Subject: Summary: Partial Charges on FAD with MOPAC

From: Patricia M Fulmer <[email-masked]>
Date: Fri, 11 Oct 1996 15:08:22 -0500 (CDT)

With appologies for the previous post....

Dear Friends,

On Sep. 23, 1996, I posted a message to you regarding calculation of partial
charges on FAD using MOPAC. I have received a number of replies to my 
question. I would like to thank each of you for your time and information. 
Here is my original question together with a collection your replies.
Please forgive me if I have left anyone out.

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        Suppose I would like a quick estimate of the partial charges
on flavin adenine dinucleotide (FAD) using MOPAC.  What keywords
would you recomend?  This poor molecule disociates with words like
        PM3 PULAY MMOK T=7200 XYZ
Will post replys to the list. Thanks in advance.
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Hi,
I saw your posting about FAD. I have done some work on flavins and 
simply used MMOK PM3 XYZ or 
MMOK PM3 GEO-OK .

Paul Heelis.
p.s why the interest in FAD. I am a flavin man so I was just curious.
Dr. P.Heelis
Faculty of Science and Innovation
North East Wales Institute
Mold Rd
Wrexham
Ll11 2AW
UK
"Paul Heelis, Research" <[email-masked]>
******************************************************************************
Hi!

Add 

EF HESS=1
or
EF HESS=3

These will use an explicit start hessian and thus stop (hopefully) the
dissociation (that is - if it is a optimiser problem).

Otherwise, free out the degrees that break up the molecule , optimise and
then free them and optimise.

Cheers

Alex

 -------------------------------------------------------------------
|Alexander J Turner         [email-masked]                  |
|Post Graduate              |http://www.bath.ac.uk/~chpajt/home.html|
|School of Chemistry        |+144 1225 8262826 ext 5137             |
|University of Bath         |                                       |
|Bath, Avon, U.K.           |Field: QM/MM modeling                  |
 ------------------------------------------------------------------- 
A J Turner <[email-masked]>
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Hi,
      Firstly it looks like you've forgotten a keyword to tell MOPAC about the
charge state of the molecule in question. If it's a dinucleotide (2 phosphates
?) then you should use the keyword CHARGE=-2. In the absence of this MOPAC will
try to treat the system as an open shell species for which it will have severe
convergence problems (hence the PULAY I guess). It will probably also be
horribly slow due to the need to treat electrons in SOMOs with the
half-electron approximation. For charges I'd use AM1 MEP-derived charges
(keywords AM1 and ESP). Also, you should probably use the EF keyword to employ
the eigenvector method of optimisation. Additionally, you may or may not wish
to include the keyword PRECISE to increase the accuracy (and CPU) of your
calculation. If the calculation finishes with a rather high gradient say >10.0
then you may also wish to include the keyword GNORM=value (e.g. 1.0) to try and
force the calculation to a better minimum. Generally, I find that below a
gradient of say 5.0 a lot of systems will change only slightly in geometry and
the resultant charges.

Hope this has been of assistance.

William

-- 
Dr. William A. Wylie             | 
Senior Scientist                 |
Computational Chemistry Dept.    |  Email: [email-masked]  
Proteus Molecular Design Ltd.    |  Phone: +44 1625 500555
Lyme Green Business Park         |  Fax  : +44 1625 500666
Macclesfield                     |
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SK11 0JL, United Kingdom         |
William Wylie <[email-masked]>
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Dear Patricia Fulmer, I have just done an optimization of FAD using the
keywords:- 

T=36000 XYZ MMOK AM1 NOINTER 

It took 43 minutes and 9.756 seconds on an SGI 4400 processor (200MHz) The
starting structure was got from a Brookhaven file (1fnb) (mainly because I
was too lazy to built it from scratch).  This structure needed to have
hydrogens added.  At this stage I ran the structure through a molecular 
mechanics package to ensure that there were no bad contacts.  In my 
experience with MOPAC, if there are bad contact, either the program will 
not run (unless you put GEO-OK as a keyword), or the structure will 
undergo a rearrangement or dissociate.  The precaution of doing molecular 
mechanics is well worth while.  I must add that the structure I used was 
not in a zwitterion form (i.e. there were hydrogens on the phosphate groups).
It would probably be netter to do the zwitterion form.  In any case if 
all you want is atom charges then the keyword 1SCF would probably do, 
and would give you the charges in a much shorter time.

I would imagine that the option PM3 would work in a similar time.

Yours sincerely,

Peter Bladon.
"P.Bladon" <[email-masked]>
******************************************************************************

You mentioned that the molecules dissociates.  Perhaps you don't want to
optimize the structure using MOPAC.  If you can obtain the crystal structure
>from the Cambridge Crystallographic database, optimization of the structure
should not be necessary.  One simply performs the MOPAC calculation for the
fixed structure which you provide.  If you don't have access to the crystal
structure, try generating it with molecular mechanics.  The Klotho Web site is
one place that will probably have a .pdb structure.  You may need Babel to
convert the format to one that your version of MOPAC can use.

Refer to my Web page,

http://pages.pomona.edu/~wsteinmetz/moldata.html

for links to sources of data.  Data for small molecules is found on the
organic chemistry page.

Wayne Steinmetz <[email-masked]>
******************************************************************************

My "default" for something like this is

AM1 NOMM CHARGES=

FAD should have some charges on it, as it is usually modeled.  If you have
protonated everything, then you won't need these.

If you are doing a geometry optimization, I recommend EF.  You may want to
better specify termination criteria (GNORM= , etc.), and a few others (DDMIN=
0.0, LET if you ar using MOPAC 93).

I do not recommend using cartesian coordinates.

Depending on the environment of your FAD, you may want to look at charging in a
dielectric medium.  Try AMSOL for an aqeous wavefunction. . .it may have
parameters for other solvents as well.  MOPAC has the COSMO model, where you 
can
specify the dielectric constant, but I don't have experience with this.

Be very careful of the charging on the phosphorus.  Stewart (or maybe Dewar or
Holder) have warned about some peculiarities of AM1 with P.

sb 
[email-masked]
******************************************************************************

Dear Patricia,
If you have a good starting geometry (e.g. from crystal structures, or 
obtained with molecular mechanics computations) the Mopac keyword 1scf 
might be what you look for.  It will give you the properties, such as 
charges, of the specified geometry without further optimizations.
Hope this helps,
Best regards,

Han Zuilhof

******************************************************************************
**   Dr. Han Zuilhof           **  e-mail: [email-masked]  **
**   Department of Chemistry   **                                           **
**   University of Rochester   **                                           **
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Han Zuilhof <[email-masked]>
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Hi, Patricia,
        It's been a long time since I checked my mail so you may already
have an answer, but have you tried using "1SCF"  This only does not alter
the geometry but it will give  you charges, and info about where the
electrons are etc..

        Of course you nedd to use a half way decent geometry for this to
give reasonable results.

        Hope this helps
                        Iain

________________________________________________________
Iain McVey
Graduate Student
Department of Chemistry
Kent State University
Kent, Ohio, U.S.A.

[email-masked]
(330) 672 3731
Iain McVey <[email-masked]>
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