From chemistry-request@ccl.net Thu Mar 4 23:29:07 2004 Received: from calmail-cl.berkeley.edu (mailfarm.Berkeley.EDU [128.32.61.106]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i254T6d4020587 for ; Thu, 4 Mar 2004 23:29:07 -0500 Received: from [128.32.198.91] (account shaji..at..calmail.berkeley.edu HELO berkeley.edu) by calmail-cl.berkeley.edu (CommuniGate Pro SMTP 4.1.8) with ESMTP id 2507685; Thu, 04 Mar 2004 20:30:42 -0800 Message-ID: <40480263.6040705..at..berkeley.edu> Date: Thu, 04 Mar 2004 20:30:27 -0800 From: Shaji Chempath User-Agent: Mozilla/5.0 (X11; U; Linux i686; en-US; rv:1.4.1) Gecko/20031114 X-Accept-Language: en-us, en MIME-Version: 1.0 To: ccl , baronp..at..uclink.berkeley.edu, Shaji Chempath Subject: Geom. Optimization in Solvent (Gaussian, Jaguar) Content-Type: text/plain; charset=ISO-8859-1; format=flowed Content-Transfer-Encoding: 7bit Hello CCLers, Few weeks beore I had asked a question about geometry optimization in the presence of a solvent. I would like to thank all the people who replied to that. ( see summary of replies below). However I still have lots of problems with optimizing in the presence of solvent. I have used both Gaussian and Jaguar for doing my polarizable continuum optimizations and still no luck. Here is what I understand about what is going on, please let me know if you have any opinions. It appears as though the gradients calculated in the presence of solvent are far less accurate. This may be because the 'Poisson Boltzmann' equation is solved numerically for the solvent region and the reaction field in the solvent is mapped on to limited number of "Tesserae" (points on the solute-solvent boundary). This somehow makes the potential energy surface very rough, compared to the smooth surface in gas phase. Look at the graphs (on my webpage) to see what I mean http://zeolites.cqe.nwu.edu/shaji/solvation.html You can see that the gas phase optimization proceeds smoothly, but liquid phase optimizations run into bumpy potnetial energy surface. (even after staring from a gas phase optimized geometry). This is a general phenomena (the roughening of the potential energy surface) I have observed for different systems I have tried . So based on this I hav ecome to the conclusion that the optimization with solvent is very tough and works only for very simple molecules. Am I wrong? Summary of help I got from others regarding PCM (Gaussian) optimizations ------------------------------------------------------------- a) initially do a gas phase geometry and then start liquid phase optimization from there b) use "OPT(calcfc)" to calculate initial hessian c) try iefpcm instead of pcm or scipcm d) try "loose" optimization e) try changing TSNUM (number of tesserae) or TSARE(ares of tesserae) in scrf f) use nosymm option Anyway none of them seem to have helped in particular for my molecules Thanks again Shaji From chemistry-request@ccl.net Thu Mar 4 14:31:23 2004 Received: from casbah.it.northwestern.edu (casbah.it.northwestern.edu [129.105.16.52]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i24JVNd4031133 for ; Thu, 4 Mar 2004 14:31:23 -0500 Received: (from mailnull@localhost) by casbah.it.northwestern.edu (8.12.10/8.12.10) id i24JWwD4003186 for ; Thu, 4 Mar 2004 13:32:58 -0600 (CST) Received: from chief (chief.chem-eng.northwestern.edu [129.105.205.171]) by casbah.it.northwestern.edu via smap (V2.0) id xma001879; Thu, 4 Mar 04 13:32:40 -0600 From: "Jim Pfaendtner" To: Subject: Gaussian 98/03 on Rocks 3 or Redhat 9 Date: Thu, 4 Mar 2004 13:30:40 -0600 Message-ID: <000201c4021f$2e070430$abcd6981@chief> MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="----=_NextPart_000_0003_01C401EC.E36C9430" X-Priority: 3 (Normal) X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook, Build 10.0.2627 Importance: Normal X-MimeOLE: Produced By Microsoft MimeOLE V6.00.2800.1165 This is a multi-part message in MIME format. ------=_NextPart_000_0003_01C401EC.E36C9430 Content-Type: text/plain; charset="us-ascii" Content-Transfer-Encoding: 7bit CCLers We are trying to install g98 and g03 on a redhat 9.0 rocks cluster. We are now unable to run either of these program using Linda(multi-processors). After contacting Gaussian support, we were told that Linda has some library incompatibilities with redhat 9.0 libraries. If we can install these new libraries over our default redhat 9.0 installation, perhaps we can overcome this problem. I am just curious now if there are people who have dealt with these issues and can help us out? Thanks! ------=_NextPart_000_0003_01C401EC.E36C9430 Content-Type: text/html; charset="us-ascii" Content-Transfer-Encoding: quoted-printable

CCLers<= font size=3D2 face=3DArial>

 

We are trying to install g98 and g03 on a redhat 9.0 rocks cluster.  We are now unable to run either of these program using Linda(multi-processors).  After contacting Gaussian support, we were told that Linda has = some library incompatibilities with redhat 9.0 libraries.  If we can = install these new libraries over our default redhat 9.0 installation, perhaps we can overcome this = problem.  I am just curious now if there = are people who have dealt with these issues and can help us = out?

 

 

 

Thanks!

 

 

