Subject: External parameters for Mopac calculations

From: "Coussens, Betty" <[email-masked]>
Date: Wed, 8 May 2002 12:16:09 +0200

Dear all,

I want to perform computations on Mg containing systems using Mopac6.0 and
found an article in which a magnesium parameter set has been published for
use with AM1 (i.e. J. Chem. Phys. B, vol. 102(41), 1998, 8083).  I want to
plug in these parameters into Mopac6.0 by using the keyword
EXTERNAL=filename with filename the name of a file containing the new
parameter set in the format <parameter> Mg <Value of parameter> and
terminated by a blank line.  However, I appear to do something wrong as I
keep getting the message 'SOME ELEMENTS HAVE BEEN SPECIFIED FOR WHICH NO
PARAMETERS ARE AVAILABLE.  CALCULATION STOPPED'.  Has anybody an idea about
what could possibly be wrong? 

Thanks in advance for the help!

Betty  

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---

From: "Mark Thompson" <[email-masked]>
Date: Wed, 8 May 2002 07:06:25 -0700

Dear Betty,

Its far easier to add new parameters to ArgusLab to run your PM3/AM1
calculations.  All parameters are stored in formatted text files for MNDO,
AM1, PM3, EHT, and ZINDO.  This approach has been particularly popular with
ZINDO users who want to calculate spectra with new or modified atomic
parameters.

You can get ArgusLab at  http://www.arguslab.com

Cheers,
Mark

=================================
Mark Thompson, Ph.D.
Planaria Software
Seattle, WA.
http://www.arguslab.com
=================================

> -----Original Message-----
> From: Computational Chemistry List [mailto:[email-masked]]On
> Behalf Of Coussens, Betty
> Sent: Wednesday, May 08, 2002 3:16 AM
> To: [email-masked]'
> Subject: CCL:External parameters for Mopac calculations
>
>
> Dear all,
>

---

From: "Julien MICHEL" <[email-masked]>
Date: Wed, 8 May 2002 19:22:58 +0200

Dear CCLers,

I am currently trying to evaluate energies of interaction between a group of
peptides and it's receptor. I am particularly interested in computing these
energies with solvated compounds. I was thinking to build a thermodynamic
cycle. The in vacuo step seems clear enough to me, but I was wondering how I
should consider the problem of solvation. It seems to me that my
calculations would be inconsistent if I'm not careful.
Assuming I need N molecules of water to solvate my ligand and M molecules to
solvate my Receptor. Upon, solvating my in vacuo complex, should I use N+M
molecules of water so that my system size is consistent ?
I can see another way to consider the cycle. I could start with a big box
filled with water, add either ligand, receptor or complex depending on the
calculation desired and eliminate overlapping water molecules. But then the
size wouldn't be consistent anymore.
I am also wondering how one can define a system as properly solvated. I
would like to keep computational expenses low and ideally I'd like to use a
layer of a few angstroms on each compounds and restrain the solvent
molecules from moving away from the system using a small distance dependant
restrain (from the centre of mass).

Best regards,

Julien MICHEL

---

From: Ernst-Ulrich Wuerthwein <[email-masked]>
Date: Wed, 8 May 2002 17:41:59 +0200 (MES)

The correct reference for the AM1-Mg parameters is as follows:

M. C. Hutter, J. R. Reimers, N. S. Hush,
J. Phys. Chem. B 1998, 102, 8080-8090

E.-U. Wuerthwein

On Wed, 8 May 2002, Coussens, Betty wrote:

> Date: Wed, 8 May 2002 12:16:09 +0200
> From: "Coussens, Betty" <[email-masked]>
> To: "[email-masked]'" <[email-masked]>
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