AMBER Archive (2009)

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

From: FyD (fyd_at_q4md-forcefieldtools.org)
Date: Thu Oct 01 2009 - 23:27:13 CDT

Quoting Jihang Wang <wangj3_at_mymail.vcu.edu>:

> Great, thanks a lot.

and you can use R.E.D. http://q4md-forcefieldtools.org/RED/ to compute
RESP or ESP charges.

regards, Francois

> On Thu, Oct 1, 2009 at 6:30 PM, Carlos Simmerling <
> carlos.simmerling_at_gmail.com> wrote:
>
>> 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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           F.-Y. Dupradeau
                 ---
http://q4md-forcefieldtools.org/FyD/

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