------=_NextPart_000_0003_01C401EC.E36C9430-- From chemistry-request@ccl.net Thu Mar 4 21:47:50 2004 Received: from postal.usc.edu (postal.usc.edu [128.125.253.6]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i252lnd4016110 for >ccl.net>; Thu, 4 Mar 2004 21:47:50 -0500 Received: from almaak.usc.edu (almaak.usc.edu [128.125.253.166]) by postal.usc.edu (iPlanet Messaging Server 5.2 HotFix 1.21 (built Sep 8 2003)) with ESMTP id <0HU300DRC16CKB<>postal.usc.edu> for CHEMISTRY<>ccl.net; Thu, 04 Mar 2004 18:49:24 -0800 (PST) Date: Thu, 04 Mar 2004 18:49:24 -0800 (PST) From: Anna Krylov >almaak.usc.edu> Subject: CCL: New website alert To: CHEMISTRY<>ccl.net Message-id: >almaak.usc.edu> MIME-version: 1.0 Content-type: TEXT/PLAIN; charset=US-ASCII Content-transfer-encoding: 7BIT Dear Colleagues, Since many of you are employing electronic structure calculations in your research, you may find the following new website that highlights certain issues re: ab initio software to be of some interest to you: http://www.bannedbygaussian.org From chemistry-request@ccl.net Wed Mar 3 11:56:57 2004 Received: from web14103.mail.yahoo.com (web14103.mail.yahoo.com [216.136.172.133]) by server.ccl.net (8.12.8/8.12.8) with SMTP id i23Guvd4012582 for ; Wed, 3 Mar 2004 11:56:57 -0500 Message-ID: <20040303164958.88020.qmail=at=web14103.mail.yahoo.com> Received: from [200.55.139.213] by web14103.mail.yahoo.com via HTTP; Wed, 03 Mar 2004 08:49:58 PST Date: Wed, 3 Mar 2004 08:49:58 -0800 (PST) From: raquel crespin Subject: excited state geometries with mopac To: chemistry=at=ccl.net MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii Hi all! I tried to find excited state geometries with mopac using keywords: AM1 C.I.=3 ROOT=2 gnorm=0.01 CHARGE=-1 MECI (the molecule have charge=-1). After 14 cycles appear the following message: NO POINT LOWER IN ENERGY THAN THE STARTING POINT COULD BE FOUND IN THE LINE MINIMIZATION. What can i do? Thanks Rachel Crespo Otero Ph.D. Student Laboratorio de Quimica Computacional y Teorica (LQCT) Universidad de la Habana Cuba __________________________________ Do you Yahoo!? Yahoo! Search - Find what you re looking for faster http://search.yahoo.com From chemistry-request@ccl.net Thu Mar 4 19:57:11 2004 Received: from mail2.qmul.ac.uk (mail2.qmul.ac.uk [138.37.6.6]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i250vAd4011306 for ; Thu, 4 Mar 2004 19:57:11 -0500 Received: from smtp.qmul.ac.uk ([138.37.6.40]) by mail2.qmul.ac.uk with esmtp (Exim 4.14) id 1Az3ft-0000T2-48 for CHEMISTRY=at=ccl.net; Fri, 05 Mar 2004 00:58:49 +0000 Received: from matpc18.mats.qmw.ac.uk ([138.37.43.64] helo=Ruzhen) by smtp.qmul.ac.uk with smtp (Exim 3.35 #5) id 1Az3fr-0004oi-00 for CHEMISTRY=at=ccl.net; Fri, 05 Mar 2004 00:58:47 +0000 Message-ID: <01aa01c4024d$09d751e0$402b258a@Ruzhen> From: "Ru-Zhen Li" To: Subject: analyse bond length distribution? Date: Fri, 5 Mar 2004 00:58:57 -0000 MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="----=_NextPart_000_01A7_01C4024D.09A2D460" X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 6.00.2800.1158 X-MimeOLE: Produced By Microsoft MimeOLE V6.00.2800.1165 X-Sender-Host-Address: 138.37.43.64 X-QM-Scan-Virus: virusscan says the message is clean X-QM-Scan-Virus: ClamAV says the message is clean This is a multi-part message in MIME format. ------=_NextPart_000_01A7_01C4024D.09A2D460 Content-Type: text/plain; charset="gb2312" Content-Transfer-Encoding: quoted-printable Dear CCLers, Does anyone know any free software that can analyse geometric properties = of solids? such as length distribution, angle distribution etc? Thank you very much in advance! Best regards, Ru-Zhen ------=_NextPart_000_01A7_01C4024D.09A2D460 Content-Type: text/html; charset="gb2312" Content-Transfer-Encoding: quoted-printable
Dear CCLers,
 
Does anyone know any free software that = can analyse=20 geometric properties of solids? such as length distribution, angle = distribution=20 etc?
 
Thank you very much in = advance!
 
