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

From: Albert <>
Date: Fri, 02 Dec 2011 00:36:50 +0100

Hi Franois:
    I've got another question about the partial charge calculation in
AMBER. I found that it use RESP for HF/6-31G* for Amber FF. I am
wondering, is CHARMM 27 or CHARMM36 use the same methods for partial
charge calculation? I may also use CHARMM FF in amber in the near future.

Thank you very much
best wishes


On 12/01/2011 09:06 AM, FyD wrote:
> 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
> See
> 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 - 16:00:03 PST
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