AMBER Archive (2009)

Subject: Re: [AMBER] method used to determine partial charges?

From: Carlos Simmerling (carlos.simmerling_at_gmail.com)
Date: Thu Oct 01 2009 - 17:30:21 CDT

Amber doesn't include partial charges, but it does include a program
(antechamber) that calculates partial charges for various organic
molecules. You could use this to generate a parameter set for
simulations. There is quite a bit of info in the manuals and
tutorials.
http://ambermd.org/antechamber/antechamber.html

On Thu, Oct 1, 2009 at 6:26 PM, Jihang Wang <wangj3_at_mymail.vcu.edu> wrote:
> Thanks again for your reply.
> Actually, I'm just trying to do some simulations of -CN groups with
> different force fields. So you are saying Amber ff only have partial charges
> available for biological systems? since in OPLS-AA ff, I found the partial
> charges for organic molecules too.
>
> On Thu, Oct 1, 2009 at 6:18 PM, Bill Ross <ross_at_cgl.ucsf.edu> wrote:
>
>> > I could not find the partial charges in some organic molecules,
>> > for example,  the nitrile group (-CN)
>>
>> If this is not a residue in the dbase, there wouldn't be charges
>> for it per se. If it is a substituent of other residues, you
>> could see how the charges vary per residue (I'm not a chemist,
>> so not sure what you expect).
>>
>> Bill
>>
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