Subject: Gaussian98W's AMBER input --SUMMARY

From: "Telkuni" <[email-masked]>
Date: Wed, 28 Aug 2002 00:36:38 +0900

Hello, CCLers

Last week, I've posted a question:
> I'm a novice user of molecular mechanics(MM) and planning to do
> Base-Pair's MM calculation with Gaussian98W's AMBER function.
>
> However, there is a guidance of  Gaussian's AMBER on the G98
> user's reference(page122), it is too short to make actual input.
>
> Maybe, I think, when one want to do AMBER calculation on a molecule,
> he must search and apply the molecule's peculiar atomic parameters
> such as Fig-5 of "W.D.Cornell et.al, J. Am. Chem. Soc. 117, p5179 (1995)".
> (on RNA, it's Fig-6.)
>
> Is above correct?
>
> And, must one search and apply the each atomic parameters even a small
> molecule? (for example, even though CH3OH ?, where is its parameters?)
>
>
> Any replies I will appreciate and make the summary.

Here is the summary of replies. Thank you very much Dr.Nicolas FERRE' and
Dr.Chandra U. Singh.

--- 1) from Nicolas -------
Hi Telkuni,

If you want to use G98 to run some Amber jobs, you always have to write
in the Z-matrix part:
"Atomic symbol"-"Amber atom type"-"Charge" coordinates ...
e.g.
C-CT--.0252 for an alpha carbon of a glycin molecule.
Actually, the RESP charges defined for Amber are not stored into G98 and
you have to write them in the input file.
For methanol, you won't find any parameter within this old Amber version
which was designed especially for amino-acids. Since this early work,
the Amber force-field has been developed to include some parameters for
organic molecules also. Maybe you should consider to buy the last
version of Amber (7, see http://www.amber.ucsf.edu/amber/), or
alternatively you can try to use - free - Tinker that includes Amber,
Charmm, MM2/3 ... (http://dasher.wustl.edu/tinker/)
If you want to derive the RESP point charges for methanol, consider the
procedure described here: http://www.amber.ucsf.edu/amber/charges.txt
... but I'm sure that someone always did it !

Hope this helps.

Nicolas

--- 2) form Chandra -------
Hello,

I have read your e-mail and I am Dr. Singh who developed the AMBER programs in the 80's. If you need to automatic calculations
without worrying about parameters, please check our new software GALAXY at www.am-tech.com.

Sincerely,

Chandra U. Singh

------------------------------------------------------
      Telkuni Tsuru     [email-masked]