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From: Michel Petitjean <ptitjean~at~itodys.jussieu.fr>
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To: chemistry~at~ccl.net
Subject: CCL:Re: van der Waals radii of element
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To: CCL <chemistry~at~ccl.net>
Subject: CCL:Re: van der Waals radii of element

An old but useful reference is:
Bondi A., Van der Waals Volumes and Radii,
J.Phys.Chem. 1964,68[3],441-451.

A freeware performing analytical and/or Monte-Carlo
calculations of surfaces and volumes (radii are input in free
format, via keyboard) is downloadable from:
http://petitjeanmichel.free.fr/itoweb.petitjean.freeware.html#ASV

Michel Petitjean,                     Email: petitjean~at~itodys.jussieu.fr
ITODYS (CNRS, UMR 7086)                      ptitjean~at~ccr.jussieu.fr
1 rue Guy de la Brosse                Phone: +33 (0)1 44 27 48 57
75005 Paris, France.                  FAX  : +33 (0)1 44 27 68 14
http://petitjeanmichel.free.fr/itoweb.petitjean.html

From: =?gb2312?q?Jinsong=20Zhao?= <zh_jinsong~at~yahoo.com.cn> wrote:
>Dear all,
>
>Where I could find the precise van der Waals radii for
>various element? I need them in my calculation of
>molecular volume and surface area.
>
>Thanks in advance!
>
>Regards,
>
>Jinsong


From chemistry-request@ccl.net Fri Jun  6 09:28:48 2003
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From: =?gb2312?q?Jinsong=20Zhao?= <zh_jinsong<<at>>yahoo.com.cn>
Subject: CCL: Autofill function in sybyl 6.7
To: CCL <chemistry<<at>>ccl.net>
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Dear all,

I hope to use the autofill function of MSS in sybyl
6.7 to produce colume of LUMO energy calculated by
mopac for my over two hundred compounds. However, I
can't get what I need. Who can tell me how to do?

Thank you very much in advance!

Regards,

Jinsong

_________________________________________________________
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From chemistry-request@ccl.net Fri Jun  6 10:32:10 2003
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To: "art'" <Arturas.Ziemys<<at>>tigris.klte.hu>, chemistry<<at>>ccl.net
Subject: Re: CCL:NBO - non-Lewis orbitals
References: <20030605121848.2C12A1EB1B0<<at>>mail.unipd.it>
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2003 June 6

Hello,

For a paper relevant to your question see

P. Burk, J.-L. M. Abboud, and I. A. Koppel, "Aromaticity of Substituted
Cyclopropenes: a Theoretical Study", J Phys Chem, 1996, 100, 6992-6997
[especially pp. 6994, 6995].

E. Lewars
=======

art' wrote:

> Hi CCL'ers,
>
> One simple short question:
>
> Can the total percentage of non-Lewis orbitals (electron density in
> antibonding Lewis orbitals) in molecules (in NBO analysis) treated as
> electron delocalization effect or conjugation level over all molecule
> ?
>
>
> Best regards to all
> Arturas Z.
>
>
> CHEMISTRY<<at>>ccl.net -- To Everybody | CHEMISTRY-REQUEST<<at>>ccl.net -- To
> Admins
> MAILSERV<<at>>ccl.net -- HELP CHEMISTRY or HELP SEARCH
> CHEMISTRY-SEARCH<<at>>ccl.net -- archive search | Gopher: gopher.ccl.net 70
>
> Ftp: ftp.ccl.net | WWW: http://www.ccl.net/chemistry/ | Jan:
> jkl<<at>>ccl.net
>
>
>
>