Best regards,
Ru-Zhen
 
------=_NextPart_000_01A7_01C4024D.09A2D460-- From chemistry-request@ccl.net Wed Mar 3 15:07:03 2004 Received: from postoffice7.mail.cornell.edu (postoffice7.mail.cornell.edu [132.236.56.22]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i23K72d4021598 for ; Wed, 3 Mar 2004 15:07:02 -0500 Received: from cornell.edu (67-41-169-107.slkc.qwest.net [67.41.169.107]) by postoffice7.mail.cornell.edu (8.12.10/8.12.6) with ESMTP id i23K8SRR021290; Wed, 3 Mar 2004 15:08:33 -0500 (EST) Message-ID: <40463B3C.8050303*at*cornell.edu> Date: Wed, 03 Mar 2004 13:08:28 -0700 From: Richard Wood User-Agent: Mozilla/5.0 (Windows; U; Windows NT 5.1; en-US; rv:1.4) Gecko/20030624 Netscape/7.1 (ax) X-Accept-Language: en-us, en MIME-Version: 1.0 To: "chemistry*at*ccl.net" Subject: Re: SDF files (summary) Content-Type: multipart/alternative; boundary="------------090002090306080709010507" X-PMX-Version: 4.5.0.90627, Antispam-Core: 4.0.4.92622, Antispam-Data: 2004.3.2.93283 This is a multi-part message in MIME format. --------------090002090306080709010507 Content-Type: text/plain; charset=us-ascii; format=flowed Content-Transfer-Encoding: 7bit Hi all A few days ago I posted a question about a problem I was having with SDF files. Here's my original post: ====================================================================================== Hi all I'm trying to glean the structures out of some SDF files that I have. I have 3 databases that have structures in them, and I'm trying to get the structures out of them. I've downloaded the SDF toolkit and the program CACTUS, but neither of those are helping me. I can get both programs to read the first structure, but I can't get any further than that. Any suggestions on how to do this, including any other programs that could be of help (free would be the best) would be most welcome. Thanks in advance, Richard ====================================================================================== Here are the responses I received: ====================================================================================== W. D. Ihlenfeldt Xemistry GmbH wdi*at*xemistry.com aber being disconnected from the Internet for a week I just learned about your problems in splitting an SD-file. The CACTVS toolkit is the right tool for this. Maybe you could send me a few record from your original file, any scripts which you may already have written, and I will see if I see any problem with your original file and/or application script. Regards ====================================================================================== Rajeshri G. Karki Ph.D. (several response) rajeshri*at*helix.nih.gov 1) Did you try reading the structures using csbr (the cactus browser GUI) or csed (cactus editor GUI)? Do you see any error message? Rajeshri and 2) I could not rest at peace so tried again. I contacted the folks at DTP and they have made changes in the sd file. So please download again and now you will be able to see the structures using csbr. With best wishes Rajeshri ====================================================================================== Dr. Tamas E. Gunda tgunda*at*puma.unideb.hu Hi, You may try Mol2Mol. It can slice SDF files. http://web.interware.hu/frenzy/mol2mol/index.html Regards ====================================================================================== Jacco van de Streek streek*at*ccdc.cam.ac.uk If all you want to do is look at them, possible do some measurements and save some of them in other file formats, you can try Mercury. Mercury is available for a number of platforms and is free: http://www.ccdc.cam.ac.uk/mercury/ ====================================================================================== Kevin P. Cross, Ph.D. kcross*at*leadscope.com You need to look at your SD file to determine whether it is ill-formed or correct. Several programs that export SD files, like ChemFinder, fail to separate individual mol entries (1 per structure) with the SD file. Commonly, they are either missing the "$$$$" delimiter between the structures or are missing an "M END" statement. I suggest you download the SDF format from the MDL web site and then examine the first mol entry of you file to see what the problem is. As the SDF toolkit includes source code, you should be able to tell what data field it is looking for to delimit individual structures. However, we have found several bugs in the SDF toolkit and use our own code for reading and verifying structures in SD files. ====================================================================================== Konrad Koehler konrad.koehler*at*karobio.se I am not sure exactly what you are trying to do, but you might try Open Babel (http://openbabel.sourceforge.net/) which can convert SD files into a number of other file formats (Sybyl mol2, pdb, SMILES, etc.). If the SDF Toolkit can't read past the first structure in your SD file, then there may be something wrong with your SD file. Are your structures seperated by "$$$$" records in your SD file? Finally, if you would indicate what program you are using to view/analyze the structures, I might be able to provide you with more specific advice. I hope this helps. Best regards, Konrad ====================================================================================== Doug Henry had two suggestions: D.Henry*at*mdl.com 1) When I have noticed trouble reading SDfiles with 3rd party programs, I look for: - There should be one blank line between the last line of the molfile, and the $$$$: ... M END $$$$ (next molfile) ... - If there are data fields in the SDfile, they should follow the M END immediately, and they should each be separated by one blank line: ... M END MFCD1234 123.45 $$$$ - Check that the $$$$ is not '$$$$ ' or something else (extra blank) Hope this helps... DH 2) If you have the sed utility (it's standard on unix; on Windows, it comes as part of unix emulation systems like Cygwin - see below...), you could try this: For Windows, create a file (called say, insert_blank) using the following commands: echo /\$\$\$\$/i\ > insert_blank echo. >> insert_blank On unix, you would type: echo /\$\$\$\$/i\ > insert_blank echo "" >> insert_blank This creates a file that has two lines: /\$\$\$\$/i\ (a blank line) Then run sed using the file insert_blank to change the old_sdfile to the new one: sed -f insert_blank old_sdfile.sdf > new_sdfile.sdf If you need sed for windows, you can download the Setup zip file http://gnuwin32.sourceforge.net/packages/sed.htm And it will install sed for you (just install the binaries if you want). It is a very useful utility. If you need to insert blanks before other things besides $$$$, you can modify the insert_blank file to have the string to look for, between the /.../ separators, and run the command as above. As an example, to insert a blank before the string "> <" the insert_blank file would look like: /> ... >... do somehting with the structure ... >... } In the body of the loop you can define various methods like Hashcode calculations, write the structures to other chemical exchange formats, modify them and so on. ======================================================================================== Carsten Detering detering*at*u.washington.edu Hi Richard, although not free, I can highly recommend MOE (Chemical Computing Group) for processing databases. It is very easy and straightforward to use, and the support is excellent. Hope this helps. Carsten ======================================================================================== Josef Scheiber Josef.Scheiber*at*mail.uni-wuerzburg.de Hi Richard, maybe the DS Viewer Pro (http://www.accelrys.com/dstudio/ds_viewer/) could be helpful for you. It is not for free, but they have a free 30-day trial version that could help you solving your problem. Another possibility is to separate the files in a text editor. In a sdf - File the different structures are separated by "$$$$". You can take every part out of there (each structure represents a mol-File, a sdf is a database of .mol-files) and save it as a mol-File that can be read by a lot of common freeware packages (e.g. VMD or VEGA). Bye, Sepp =================================================================================================== Ajit Jadhav Ajit.Jadhav*at*amphoracorp.com Cactus should work fine for the sdf browsing. Another program you can try (go through evaluation agreement) is Vida by OpenEye http://www.eyesopen.com/products/applications/vida.htm. It's an excellent 3d browser but can depict 2d as well. -Ajit ======================================================================================== Marc Niclaus mn1*at*helix.nih.gov Hmm, that's a bit surprising. Usually, these tools have no problems reading databases of >100,000 compounds. Are you sure your SD file is not somehow corrupted? Or that the second structure has illegal molfile syntax? If you can send me one of these databases (the smallest one, preferably), I could have a look at it. Marc =================================================================================================== Gyandera Kumar gyan*at*mbu.iisc.ernet.in You can try babel. you can seperate individual structures from a SDF database using this free program downloadable from the net. Gyan. =================================================================================================== Jolanta Lotasinska jolanala*at*amu.edu.pl As far as i remember SDF is MDL format. Babel read sdf structures. best, Jola =================================================================================================== Thanks to everyone who responded. I apologize if I missed anyone. The problem was the database I was using was formatted incorrectly. The people at the NCI fixed it, and now I can read the structures. Thanks to all. Richard -- Richard L. Wood, Ph. D. Computational Chemist SynVax, Inc. N. Logan, UT 84341 --------------090002090306080709010507 Content-Type: text/html; charset=us-ascii Content-Transfer-Encoding: 7bit 
Hi all

A few days ago I posted a question about a problem I was having with SDF files.  Here's my original post:

======================================================================================

Hi all

I'm trying to glean the structures out of some SDF files that I have. I 
have 3 databases that have structures in them, and I'm trying to get the 
structures out of them.  I've downloaded the SDF toolkit and the program 
CACTUS, but neither of those are helping me.  I can get both programs to 
read the first structure, but I can't get any further than that.

Any suggestions on how to do this, including any other programs that 
could be of help (free would be the best) would be most welcome.

Thanks in advance,
Richard

======================================================================================

Here are the responses I received:

======================================================================================
W. D. Ihlenfeldt
Xemistry GmbH
wdi*at*xemistry.com

aber being disconnected from the Internet for a week I just learned
about your problems in splitting an SD-file. The CACTVS toolkit is the
right tool for this. Maybe you could send me a few record from your
original file, any scripts which you may already have written, and I
will see if I see any problem with your original file and/or application
script.

Regards

======================================================================================

Rajeshri G. Karki Ph.D. (several response)
rajeshri*at*helix.nih.gov

1) Did you try reading the structures using csbr (the cactus browser GUI) or
csed (cactus editor GUI)?
Do you see any error message?

Rajeshri

and 

2) I could not rest at peace so tried again.
I contacted the folks at DTP and they have made changes in the sd file.
So please download again and now you will be able to see the structures
using csbr.

With best wishes
Rajeshri

======================================================================================

Dr. Tamas E. Gunda
tgunda*at*puma.unideb.hu

Hi,
You may try Mol2Mol. It can slice SDF files.
http://web.interware.hu/frenzy/mol2mol/index.html
Regards

======================================================================================

Jacco van de Streek
streek*at*ccdc.cam.ac.uk

If all you want to do is look at them, possible do some measurements and save
some of them in other file formats, you can try Mercury. Mercury is available
for a number of platforms and is free:

http://www.ccdc.cam.ac.uk/mercury/

======================================================================================

Kevin P. Cross, Ph.D.
kcross*at*leadscope.com

You need to look at your SD file to determine
whether it is ill-formed or correct. Several programs
that export SD files, like ChemFinder, fail to separate
individual mol entries (1 per structure) with the SD file.
Commonly, they are either missing the "$$$$" delimiter
between the structures or are missing an "M END" statement.
I suggest you download the SDF format from the MDL web site
and then examine the first mol entry of you file to see what
the problem is. As the SDF toolkit includes source code, you
should be able to tell what data field it is looking for
to delimit individual structures. However, we have found several
bugs in the SDF toolkit and use our own code for reading and
verifying structures in SD files.

