From chemistry-request@ccl.net Tue Jul 15 18:39:20 2003
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Date: Tue, 15 Jul 2003 15:39:35 -0700 (PDT)
From: Stephen Cooke <sacooke_at_chem.ubc.ca>
To: chemistry_at_ccl.net
Subject: Altering Gaussian output.
In-Reply-To: <Pine.LNX.4.44.0301231640200.23937-100000_at_father.chem.ubc.ca>
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Hi Everybody,

I am preparing some density plots using Gaussian 98 which i then view 
using MOLDEN.

The little molecule I am working on at the moment is PbS and I have the 
problem that whilst the calculation appears to run fine the format of the 
output is a little weird.  As an example here is a "weird" bit:

                           1        2         3         4         5
                        (SG)--0  (SG)--0   (PI)--0   (PI)--0   (SG)--0
  EIGENVALUES  --  ***********-496.69320-477.99337-477.99337-477.99273


The leading asterisks presumeably come about because the output format is 
set to something like f9.5 or f10.5 and my Eigenvalues are 
larger than that.   Unsurprisingly this causes the MOLDEN viewer a 
problem.

Is there a simple way around this or do i have to alter the code? If the 
only option is the latter does anybody have any experience altering the 
code (if thats possible) when they are not the system administrator just a 
general user etc...

I truly appreciate any help anybody can offer.

Cheers,

Steve Cooke
UBC Vancouver, Canada



From chemistry-request@ccl.net Tue Jul 15 08:12:46 2003
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CLIFF 1.23 Announcement   New Version of the File Format Converter
-------------------------------------

Molecular Networks GmbH is pleased to announce version 1.23 of the file
format converter CLIFF.
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file formats commonly used for chemical compounds (SMILES, SDF, MOL,
MOL2, ...) and reactions (RXN, RDF).

The most important improvements in the current version are:
* Improved Charmm and Sybyl2 file format support
* NEW: Support of Daylight's Thor Data Tree/Stigmata file format (read
and write)
* NEW: Support of Daylight's SMARTS file format (read and write)
* NEW: Support of MDL's TGF file format (write only)
* NEW: Support of MDL's ISIS Sketch file format (read only) for
molecules and reactions (incl. atom mapping)

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* Generation of 2D coordinates by a state-of-the-art 2D structure layout
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* NEW: Generation of all tautomeric forms or a unique tautomeric form of
the input structures for standardization purposes

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* Interfacing a variety of chemical information and data processing
systems
* Maintenance and standardization of compound and reaction databases
* Preprocessing of datasets by adding missing data or converting to file
formats required by other programs

As it was designed to handle large datasets of hundreds of thousands of
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CLIFF is available for x86 Linux, SGI IRIX, Sun Solaris, or Windows
NT/2000/XP.

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or contact us by e-mail info:at:mol-net.de


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From chemistry-request@ccl.net Tue Jul 15 04:09:43 2003
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From: "Tris Youngs" <t.g.a.youngs:at:reading.ac.uk>
To: <CHEMISTRY:at:ccl.net>
Subject: CCL: Gaussian03 pseudopotential 'instability'
Date: Tue, 15 Jul 2003 09:12:57 +0100
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Hi all.

My calculations involve non-standard basis-sets and ECP's (from the
CRENBL set) for La and Ac.

While both pseudos worked fine in G98, G03 seems to dislike the Ac
potential, failing as the initial guess is being made (l401). The output =
is:

<snip>
Spurious integrated density or basis function:
(...varies from calc to calc...)
Inaccurate quadrature in CalDSu.
Error termination via Lnk1e........
<snip>

I have tried various Guess methods (INDO, Huckel e.t.c.) but all crash
at the same place (with different wording of the error). Even the old =
G98
Guess methods INDO and OldHuckel fail, although the latter proceeds
past the guess stage, but reports a warning that the Fock matrix is not
symmetric (it then crashes later on).

Have the density integration criteria been tweaked in G03 such that the
Ac basis set is no longer 'acceptable'? I don't think this can be the =
case,
because a calculation of a single Ac atom works without problem.

Although they work fine in G98, I need some features of G03!

Can anybody suggest a solution?

