AMBER Archive (2008)

Subject: Re: AMBER: Which CO2 potential?

From: Gustavo Seabra (gustavo.seabra_at_gmail.com)
Date: Thu Jul 24 2008 - 08:08:53 CDT

I don't recall seeing any CO2 parametrization for Amber, although
someone may have done that in the past. Anyways, for a molecule as
small as CO2, producing a force field with Antechamber may be faster
then looking in the literature for a pre-made potential, and that's
including the time to learn how to do it.

Good luck,
Gustavo.

On Wed, Jul 23, 2008 at 11:45 PM, Jones de Andrade <johannesrs_at_gmail.com> wrote:
> Thanks a lot Gustavo.
>
> I though about this possibility, but for me it looks like making an AMBER
> water potential to make simulations with water instead of... spc/e or tip3p.
> I was thinking if there isn't in the literature any "commonly used" CO2
> potential together with AMBER parameters of other molecules in the
> simulation. ;) Is there such a reference flying around?
>
> Thanks a lot,
>
> Jones
>
> On Thu, Jul 24, 2008 at 12:32 AM, <gustavo.seabra_at_gmail.com> wrote:
>>
>> Hi,
>>
>> AFAIK, Amber doesn't have parameters for CO2. I believe that, in your
>> situation, your best bet is to generate the parameters yourself. You
>> can use Antechamber to generate GAFF parameters for it. Take a look
>> at:
>> www.ambermd.org/tutorials/basic/tutorial4/index.htm
>> For details on using Antechamber.
>>
>> HTH,
>> Gustavo.
>>
>> On 7/23/08, Jones de Andrade <johannesrs_at_gmail.com> wrote:
>> > Hi all.
>> >
>> > I have a really direct question: I have to make a few simulations
>> > involving
>> > interation of CO2 molecules with other, with the other molecules,
>> > solvents,
>> > etc, all within the AMBER ff.
>> >
>> > Which potential should I choose to describe the CO2 molecule? Any
>> > suggestion, please?
>> >
>> > Thanks a lot in advance,
>> >
>> > Jones
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