======================================================================================

Konrad Koehler
konrad.koehler*at*karobio.se

I am not sure exactly what you are trying to do, but you might
	try Open Babel (http://openbabel.sourceforge.net/) which can convert SD
	files into a number of other file formats (Sybyl mol2, pdb, SMILES,
	etc.).  If the SDF Toolkit can't read past the first structure in your
	SD file, then there may be something wrong with your SD file.  Are your
	structures seperated by "$$$$" records in your SD file?  Finally, if you
	would indicate what program you are using to view/analyze the
	structures, I might be able to provide you with more specific advice.
	
		I hope this helps.  Best regards,
	
	Konrad

======================================================================================

Doug Henry had two suggestions:
D.Henry*at*mdl.com

1) When I have noticed trouble reading SDfiles with 3rd party programs, I look
for:
- There should be one blank line between the last line of the molfile, and
the $$$$:

...
M  END

$$$$
(next molfile)
...

- If there are data fields in the SDfile, they should follow the M  END
immediately, and they should each be separated by one blank line:

...
M  END
      
<EXTREG>    

MFCD1234

<MOLWEIGHT> 
123.45

$$$$

- Check that the $$$$ is not '$$$$ ' or something else (extra blank)

Hope this helps...
DH
2) If you have the sed utility (it's standard on unix; on Windows, it comes as part of unix emulation systems like Cygwin - see below...), you could try this:
 
For Windows, create a file (called say, insert_blank) using the following commands:
 
echo /\$\$\$\$/i\ > insert_blank
echo. >> insert_blank
 
On unix, you would type:
 
echo /\$\$\$\$/i\ > insert_blank
echo "" >> insert_blank
 
This creates a file that has two lines:
 
/\$\$\$\$/i\
(a blank line)
 
Then run sed using the file insert_blank to change the old_sdfile to the new one:
 
sed -f  insert_blank  old_sdfile.sdf  > new_sdfile.sdf
 
 
If you need sed for windows, you can download the Setup zip file
 
And it will install sed for you (just install the binaries if you want). 
It is a very useful utility.
 
If you need to insert blanks before other things besides $$$$, you can modify the insert_blank file to have the string to look for, between the /.../ separators, and run the command as above.
 
As an example, to insert a blank before the string ">  <" the insert_blank file would look like:
 
/>  </i\
(blank line)
 
The reason we have to add "\" in front of each $ is because $ is a special character to sed.
 
DH

===================================================================================================

 
Dr. Frank Oellien
Frank.Oellien*at*intervet.com

you start with a SD File, right?
What do you want to do with the structures?
Are you searching for specific structures?

If you are using CACTVS, do this:

1. Start csts
2. Write the following code

set infile [molfile open your_sdfile.sdf r]
molfile loop $infile ehandle {

>...
>... do somehting with the structure ...
>...

}

In the body of the loop you can define various methods like Hashcode
calculations, write the structures to other chemical exchange formats,
modify them and so on.
========================================================================================

Carsten Detering
detering*at*u.washington.edu

Hi Richard,

although not free, I can highly recommend MOE (Chemical Computing Group) for processing databases. It is very easy and straightforward to use, and the support is excellent.

Hope this helps.

Carsten

========================================================================================

Josef Scheiber
Josef.Scheiber*at*mail.uni-wuerzburg.de
Hi Richard,

maybe the DS Viewer Pro (http://www.accelrys.com/dstudio/ds_viewer/) could be 
helpful for you. It is not for free, but they have a free 30-day trial version 
that could help you solving your problem.
Another possibility is to separate the files in a text editor. In a sdf - File 
the different structures are separated by "$$$$". You can take every part out of 
there (each structure represents a mol-File, a sdf is a database of .mol-files) 
and save it as a mol-File that can be read by a lot of common freeware packages 
(e.g. VMD or VEGA). 

Bye, Sepp

===================================================================================================

Ajit Jadhav
Ajit.Jadhav*at*amphoracorp.com

Cactus should work fine for the sdf browsing. Another program you can
try (go through evaluation agreement) is Vida by OpenEye
http://www.eyesopen.com/products/applications/vida.htm. It's an
excellent 3d browser but can depict 2d as well.

-Ajit
========================================================================================

Marc Niclaus
mn1*at*helix.nih.gov
Hmm, that's a bit surprising.  Usually, these tools have no problems reading
databases of >100,000 compounds.  Are you sure your SD file is not somehow
corrupted?  Or that the second structure has illegal molfile syntax?

If you can send me one of these databases (the smallest one, preferably),
I could have a look at it.

Marc

===================================================================================================

Gyandera Kumar
gyan*at*mbu.iisc.ernet.in

You can try babel. you can seperate individual structures from a SDF 
database using this free program downloadable from the net.

Gyan.

===================================================================================================

Jolanta Lotasinska
jolanala*at*amu.edu.pl

As far as i remember SDF is MDL format.
Babel read sdf structures.
best,
Jola

===================================================================================================

Thanks to everyone who responded.  I apologize if I missed anyone.

The problem was the database I was using was formatted incorrectly.  The people at the NCI fixed it, and now I can read the structures.

Thanks to all.