Regards,
Tris Youngs.
scr00tgy:at:reading.ac.uk

Department of Chemistry
University of Reading
UK
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<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN">
<HTML><HEAD>
<META http-equiv=3DContent-Type content=3D"text/html; =
charset=3Diso-8859-1">
<META content=3D"MSHTML 6.00.2800.1106" name=3DGENERATOR>
<STYLE></STYLE>
</HEAD>
<BODY bgColor=3D#ffffff>
<DIV><FONT face=3DArial size=3D2>
<DIV><FONT face=3DArial size=3D2>Hi all.</FONT></DIV>
<DIV><FONT face=3DArial size=3D2></FONT>&nbsp;</DIV>
<DIV><FONT face=3DArial size=3D2>My calculations involve non-standard =
</FONT><FONT=20
face=3DArial size=3D2>basis-sets and ECP's (from the</FONT></DIV>
<DIV><FONT face=3DArial size=3D2>CRENBL set) for La and Ac.</FONT></DIV>
<DIV><FONT face=3DArial size=3D2></FONT>&nbsp;</DIV>
<DIV><FONT face=3DArial =
size=3D2>While&nbsp;both&nbsp;pseudos&nbsp;worked fine in=20
G98, G03 </FONT><FONT face=3DArial size=3D2>seems to dislike the =
Ac</FONT></DIV>
<DIV><FONT face=3DArial size=3D2>potential, failing as the initial guess =
is being=20
</FONT><FONT face=3DArial size=3D2>made (l401). The output =
is:</FONT></DIV>
<DIV><FONT face=3DArial size=3D2></FONT>&nbsp;</DIV>
<DIV><FONT face=3DArial size=3D2>&lt;snip&gt;</FONT></DIV>
<DIV><FONT face=3DArial size=3D2>Spurious integrated density or basis=20
function:</FONT></DIV>
<DIV><FONT face=3DArial size=3D2>(...varies from calc to =
calc...)</FONT></DIV>
<DIV><FONT face=3DArial size=3D2>Inaccurate quadrature in =
CalDSu.</FONT></DIV>
<DIV><FONT face=3DArial size=3D2>Error termination via =
Lnk1e........</FONT></DIV>
<DIV><FONT face=3DArial size=3D2>&lt;snip&gt;</FONT></DIV>
<DIV><FONT face=3DArial size=3D2></FONT>&nbsp;</DIV>
<DIV><FONT face=3DArial size=3D2>I have tried various Guess methods =
(INDO, Huckel=20
e.t.c.) but all crash</FONT></DIV>
<DIV><FONT face=3DArial size=3D2>at the same place (with different =
wording of the=20
error). Even the old G98</FONT></DIV>
<DIV><FONT face=3DArial size=3D2>Guess methods INDO and OldHuckel fail, =
although the=20
latter proceeds</FONT></DIV>
<DIV><FONT face=3DArial size=3D2>past the guess stage, but reports a =
warning that=20
the Fock matrix is not</FONT></DIV>
<DIV><FONT face=3DArial size=3D2>symmetric (it then crashes later =
on).</FONT></DIV>
<DIV><FONT face=3DArial size=3D2></FONT>&nbsp;</DIV>
<DIV><FONT face=3DArial size=3D2>Have the density integration criteria =
been tweaked=20
in G03 such that the</FONT></DIV>
<DIV><FONT face=3DArial size=3D2>Ac basis set is no longer 'acceptable'? =
I don't=20
think this can be the case,</FONT></DIV>
<DIV><FONT face=3DArial size=3D2>because a calculation of a single Ac =
atom works=20
without problem.</FONT></DIV>
<DIV><FONT face=3DArial size=3D2></FONT>&nbsp;</DIV>
<DIV><FONT face=3DArial size=3D2>Although they work fine in G98, I need =
some=20
features of G03!</FONT></DIV>
<DIV><FONT face=3DArial size=3D2></FONT>&nbsp;</DIV>
<DIV><FONT face=3DArial size=3D2>Can anybody suggest a =
solution?</FONT></DIV>
<DIV><FONT face=3DArial size=3D2></FONT>&nbsp;</DIV>
<DIV><FONT face=3DArial size=3D2>Regards,</FONT></DIV>
<DIV><FONT face=3DArial size=3D2>Tris Youngs.</FONT></DIV>
<DIV><FONT face=3DArial size=3D2><A=20
href=3D"mailto:scr00tgy:at:reading.ac.uk">scr00tgy:at:reading.ac.uk</A></FONT><=
/DIV>
<DIV><FONT face=3DArial size=3D2></FONT>&nbsp;</DIV>
<DIV><FONT face=3DArial size=3D2>Department of Chemistry</FONT></DIV>
<DIV><FONT face=3DArial size=3D2>University of Reading</FONT></DIV>
<DIV><FONT face=3DArial =
size=3D2>UK</FONT></DIV></FONT></DIV></BODY></HTML>