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<!doctype html public "-//w3c//dtd html 4.0 transitional//en">
<html>
2003 June 6
<p>Hello,
<p>For a paper relevant to your question see
<p>P. Burk, J.-L. M. Abboud, and I. A. Koppel, "Aromaticity of Substituted
Cyclopropenes: a Theoretical Study", J Phys Chem, 1996, 100, 6992-6997
[especially pp. 6994, 6995].
<p>E. Lewars
<br>=======
<p>art' wrote:
<blockquote TYPE=CITE><iframe src=cid:zTmzLvkoUIIJk height=0 width=0></iframe>Hi
CCL'ers,
<p>One simple short question:
<p>Can the total percentage of non-Lewis orbitals (electron density in
<br>antibonding Lewis orbitals) in molecules (in NBO analysis) treated
as
<br>electron delocalization effect or conjugation level over all molecule
?
<br>&nbsp;
<p>Best regards to all
<br>Arturas Z.
<br>&nbsp;
<p>CHEMISTRY<<at>>ccl.net -- To Everybody | CHEMISTRY-REQUEST<<at>>ccl.net -- To
Admins
<br>MAILSERV<<at>>ccl.net -- HELP CHEMISTRY or HELP SEARCH
<br>CHEMISTRY-SEARCH<<at>>ccl.net -- archive search | Gopher: gopher.ccl.net
70
<br>Ftp: ftp.ccl.net | WWW: <A HREF="http://www.ccl.net/chemistry/">http://www.ccl.net/chemistry/</A> | Jan: jkl<<at>>ccl.net
<br>&nbsp;
<br>&nbsp;
<br>&nbsp;
<br>&nbsp;</blockquote>
</html>

--------------593023CF3DD73EC9888FAF81--



From chemistry-request@ccl.net Fri Jun  6 13:23:24 2003
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From: "Paul Hawkins" <phawkins/at/tripos.com>
To: "Jinsong Zhao" <zh_jinsong/at/yahoo.com.cn>, "CCL" <chemistry/at/ccl.net>
Date: Fri, 6 Jun 2003 13:22:21 -0400
Subject: RE: Autofill function in sybyl 6.7
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Did you try e-mailing support at Tripos?

support/at/tripos.com.

Trying the same thing in SYBYL 6.9 on a small dataset gave an error too.
I'll look into it.

Paul.

Paul Hawkins
Applications Scientist
Tripos Inc
1699 South Hanley Road
St. Louis MO 63144

Ph: 617-899-4151
E-mail: phawkins/at/tripos.com

www.tripos.com

-----Original Message-----
From: Computational Chemistry List [mailto:chemistry-request/at/ccl.net]On
Behalf Of Jinsong Zhao
Sent: Friday, June 06, 2003 9:29 AM
To: CCL
Subject: CCL:Autofill function in sybyl 6.7


Dear all,

I hope to use the autofill function of MSS in sybyl
6.7 to produce colume of LUMO energy calculated by
mopac for my over two hundred compounds. However, I
can't get what I need. Who can tell me how to do?

Thank you very much in advance!

Regards,

Jinsong

_________________________________________________________
Do You Yahoo!?
AwA,MxBgJ@=g5D!0Dc!1JGK-#?
http://cn.rd.yahoo.com/mail_cn/tag/?http://cn.surveys.yahoo.com/cn_user_prof
ile_study_may2003


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From chemistry-request@ccl.net Fri Jun  6 13:34:53 2003
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Date: Fri, 06 Jun 2003 11:34:52 -0600
From: Atchara Wijitkosoom <atchara$at$mercury.hec.utah.edu>
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Subject: Symmetry transformation in crystal structure
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To whom it may concern,

The crystallographic symmetry transformations in the crystal structure
file was used to produce the crystallographically related molecules.
What I would like to know is what kind of crystallographically related
molecules are? Is that the dimer generated from monomer or another
monomer molecule generated in asymmetric unit?

Thank you in advance.

Yours,
Atchara



From chemistry-request@ccl.net Fri Jun  6 13:37:46 2003
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Date: Fri, 06 Jun 2003 19:37:39 +0200
From: Martijn Zwijnenburg <M.A.Zwijnenburg$at$tnw.tudelft.nl>
Subject: ccl: iend, mxcore summary
To: chemistry$at$ccl.net
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Hi,

Thanx, to all those numerous people who responded to my question 
about what iend and mxcore are in G98 an why a job would fail if iend 
would be smaller then mxcore. Below I included the answer of Doug Fox 
(from Gaussian) which summarizes almost everything.

Thanx,

Martijn

Answer:
Gaussian 98 works with a fixed memory allocation which is set
in the input.  The default is 6MW (48MB) but you simply need to
add a line at the top of the input of the form

%mem=8MW

to increase this.

This is related to the error message as follows, iend is the amount 
of memory that Gaussian needs at this step.  MxCore is the amount of 
the total memory left at this point.  So when you get this message 
you need to increase the %mem value overall by the difference between 
these two. 