Richard

-- 
Richard L. Wood, Ph. D.
Computational Chemist
SynVax, Inc.
N. Logan, UT 84341
--------------090002090306080709010507-- From chemistry-request@ccl.net Thu Mar 4 04:37:34 2004 Received: from mail-gw0.york.ac.uk (mail-gw0.york.ac.uk [144.32.128.245]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i249bXd4031746 for ; Thu, 4 Mar 2004 04:37:34 -0500 Received: from [144.32.52.130] (thallium.york.ac.uk [144.32.52.130]) by mail-gw0.york.ac.uk (8.12.10/8.12.10) with ESMTP id i249d2Qm022108 for ; Thu, 4 Mar 2004 09:39:02 GMT Subject: Dummy atoms in Dalton From: Grant Hill To: chemistry*at*ccl.net Content-Type: text/plain Message-Id: <1078393134.3767.8.camel@thallium> Mime-Version: 1.0 X-Mailer: Ximian Evolution 1.4.5 (1.4.5-7) Date: Thu, 04 Mar 2004 09:38:55 +0000 Content-Transfer-Encoding: 7bit X-York-MailScanner: Found to be clean Hi list, I was wondering if anyone has any experience of adding dummy atoms to an xyz molecule specification in Dalton, if it is even possible? If so, I'd appreciate some brief instructions on how to do it. I'll summarise any replies. Thanks in advance, Grant Hill From chemistry-request@ccl.net Wed Mar 3 07:24:23 2004 Received: from collapsed.wormhole.hu (collapsed.wormhole.hu [195.70.35.130]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i23COMd4029057 for ; Wed, 3 Mar 2004 07:24:22 -0500 Received: from szilva (helo=localhost) by collapsed.wormhole.hu with local-esmtp (Exim 3.36 #1 (Debian)) id 1AyVRf-0000es-00 for ; Wed, 03 Mar 2004 13:25:51 +0100 Date: Wed, 3 Mar 2004 13:25:51 +0100 (CET) From: szilva-.at.-computer.org X-X-Sender: szilva-.at.-collapsed.wormhole.hu To: CCL Subject: Re: CCL:Docking software vithout validation In-Reply-To: Message-ID: References: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Sender: Szilveszter JUHOS Dear All, I know very well that validating a docking software is rather time consuming and needs some experience. Note I spent some time (years) in a group with validating and developing a docking software that is used in-house at a durg-discovery company. Docking softwares originally were developed to restore Xtal ligand structures quickly and virtual screening were not always in mind at the birth of these tools. Luckily, they can be used for hit-id as well, that is a very handy "by-product". Though validation is expensive but necessary: as it is unacceptable from a car-manufacturer to leave its products validation for the customers, it is true for all other products - for software as well. Choice is a result of comparison: with validation data I can choose between A_dock and B_dock. I do not want to impose a compulsory validation set on any developer but sticking to a cleared set that is used by other programs also makes the choice easier for the customer. The source of these programs likely will not be freely available for quite a while and it is understandable. Docking is still a new technology and the competition is already strong. As for me the main validation points would be (and it is about the scheduling the validation also): i) reproducing RMSD on a large target set ii) checking selectivity (ie with cross-docking matrix) iii) proving docking can select active compounds from a random library iv) providing tools for post-processing (discarding false positives, opportunistic binders) One can argue the last step is not the docking software's task but I want to emphasize my point of view is that such a "docking platform" has a role to select putative leads from a large virtual library. As for this step iv) is required because the crude run-results are heavily polluted with false positives. Usually people are expecting docking to reproduce not only the exact X-ray conformation of the ligand but the free energy (dG) values as well. My opinion is that this is not the task of docking: the dG values in the literature are quite unreliable and there are other problems with the scoring functions also. Cheers: Szilva PS: sorry not to include all the mails I responded to, but this lengthy email would be even longer. From chemistry-request@ccl.net Thu Mar 4 03:01:20 2004 Received: from gveu50.emea.givaudan.com (mail-external3.givaudan.com [57.66.141.4]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i2481Id4023871; Thu, 4 Mar 2004 03:01:19 -0500 To: chemistry-.at.-ccl.net, "Computational Chemistry List" Subject: software evaluation / validation MIME-Version: 1.0 X-Mailer: Lotus Notes Release 5.0.11 July 24, 2002 Message-ID: From: Andras.Borosy-.at.-givaudan.com Date: Thu, 4 Mar 2004 09:02:41 +0100 X-MIMETrack: Serialize by Router on gvedoh01/H/Givaudan(Release 5.07a |May 14, 2001) at 04/03/2004 09:03:06, Serialize complete at 04/03/2004 09:03:06 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id i2481Kd4023878 Dear Colleagues, On February 27, 2004 07:40 am, Csaba wrote: ... > In my view, using commercial modelling (e.g. docking, MD, > etc.) softwares is quite questionable from a scientific point of view. > The main criterion of scientific work is reproducibility. My question: how > is it possible to reproduce scientific results obtained by commercial > softwares which are not available for the whole scientific community??? > (That is, if you do not have several thousands of dollars just for yearly > licences you cannot check the reliability of data published with > commercial softwares by others. Not to speak about the > availability of source codes...) > There are good initiatives, like the AutoDock, GROMACS, etc. projects > (free programs for academic users) which should be considered by > software developers in the future. I think that ALL of the software providers (commercial, non-profit, academic etc.) would freely give a copy for a limited time period (e.g. 1-2 months) for evaluation / validation purposes. This time period should be enough to run the software through the validation set of your choice. Source code is not necessary for testing or validation. It is only necessary if you want to modify, enhance, integrate, build onto an existing code base. I agree with the first part, which is indeed a _VERY_ important point: "The main criterion of scientific work is reproducibility." However, my question about this would be: How is it possible to reproduce scientific results obtained by commercial _OR_ academic software which relies on _RANDOM_ methods ? (e.g. GOLD, AutoDock, ICM-dock etc. employ random methods). Best regards, Andras Borosy PhD Computational Chemist Givaudan Schweiz AG Fragrance Research Ueberlandstr. 138 8600 D|bendorf Switzerland tel: + 41-1-8242164 fax: +41-1-8242926 e-mail: andras.borosy-.at.-givaudan.com From chemistry-request@ccl.net Fri Mar 5 12:39:48 2004 Received: from cuces.unisi.it (cuces.unisi.it [193.205.4.2]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i25Hdjd4025432 for ; Fri, 5 Mar 2004 12:39:48 -0500 Received: from CONVERSION-DAEMON.cuces.unisi.it by cuces.unisi.it (PMDF V6.2-X17 #30546) id <01L7DMH4FC5C00802V.-at-.cuces.unisi.it> for chemistry.-at-.ccl.net; Fri, 05 Mar 2004 18:41:26 +0100 (MET) Received: from student.unisi.it (morgana.smin.unisi.it [172.16.53.95]) by cuces.unisi.it (PMDF V6.2-X17 #30546) with ESMTPA id <01L7DMH3ALY20086FC.-at-.cuces.unisi.it> for chemistry.-at-.ccl.net; Fri, 05 Mar 2004 18:41:25 +0100 (MET) Date: Fri, 05 Mar 2004 18:46:48 +0100 From: Lucilla angeli Subject: MOPAC To: chemistry.-at-.ccl.net Message-id: <4048BD08.9060307.-at-.student.unisi.it> MIME-version: 1.0 Content-type: text/plain; charset=us-ascii; format=flowed Content-transfer-encoding: 7bit X-Accept-Language: en-us, en User-Agent: Mozilla/5.0 (X11; U; IRIX64 IP30; en-US; rv:1.4) Gecko/20030711 Dear CCL I am trying to use MOPAC to optimize a structure with heme. Unfortunately I have not the Iron parameters that are necessary to the calculation. In particular these parameters are necessary: USS, UPP, UDD, ZS, ZP, ZD, BETAS, BETAP, BETAD, GSS, GSP, GPP, GP2, HSP, ALP. May anyone help me to find them? Thanks in advance ********************************* Lucilla Angeli c/o Prof. Botta Dip. Farmaco Chimico Tecnologico Universita' degli Studi Di Siena Via Aldo Moro I-53100 Siena, Italy Phone: ++39 0577 234307 Fax: ++39 0577 234333 ********************************** From chemistry-request@ccl.net Thu Mar 4 15:08:18 2004 Received: from copland.udel.edu (copland.udel.edu [128.175.13.92]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i24K8Hd4032621 for ; Thu, 4 Mar 2004 15:08:18 -0500 Received: from [128.175.138.90] ([128.175.138.90]) by copland.udel.edu (8.12.10/8.12.10) with ESMTP id i24K9s8L005273 for ; Thu, 4 Mar 2004 15:09:55 -0500 (EST) Message-Id: <200403042009.i24K9s8L005273.-at-.copland.udel.edu> X-Mailer: Microsoft Outlook Express Macintosh Edition - 4.5 (0410) Date: Thu, 04 Mar 2004 15:00:03 -0500 Subject: relative stabilities in water: zwitterion vs anion From: "Olga Dmitrenko" To: chemistry.-at-.ccl.net Mime-version: 1.0 X-Priority: 3 Content-type: multipart/alternative; boundary="MS_Mac_OE_3161257203_838915_MIME_Part" X-Spam-Score: 1.7 HTML_FONT_FACE_ODD,MIME_LONG_LINE_QP,SPAM_PHRASE_03_05 X-Scanned-By: MIMEDefang 2.37 > THIS MESSAGE IS IN MIME FORMAT. Since your mail reader does not understand this format, some or all of this message may not be legible. --MS_Mac_OE_3161257203_838915_MIME_Part Content-type: text/plain; charset="ISO-8859-1" Content-transfer-encoding: quoted-printable Dear CCLers, The molecule I am studying is bifunctional and can exist in aqueous solutions as zwitterion or anion depending on pH. I am trying to compare the energies of zwitterionic and anionic forms by optimizations of the following H-bonded systems put into water media (using COSMO model): 1) zwitterion/OH- and anion/H2O - this system has net charge =B3-1=B2 2) zwitterion/H2O and anion/H3O+ - this system is neutral, which is better > from the computational point of view. I=B9ve got VERY different results. In case #1, the anionic form of my molecul= e was more stable. In the second case, the zwitterion was the preferred form. I feel that this is a wrong approach, but I can not compare directly the energies of zwitterion and anion because of different number of atoms. I would greatly appreciate if someone will point out the publications which rise similar questions. Best regards, Olga --MS_Mac_OE_3161257203_838915_MIME_Part Content-type: text/html; charset="ISO-8859-1" Content-transfer-encoding: quoted-printable relative stabilities in water: zwitterion vs anion Dear CCLers,