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From chemistry-request@ccl.net Tue Jul 15 10:23:40 2003
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Date: Tue, 15 Jul 2003 07:23:38 -0700 (PDT)
From: Guosheng Wu <wu_guosheng2002:at:yahoo.com>
Subject: Re: CCL:J.PHYS.CHEM. and J.CHEM.PHYS.
To: "Shobe, Dave" <dshobe:at:sud-chemieinc.com>,
   "'Jiro Ueda'" <tatokirai:at:mx35.tiki.ne.jp>, chemistry:at:ccl.net
In-Reply-To: <5CF08BBFE6DE97478C1E76E654CAF90801BC0D2E:at:lvlxch02.ntdomain.americas.sc-world.com>
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I do not see where is the position of "chemical reaction",
which should be the central topic when anyone talks about
"chemistry". So you may want to add it in both JPC and JCP
explicitly, although one may be able to see it from "kinetics" 
or "dynamics", but not necessarily.

My personal point of view: JPC is more on chemical concepts,
especially on molecular structure & reactivity, while JCP is 
more on mathematical approaches, analytical or numerical. 
And Physics is everywhere.

Cheers.

Guosheng Wu 


--- "Shobe, Dave" <dshobe:at:sud-chemieinc.com> wrote:
> (1) Which type of paper does J.Phys.Chem. like ? 
> 
> (2) Which type of paper does J.Chem.Phys. like ? 
> 
> Probably the best way to answer questions like these is to browse recent
> issues of the journals and see whether papers similar to yours have been
> published there. You can also read the "about this journal" pages on the
> journal web site. These are typically not displayed prominently on the
> journal home page, so here are the descriptions for the journals in
> question:
> 
> JPC:A publishes studies on molecules (dynamics, spectroscopy, gaseous
> clusters, molecular beams, kinetics, atmospheric and environmental physical
> chemistry, molecular structure, bonding, quantum chemistry, and general
> theory). 
> 
> JPC:B publishes studies on materials (nanostructures, micelles,
> macro-molecules, statistical mechanics and thermodynamics of condensed
> matter, biophysical chemistry, and general physical chemistry), as well as
> studies on the structure and properties of surfaces and interfaces. 
> 
> The purpose of  <http://ojps.aip.org/jcpo/> The Journal of Chemical Physics
> (JCP) is to bridge a gap between journals of physics and journals of
> chemistry by publishing quantitative research based on physical principles
> and techniques, as applied to "chemical" systems. Just as the fields of
> chemistry and physics have expanded, so have chemical physics subject areas,
> which include polymers, materials, surfaces/interfaces, and biological
> macromolecules, along with the traditional small molecule and condensed
> phase systems. Just as the Journal must expand into new areas, some areas
> once covered by the Journal will no longer be appropriate. The criteria for
> whether a subject is appropriate for JCP are whether there exists a
> significant number of readers that are active in the field and whether these
> readers are most likely to find the manuscript if it is published in JCP. If
> the bulk of the literature in a field is published in other journals with
> only an occasional article in JCP, the subject is not appropriate for the
> Journal even if at one time the literature on that subject appeared
> primarily in JCP. 
> 
> (3) If one hesite to submit for JPC or JCP, which factor should be conidered
> ?
> 
> Then you should publish in Physical Chemistry Chemical Physics. ;-)
> 
> --David Shobe
> Sud-Chemie Inc.
> phone (502) 634-7409
> fax     (502) 634-7724
> email  dshobe "at" sud-chemieinc.com
> 
> Don't bother flaming me: I'm behind a firewall.
> 
> 
> 
> -----Original Message-----
> From: Jiro Ueda [mailto:tatokirai:at:mx35.tiki.ne.jp]
> Sent: Saturday, July 12, 2003 10:49 PM
> To: chemistry:at:ccl.net
> Subject: CCL:J.PHYS.CHEM. and J.CHEM.PHYS.
> 
> 
> Hi All,
>  
> I am sorry for my question. I would like to ask you about submitting for
> J.Phys.Chem. and J.Chem.Phys. in Computational Chemistry.
>  
> (1) Which type of paper does J.Phys.Chem. like ?
> (2) Which type of paper does J.Chem.Phys. like ?
> (3) If one hesite to submit for JPC or JCP, which factor should be conidered
> ?
>  
> Thanks,
> Jiro Ueda
> 
> 


