: FyD <>
Date: Thu, 01 Dec 2011 09:06:09 +0100

Dear Albert,

If you look at literature, you can find:
- the work of the group of Woods:
  -> i.e. for GLYCAM based on RESP charges
- the work of the group of Gould
  -> i.e. for GAFF.
You could look at the work of Stephane Abel about glycolipids

Thus, I think you should follow your idea & demonstrate it works ;-)

You could use R.E.D. Server to derive RESP or ESP charges and build
the corresponding force field libraries for POPE and derivatives.

I CC this email to Stephane in case it does not read it...

regards, Francois

> I am going to build a membrane system with POPE lipids with
> Amber99SB-ILDN (for protein) + GAFF (for both lipids and ligand). The
> system would be built from Desmond and I am going to assign the above FF
> in Amber. Since partial charge is quite important for MD, I am wondering
> will the AM1-BCC method good enough for membrane lipids? If it not, what
> kind of method should I use for assign partial charges?
> Someone suggested me that the partial charges calculation method should
> be at least "Fit to electrostatic potential charges" for MD system. I am
> wondering, is it possible to achieve this in Amber partial charge
> calculation methods?

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Received on Thu Dec 01 2011 - 00:30:03 PST
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