The molecule I am studying is bifunctional and can exist in aqueous solutio= ns as zwitterion or anion depending on pH.
 I am trying to compare the energies of zwitterionic
and anionic forms by optimizations of the following H-bonded systems put in= to water media (using COSMO model):

1) zwitterion/OH-  and anion/H2O    - this system has n= et charge =B3-1=B2
2) zwitterion/H2O and anion/H3O+  - this system is neutral, which is b= etter from the computational point of view.

I=B9ve got VERY different results. In case #1, the anionic form of my molecul= e was more stable. In the second case, the zwitterion was the preferred form= .
I feel that this is a wrong approach, but I can not compare directly the en= ergies of zwitterion and anion because of different number of atoms.

I would greatly appreciate if someone will point out the publications which= rise similar questions.

Best regards,
Olga
 --MS_Mac_OE_3161257203_838915_MIME_Part-- From chemistry-request@ccl.net Wed Mar 3 05:44:06 2004 Received: from ulys.POSTE.UMontreal.CA (ulys.POSTE.UMontreal.CA [132.204.2.41]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i23Ai6d4024310 for ; Wed, 3 Mar 2004 05:44:06 -0500 Received: from umontreal.ca (d71-23.D-FAC.UMontreal.CA [132.204.71.23]) by ulys.POSTE.UMontreal.CA (8.12.10/8.12.10) with ESMTP id i23AjdXg6889173 for ; Wed, 3 Mar 2004 05:45:39 -0500 (EST) Message-ID: <4045B752.15D5170D.-at-.umontreal.ca> Date: Wed, 03 Mar 2004 05:45:39 -0500 From: Tucker Carrington X-Mailer: Mozilla 4.77 [en] (Windows NT 5.0; U) X-Accept-Language: en,fr,fr-CA,fr-FR,de,de-DE MIME-Version: 1.0 CC: Computational Chemistry List Subject: canadian theory meeting References: <20040302125533.GA6936.-at-.chemie.uni-marburg.de> Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Dear Colleague: The 15th Canadian Symposium on Theoretical Chemistry (CSTC 2004) will be held this July 10-14 at the Hotel Le Chantecler resort and convention centre in Ste-Adele, Quebec. You are invited to join us for several days of science, conversation, fine dining, and summer recreation in the Laurentian mountains, 45 minutes north of Montreal. Held every three years, the CSTC brings together theoretical chemists from across Canada and around the world. CSTC 2004 will feature invited and contributed presentations with a focus on new quantum mechanical approaches in electronic structure and chemical dynamics. Invited speakers: Paul Ayers (McMaster) Evert Jan Baerends (Amsterdam) Joel Bowman (Emory) Paul Brumer (Toronto) Mark Casida (Grenoble) Matthias Ernzerhof (Montreal) Stephen Gray (Argonne) Martin Head-Gordon (Berkeley) Martin Kaupp (Wurzburg) Claude Leforestier (Montpellier) Daniel Lidar (Toronto) David Luckhaus (Goettingen) Vladimir Mandelshtam (UC Irvine) William Miller (Berkeley) John Perdew (Tulane) William Poirier (Texas Tech) Martin Quack (ETH Zurich) Krishnan Raghavachari (Indiana) Pierre-Nicholas Roy (Alberta) Bernhard Schlegel (Wayne State) Georg Schreckenbach (Manitoba) Gustavo Scuseria (Rice) Viktor Szalay (Budapest) David Tannor (Weizmann) Donald Truhlar (Minnesota) Mark Tuckerman (NYU) John Tully (Yale) Alexander Wang (UBC) Joshua Wilkie (Simon Fraser) Weitao Yang (Duke) Invited chairs: Russell Boyd (Dalhousie) Alexander Brown (Alberta) Natalie Cann (Queen's) Randall Dumont (McMaster) Peter Kusalik (Dalhousie) Tung Nguyen-Dang (Laval) Marcel Nooijen (Waterloo) Gren Patey (UBC) Raymond Poirier (Memorial) Dennis Salahub (Calgary) Mark Thachuk (UBC) Ajit Thakkar (New Brunswick) David Wardlaw (Queen's) Please visit our website at www.chem.queensu.ca/cstc2004 for further information. We are now accepting online registrations. Please register early (before March 31) to take advantage of our lower early registration fee. Hoping to see you in Ste-Adele! Axel D. Becke Department of Chemistry Queen's University Kingston, Ontario K7L 3N6 CANADA --------------------- e-mail: becke.-at-.chem.queensu.ca tel: (613) 533-2634 fax: (613) 533-6669 Tucker Carrington Jr. Departement de chimie Universite de Montreal Case postale 6128 succursale Centre-ville Montreal (Quebec) H3C 3J7 CANADA ------------------------- e-mail: Tucker.Carrington.-at-.umontreal.ca tel: (514) 343-2123 fax: (514) 343-7586 From chemistry-request@ccl.net Thu Mar 4 11:16:29 2004 Received: from FRESNO.NET.UNIOVI.ES (fresno.net.uniovi.es [156.35.11.2]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i24GGSd4022552 for ; Thu, 4 Mar 2004 11:16:28 -0500 Received: from CONVERSION-DAEMON.fresno.net.uniovi.es by fresno.net.uniovi.es (PMDF V6.2-X17 #30549) id <01L7C59G470G003JH5.-at-.fresno.net.uniovi.es> for chemistry.-at-.ccl.net; Thu, 04 Mar 2004 17:18:04 +0100 (MET) Received: from webuniovi.innova.uniovi.es (webuniovi.innova.uniovi.es [156.35.33.99]) by fresno.net.uniovi.es (PMDF V6.2-X17 #30549) with ESMTP id <01L7C59FTR7W003D7V.-at-.fresno.net.uniovi.es> for chemistry.-at-.ccl.net; Thu, 04 Mar 2004 17:18:04 +0100 (MET) Received: from localhost ([127.0.0.1] helo=cachewww2.si.uniovi.es) by webuniovi.innova.uniovi.es with esmtp (Exim 3.35 #1 (Debian)) id 1AyvXI-0006PF-00 for ; Thu, 04 Mar 2004 17:17:24 +0100 Date: Thu, 04 Mar 2004 17:12:41 +0100 From: =?UNKNOWN?Q?Rub=E9n?= Meana =?UNKNOWN?Q?Pa=F1eda?= Subject: Radius solvent of tert-butanol X-Sender: rubenmp.-at-.correo.uniovi.es To: chemistry.-at-.ccl.net Reply-to: rubenmp.