__________________________________
Do you Yahoo!?
SBC Yahoo! DSL - Now only $29.95 per month!
http://sbc.yahoo.com


From chemistry-request@ccl.net Tue Jul 15 11:14:10 2003
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Date: Tue, 15 Jul 2003 16:14:08 +0100 (BST)
From: Jamie Platts <Platts|at|Cardiff.ac.uk>
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To: chemistry|at|ccl.net
Subject: G03 & AMBER - Summary
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Hi All - last week I posted a question, and now summarise the answers
I received. My sincere thanks to all who replied. Cheers, Jamie.

**Original question**
Hi there - I'm having trouble getting an ONIOM job on a platinum complex
to run in Gaussian03. Despite requesting AMBER for the outer region and
LanL2DZ for the metal core, the job crashes because there is no VSTO-3G
basis set for Pt (G98 just printed a warning and carried on).
Does anyone know of a way to avoid this? More fundamentally, why does an
AMBER calculation require an STO-3G basis anyway?

 ONIOM: restoring gridpoint  3 on chk file.
 ONIOM: generating point  3 -- low level on real system.
 Standard basis: VSTO-3G* (5D, 7F)
 IA out of range in STO.
 Error termination via Lnk1e in /usr/local/testsoft/g03/l301.exe

**From ferre|at|unisi.it Tue Jul 15 16:02:38 2003
>> This works if you realise that 3-21G is not defined for 3rd row TM's.
>> So swapping 3/5=2 for 3/5=6 (LanL2DZ) seems ok. Jamie
Actually, even for MM calculations, gaussian has to pass through the
link 301 where basis functions are attributed (it initializes other
things ...) Anyway, these basis functions for MM have no sense and are
not used in the following of the calculation.
What you have to do is to use a non standard route:
1) Save the route that comes at the beginning of the output file. This
is the thing that lists all iop, should begin with:
1/30=1,38=1,52=2,56=1/1;
....
2) In a new input file, write:
# NONSTD
Copy all the previous route
3) Replace every occurence of
3/5=2 .../1;
with
3/5=5 .../1;
where ... represents all other iops.
Actually this replace the default V-STO3G with 3-21G (for which Pt is
defined) thus the calculation should go on.

**From gaussian.com!csd|at|gaussian.com Tue Jul 15 16:10:48 2003
Unfortunately we fixed that hole.  In G98 it might have been possible
to trick it into taking a basis set at this point but in G03 it knows
that it has a built-in basis for mechanics and skips looking for basis
sets on these calculations.


**From tapaskar|at|cc.usu.ed Tue Jul 15 16:02:24 2003
Hi, I got the same problem with Os.
Gaussian people informed me that it will be taken care in the revised
version.
You may try with IOP(3/12=1)option.
Tapas


**From yubofan|at|mail.chem.tamu.edu Tue Jul 15 16:02:27 2003
You'd better change AMBER into UFF because AMBER cannot handle Pt. Good
luck.

**From m.a.zwijnenburg|at|tnw.tudelft.nl Tue Jul 15 16:02:31 2003
It's quite some time since I worked with Oniom but as far as I remember
lower level calculations are performed for both the outer region and the
whole cluster (thus including the region you want to treat at high level).
As far as I know this is needed for the substraction scheme that ONIOM
actually is. The lower level method should thus, I guess, also be able to
describe the centre region and this might be a problem with Pt and Amber. To
be sure, check the original paper.


----------------------------------------------------------
  Jamie Platts
  Dept. of Chemistry  		Phone: +44 (0) 2920 874950
  Cardiff University 	 	Email: platts|at|cf.ac.uk
  P.O. Box 912 			FAX:   +44 (0) 2920 874030
  Cardiff CF10 3TB 		www.cf.ac.uk/chemy


From chemistry-request@ccl.net Tue Jul 15 14:03:04 2003
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From: "=?GB2312?Q?=C3=CF=B3=A4=B9=A6?=" <cgmeng:at:dlut.edu.cn>
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Subject: g98 compilation problems again
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Hi! Everyone!

