AMBER Archive (2008)

Subject: Re: AMBER: Ac-Co Parameters for Amber

From: FyD (fyd_at_q4md-forcefieldtools.org)
Date: Wed Oct 01 2008 - 16:26:54 CDT

Quoting suhaib sh <suhaib.shekfeh_at_gmail.com>:

> I appreciate your quick help ... actually I would prefer to try firstly
> Amberff99 which is more related to cornelly et. all amberff94 ,

Yes, by Cornell et al. I thought RESP charges derived using HF/6-31G*
as in Cornell et al. (parm94) and its different adaptations (parm96,
parm98 & parm99).

> but I would like also to try Amberff03 (Duan et al ff) ..
> it is rcommended for me to use
> amber99 as it is better for drug-protein complex .. what do u think ?

My understanding is that the Duan et al. force field has been designed
for globular proteins: This is why we developped two versions of our
force field topology database (FFTopDB), one for parm99 and the other
for ff03.

If your drug is in hydrophobic environment it might be interesting to
test the ff03 version of our FFTopDB...

> are you from the group which develops AmberFFC?

Yes

"Which" Acetyl-coA do you wish ?
If we consider http://en.wikipedia.org/wiki/Acetyl-CoA:
* terminal -SH or -SAc ?
* phosphate @ position C3' of the base: charge value = -2 or -1 ?
* which base: A, C, G or U ?

regards, Francois

> On Wed, Oct 1, 2008 at 8:14 AM, FyD <fyd_at_q4md-forcefieldtools.org> wrote:
>
>> Quoting suhaib sh <suhaib.shekfeh_at_gmail.com>:
>>
>> any hints please .. I searched many sites but I found nothing
>>>
>>
>> We have a force field topology database for many coenzymes with Acetyl-CoA
>> and more... Which force field do you want to use: the Cornell et al. force
>> field or the Duan et al. force field ? If you are interested in I can send
>> you the corresponding Tripos mol2 file in private...
>> All will be available in R.E.DD.B. @
>> http://q4md-forcefieldtools.org/REDDB/
>>
>> regards, Francois

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