-at-.correo.uniovi.es Message-id: MIME-version: 1.0 X-Mailer: Mailreader.com v2.3.29 (2001-07-20) Content-type: text/plain; charset=iso8859-1 Content-transfer-encoding: 8BIT X-Originating-Host: cachewww2.si.uniovi.es [156.35.14.7]; Thu, 4 Mar 2004 16:17:24 GMT X-Browser: Mozilla/4.0 (compatible; MSIE 6.0; Windows NT 5.1), JavaScript: On Hello CCLers, I4m trying to carry out single point PCM calculations in tert- butanol with ECP4s. Where can I obtain the solvent-radius of tert- butanol? and how is the input file (gaussian) of this type of calculations? Thanks in advanced Rubin From chemistry-request@ccl.net Thu Mar 4 16:33:23 2004 Received: from shark.us.lionbioscience.com (french.us.lionbioscience.com [66.228.90.51]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i24LXMd4003516 for ; Thu, 4 Mar 2004 16:33:22 -0500 Received: from localhost (localhost [127.0.0.1]) by shark.us.lionbioscience.com (8.12.10/8.11.6) with ESMTP id i24LYwHh003570; Thu, 4 Mar 2004 16:34:59 -0500 Received: from shark.us.lionbioscience.com ([127.0.0.1]) by localhost (shark [127.0.0.1]) (amavisd-new, port 10024) with ESMTP id 03495-03; Thu, 4 Mar 2004 16:34:57 -0500 (EST) Received: from MFORTIN (dhcp-20 [10.19.2.20]) by shark.us.lionbioscience.com (8.12.10/8.11.6) with ESMTP id i24LYsrC003566; Thu, 4 Mar 2004 16:34:56 -0500 Message-Id: <200403042134.i24LYsrC003566.-at-.shark.us.lionbioscience.com> From: Martina Fortin To: chemistry.-at-.ccl.net Subject: ChemCart - a universal interface to chemical cartridges Date: Thu, 4 Mar 2004 16:34:59 -0500 X-Sent-Folder-Path: Sent Items X-Mailer: Oracle Connector for Outlook 9.0.4 50822 (9.0.6627) MIME-Version: 1.0 Content-Type: text/plain; charset=iso-8859-1 X-Virus-Scanned: by amavisd-new at us.lionbioscience.com Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id i24LXNd4003517 LION bioscience is pleased to announce the distribution of these products from DeltaSoft Inc.: ChemCart - A universal interface to chemical cartridges DeltaBook - An electronic laboratory notebook CRISTAL - A chemical reagent tracking system ChemCart is a universal chemical search application for databases built upon Oracle chemistry data cartridges. Its web-based forms interface satisfies the needs of both, research scientists and IT staff. From this user-friendly application, a scientist can search, view, sort, and report on structures, data, and images. Other powerful features include flexible form building and extensive 'hit list management'. Optional links to Spotfire DecisionSite and IBM DiscoveryLink/InsightLink further expands ChemCart's functionality. For developers and IT staff, a universal front end means a choice in data cartridge technology and chemical sketchers/renders; the fact that the application is web-based eases deployment. DeltaBook is an electronic laboratory notebook that provides tools to electronically record, organize and report all of the data related to performing synthetic reactions. It is optimized to handle chemical structures and reactions as well as the specific types of data generated during the R&D process. Its features include structure searching, the capability to link other files to the notebook page, automatic calculations based on limiting reagent, and areas to save information about reaction, reagents and products. In addition, DeltaBook gives users the option to duplicate notebook pages for similar reactions, links to ACD reagents and safety information, and a variety of output forms. CRISTAL (Chemical Reagent Inventory System for Tracking And Locating) is a "cradle to grave" reagent tracking application - from purchasing and receiving to movement through laboratories and disposal. With CRISTAL, users can search for in-house and supplier reagents using a single structure query, order chemicals from a stockroom or from suppliers, utilize barcodes to retrieve bottle information, access Material Safety Data Sheets over the Internet, and track inventory history. For more information on DeltaSoft products, please visit our website www.lionbioscience.com or contact us at deltasoft.-at-.lionbioscience.com ChemCart, DeltaBook and CRISTAL are trademarks of DeltaSoft, Inc. Other copyrights and trademarks belong to the respective owners. Martina Fortin, Ph.D. Director US Marketing LION bioscience Inc. Voice: +1 617 245 5411 http://www.lionbioscience.com email: martina.fortin.-at-.lionbioscience.com From chemistry-request@ccl.net Fri Mar 5 22:28:06 2004 Received: from smtpout.mac.com (smtpout.mac.com [17.250.248.97]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i263S5d4013550 for ; Fri, 5 Mar 2004 22:28:05 -0500 Received: from webmail27-en1.mac.com (webmail27-en1 [10.13.10.127]) by smtpout.mac.com (Xserve/MantshX 2.0) with ESMTP id i263TgNH014705; Fri, 5 Mar 2004 19:29:42 -0800 (PST) Received: from webmail27 (localhost.mac.com [127.0.0.1]) by webmail27-en1.mac.com (8.12.6/8.12.6) with ESMTP id i263TcsK014822; Fri, 5 Mar 2004 19:29:42 -0800 (PST) Message-ID: <16062988.1078543778225.JavaMail.gaussian)at(mac.com> Date: Fri, 05 Mar 2004 22:29:38 -0500 From: Gaussian Email To: chemistry)at(ccl.net Subject: RE:CCL:New website alert Cc: frisch)at(gaussian.com Mime-Version: 1.0 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Anna Krylov writes: > > Dear Colleagues, > > Since many of you are employing electronic structure calculations in your > research, you may find the following new website that highlights certain > issues re: ab initio software to be of some interest to you: > > > http://www.bannedbygaussian.org > > Our rebuttal to this self-serving collection of misrepresentations, half-truths, and outright lies can be found at: http://www.gaussian.com/libel.htm Michael Frisch Gaussian, Inc. 340 Quinnipiac St., Bldg. 40 Wallingford, CT 