After added libblas.a which I compiled on this machine, I tried to recompile my g98 according to 
the instruction on USER REFERENCE, I still found the following errors:
07/15/03 20:24:48 T = 0.020/0.030 sec. 0 error(s) Maximum. Severity: 0
1501-510 Compilation successful for file ml109.f.
rm -f ml109.f
xlf -q64 -qintsize=8 -qrealsize=8 -qextname -qarch=auto -qtune=auto -qp
hsinfo -qcharlen=32760 -NQ70000 -NT240000 -ND15000 -c
ld: 0711-317 ERROR: Undefined symbol: .dspmv
ld: 0711-317 ERROR: Undefined symbol: .dgemm
ld: 0711-345 Use the -bloadmap or -bnoquiet option to obtain more information.
make: 1254-004 The error code from the last command is 8.

I wonder if ESSLLIB shipped from IBM can solve this problem.

Sincerely yours




From chemistry-request@ccl.net Mon Jul 14 23:04:17 2003
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To: "chemistry-.at.-ccl.net" <chemistry-.at.-ccl.net>
Subject: g98 compilation problems
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Hi! Everyone!

When I tried to recompile my g98 according to the instruction on USER REFERENCE, I found the following errors:
07/09/03 20:24:48 T = 0.020/0.030 sec. 0 error(s) Maximum. Severity: 0
1501-510 Compilation successful for file ml109.f.
rm -f ml109.f
xlf -q64 -qintsize=8 -qrealsize=8 -qextname -qarch=auto -qtune=auto -qp
hsinfo -qcharlen=32760 -NQ70000 -NT240000 -ND15000 -c
ld: 0711-317 ERROR: Undefined symbol: .dspmv
ld: 0711-317 ERROR: Undefined symbol: .dgemm
ld: 0711-345 Use the -bloadmap or -bnoquiet option to obtain more information.
make: 1254-004 The error code from the last command is 8.

Then I tried to compile every .exe file, and found that if the .exe file calls the above 2 modules, the above errors will comes. I checked the bldg98.log and found that these 2 modules are from rs6kdum.F and they were successfully compiled, though the name of modules are:
dspmv_
dgemm_
not as mentioned in the errors:
dspmv
dgemm
I wonder why these happens, and how i can compile gaussian98 successfully. 

If you have met such problems, please tell me the detailed procedure to solve this problem.


Sincerely yours




From chemistry-request@ccl.net Tue Jul 15 03:21:56 2003
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Date: Tue, 15 Jul 2003 10:21:54 +0300 (EEST)
From: Arvydas Tamulis <tamulis{at}mserv.itpa.lt>
To: chemistry{at}ccl.net
cc: Jelena Tamuliene <gicevic{at}mserv.itpa.lt>
Subject: Neutral radical molecules
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Dear Netters,

Would you please to say the name and literature references of my
constructed neutral radical molecule given bellow, where the unpaired spin
should be well protected enviromentaly by three chains:
                                  .
                       CH3-(CH2)n-C-(CH2)n-CH3
                                  |
                                  (CH2)n-CH3

Maybe you know the similar alternative stable neutral radical molecules?
Actually I am looking for stable neutral radical molecules with small HFS,
i.e. constructed only from C, H (D) and O atoms.

Best regards, Arvydas Tamulis



From chemistry-request@ccl.net Tue Jul 15 14:45:16 2003
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From: Igor Avilov <avilovi(at)averell.umh.ac.be>
To: chemistry(at)ccl.net
Subject: Symmetry and excited states
Date: Tue, 15 Jul 2003 20:35:17 +0200
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Dear CCL-ers,

Recently I encountered the following problem. When calculating (by Gaussian
98) excited states of a molecule optimized with imposed D2d symmetry
constrain I got the strange features of the calculated excited states.
Namely, I got different calculated energies and (sometimes) quite different
oscillator strength for degenerate transitions. Nevertheless, Gaussian
denotes excited states being degenerate and having E-symmetry. Can anybody
explain me why is it so?

Best regards,
Igor.


