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

From: Albert <>
Date: Thu, 01 Dec 2011 09:37:16 +0100

Hi Francois:
   I try to login R.E.D webpage, but there is some errors. it said:

/The way you access to R.E.DD.B. is _NOT_ correct.
Please, start again from the R.E.DD.B. Home Page...

Since R.E.DD.B. uses 'PHP sessions', the problem you encounter might be:

# The current 'session' is finished i.e. you successfully submit a project
in R.E.DD.B.
You can check this by looking for the project you just submitted using
the "download section" of R.E.DD.B.
(using for instance your lastname as "Author lastname")

# The current 'session' has expired: A session is automnatically closed
after 20 minutes
Consequently, nothing has been recorded in R.E.DD.B., and you need to
start all over from the beginning.
You can check this by looking for your project in R.E.DD.B. if it has
been (or not) recorded.
(using the "download section" of R.E.DD.B.)

# You did not allow our web server to use Cookies.
(Change the setting of your browser and accept the Cookies)

# Or you did not start a 'session' yet, and the way you access R.E.DD.B.
is forbidden...

I also try to download the installation of R.E.D and there is also some
problem for registration. Is it possible for your check for it?

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 - 01:00:02 PST
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