06492 USA 203-284-2501 * Fax 203-284-2521 frisch)at(gaussian.com From chemistry-request@ccl.net Fri Mar 5 18:45:05 2004 Received: from TheWorld.com (pcls2.std.com [192.74.137.142]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i25Nj4d4027319 for ; Fri, 5 Mar 2004 18:45:04 -0500 Received: from [206.15.128.10] (206-15-128-10.dialup.ziplink.net [206.15.128.10]) by TheWorld.com (8.12.8p1/8.12.8) with ESMTP id i25NkhbI008627 for ; Fri, 5 Mar 2004 18:46:44 -0500 Mime-Version: 1.0 (Apple Message framework v609) In-Reply-To: References: Content-Type: text/plain; charset=US-ASCII; format=flowed Message-Id: Content-Transfer-Encoding: 7bit From: Joe Leonard Subject: Re: CCL:New website alert Date: Fri, 5 Mar 2004 18:49:16 -0500 To: chemistry)at(ccl.net X-Mailer: Apple Mail (2.609) On Mar 4, 2004, at 9:49 PM, Anna Krylov wrote: > Dear Colleagues, > > Since many of you are employing electronic structure calculations in > your > research, you may find the following new website that highlights > certain > issues re: ab initio software to be of some interest to you: > > > http://www.bannedbygaussian.org > This is old news. A quick look at many of the names listed on this web site reveal competitors (forgive me if my memory is out of date): Bartlett (ACES?) Friesner (Schrodinger) Goddard (formerly Schrodinger?) Gordon (GAMESS) Head-Gordon (forget this one) Pople (mentioned above, Q-Chem?) Schaefer (forget name, doesn't belong?) Schmidt (GAMESS?) It's been a while since I worked in the QM area, and I apologize if I've associated people with programs incorrectly. QM, particularly ab initio, uses extremely precise codes - one can refer to a 6-31G* calculation rather than an XXX 6-31G* calculation. Classical methodology is, unfortunately, (far?) less precise. Since codes can't compete on results, they have to compete on features, price or performance. There are a number of codes which are available for little or no money, so price presents a problem. Features tend to be well published, and eventually end up in many programs. This leaves performance, perhaps the single most important information for hardware and software vendors - benchmark performance. I also speak from experience - it's FAR easier to (a) test one's implementation and/or (b) tune one's performance if you have access to competitor's code. Thus, Gaussian acts reasonably to preserve its competitive advantage, denying close examination by its competitors. However, since the sun DOES come up in the east, said competitors can gain access if they put a little effort in. And, given the wide range of codes, if you don't like Gaussian or any other free or commercial product, DON'T USE IT. The marketplace has a pretty amazing tendency to fix problems as they crop up... Sorry for the rant, Joe Leonard jle)at(theworld.com From chemistry-request@ccl.net Fri Mar 5 17:04:09 2004 Received: from mail1.engr.sc.edu (mail1.engr.sc.edu [129.252.21.14]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i25M49d4019736 for ; Fri, 5 Mar 2004 17:04:09 -0500 Received: from yayay ([129.252.22.24]) by mail1.engr.sc.edu with Microsoft SMTPSVC(5.0.2195.6713); Fri, 5 Mar 2004 17:05:51 -0500 Message-ID: <025a01c402fe$08779560$1816fc81@yayay> From: "Liuming Yan" To: References: Subject: How to read the 2 electron integrasl from Gaussian scratch file! Date: Fri, 5 Mar 2004 17:05:55 -0500 MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 7bit X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 6.00.2800.1106 X-MIMEOLE: Produced By Microsoft MimeOLE V6.00.2800.1106 X-OriginalArrivalTime: 05 Mar 2004 22:05:51.0614 (UTC) FILETIME=[05D6F9E0:01C402FE] Dear CCL I am trying to read the 2 electron integrals from Gaussian scratch file, unfortunately I failed to figure out the format of the two electron integral scratch file "*.int". Does any know how to read that file in a program? Thanks! ********************************************* Dr. Liuming Yan Electrical Engineering Department University of South Carolina Columbia, SC29208 Phone: 803-777-0392 e-mail: yanli)at(engr.sc.edu From chemistry-request@ccl.net Fri Mar 5 18:49:37 2004 Received: from TheWorld.com (pcls2.std.com [192.74.137.142]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i25Nnad4027660 for ; Fri, 5 Mar 2004 18:49:36 -0500 Received: from [206.15.128.10] (206-15-128-10.dialup.ziplink.net [206.15.128.10]) by TheWorld.com (8.12.8p1/8.12.8) with ESMTP id i25NpGbI017480 for ; Fri, 5 Mar 2004 18:51:17 -0500 Mime-Version: 1.0 (Apple Message framework v609) In-Reply-To: References: Content-Type: text/plain; charset=US-ASCII; format=flowed Message-Id: <57CA34D4-6F00-11D8-BB70-000A95C5DECA!at!theworld.com> Content-Transfer-Encoding: 7bit From: Joe Leonard Subject: Re: CCL:New website alert Date: Fri, 5 Mar 2004 18:53:47 -0500 To: chemistry!at!ccl.net X-Mailer: Apple Mail (2.609) On Mar 4, 2004, at 9:49 PM, Anna Krylov wrote: > Dear Colleagues, > > Since many of you are employing electronic structure calculations in > your > research, you may find the following new website that highlights > certain > issues re: ab initio software to be of some interest to you: > > > http://www.bannedbygaussian.org > Sorry for the double posting - Jan & co, feel free to combine these two emails if they're passed to the list... 1) I have no current involvement with Gaussian, Inc, nor have I in the last 2-3 years. 2) It's rather childish to put a "critical screed" website up and omit who is responsible and a means of replying. If you feel the need to criticize a business, do it openly. Joe