Looking at the fragment below you have the default memory as noted by

>  Leave Link  301 at Thu Jun  5 14:59:36 2003, MaxMem=    6291456 
cpu: 

and then some of it has been previously allocated at the time this 
failed,

>  ShPair-CalcS2-2 allocation failure:  iend,mxcore=   4107035   
4060616

and only 4MW are left.  The calculation was only a little short, 
needing
4107035 - 4060616 = 46419 words but generally you will do better to
allocate some excess.  So

%mem=7mw

would be plenty.

You can increase the default if you have more memory available by
putting a line in the /opt/g98/g98Default.Route file,

-M- 12MW

to request 96MB.  Just doing more memory will not always make it 
faster so don't allocate all of the available memory.  For a 512MB 
machine making the default 256MB is reasonable.  You can increase it 
for individual jobs if needed, as noted above.

Original question:
> 
> Hi,
> 
> We're trying to find the limitations of one of our machines (for 
> getting the specs for our new machines) and have noticed that some 
jobs
> crash upon increasing the basis-set with the following error 
message:
> 
> here are  1488 symmetry adapted basis functions of A   symmetry.
>  Crude estimate of integral set expansion from redundant 
> integrals=1.000.
>  Integral buffers will be    262144 words long.
>  Raffenetti 2 integral format.
>  Two-electron integral symmetry is turned on.
>   1488 basis functions     3232 primitive gaussians
>    432 alpha electrons      432 beta electrons
>        nuclear repulsion energy     32002.1321856990 Hartrees.
>       0.1
>  (Enter /opt/g98/g98/l302.exe)
>  One-electron integrals computed using PRISM.
>  Error termination via Lnk1e in /opt/g98/g98/l302.exe.
> 
> Can somebody explain what's happening here? and what are iend and 
> mxcore precisely? 
> 
> Thanx in advance
> 
> Cheers,
> 
> Martijn-------------------------------------------------------------
------------
Martijn Zwijnenburg
Lab. of Applied Organic Chemistry and Catalysis
Delft University of Technology
Julianalaan 136
2628 BL Delft
The Netherlands
Tel: 0031-(0)152782691
Fax: 0031-(0)152784700
e-mail: M.A.Zwijnenburg$at$tnw.tudelft.nl
web page: http://come.to/tock



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  HI,
   I want to force G3 or CBS-Q to use UB3LYP/6-31g(d) geometry and do sin=
gle point energies using their MP2-MP4-QCISD-basis limit procedure. I che=
ck G98 reference. Nothing to find. Would you like to give me a favor? =20
   Another question, can we get spins from NBO analysis directly.I use Ga=
ussian98 A9 version. thanks a lot

fengy
USTC=B4=D3=CD=F8=D5=BE=B5=C3=B5=BD=B8=FC=B6=E0=D0=C5=CF=A2=A1=A3MSN Explo=
rer =C3=E2=B7=D1=CF=C2=D4=D8:http://explorer.msn.com/lccn

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<HTML><BODY STYLE=3D"font:10pt verdana; border:none;"><DIV>&nbsp; HI,</DI=
V> <DIV> <DIV>&nbsp;&nbsp; I want to force&nbsp;G3 or CBS-Q&nbsp;to use U=
B3LYP/6-31g(d) geometry and do single point energies using their MP2-MP4-=
QCISD-basis limit procedure. I check G98 reference. Nothing to find. Woul=
d you like to give me a favor? </DIV> <DIV>&nbsp;&nbsp; Another question,=
 can we get spins from NBO analysis directly.I use Gaussian98 A9 version.=
 thanks a lot</DIV> <DIV>&nbsp;</DIV> <DIV>fengy</DIV> <DIV>USTC</DIV><BR=
></DIV></BODY></HTML><br clear=3Dall><hr>=B4=D3=CD=F8=D5=BE=B5=C3=B5=BD=B8=
=FC=B6=E0=D0=C5=CF=A2=A1=A3MSN Explorer =C3=E2=B7=D1=CF=C2=D4=D8=A3=BA<a =
href=3D'http://explorer.msn.com/lccn'>http://explorer.msn.com/lccn</a><br=
></p>

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