From chemistry-request@server.ccl.net Wed Jan 10 05:12:14 2001 Received: from xena.oai.co.uk ([195.172.92.249]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f0AACBp11235 for ; Wed, 10 Jan 2001 05:12:11 -0500 Received: by XENA with Internet Mail Service (5.5.2650.21) id ; Wed, 10 Jan 2001 10:09:58 -0000 Message-ID: <5FD8C12EECBBD4119DD10002B3027B9A023578@GABRIELLE> From: "Charlton, Michael" To: "'CHEMISTRY@ccl.net'" Subject: viewing SDfiles Date: Wed, 10 Jan 2001 10:09:57 -0000 MIME-Version: 1.0 X-Mailer: Internet Mail Service (5.5.2650.21) Content-Type: text/plain; charset="iso-8859-1" Hi, does anyone know of a free/cheap tool for looking at MDL SDfiles ? It would be good to be able to be able to rapidly examine the structures. A web-based system would be ideal. Alternatively, are there tools for turning a structure into a gif format ? (It would bve good if it would run on an SGI machine.) Thanks in advance, Michael Charlton. From chemistry-request@server.ccl.net Wed Jan 10 05:35:41 2001 Received: from ms1.uibk.ac.at (ms1.uibk.ac.at [138.232.1.201]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f0AAZep11283 for ; Wed, 10 Jan 2001 05:35:41 -0500 Received: from ea1-c724.uibk.ac.at (ea1-c724.uibk.ac.at [138.232.32.18] Hannes.Loeffler@uibk.ac.at) by ms1.uibk.ac.at (8.9.3/D3) with SMTP id LAA03669 for ; Wed, 10 Jan 2001 11:35:39 +0100 (MET) Sender: hal@ea1-c724.uibk.ac.at To: chemistry@ccl.net Subject: document format for ACS journals? From: Hannes Loeffler Date: 10 Jan 2001 11:38:29 +0100 Message-ID: Lines: 14 User-Agent: Gnus/5.0807 (Gnus v5.8.7) XEmacs/21.1 (Crater Lake) MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii Hello all, one of our co-workers just told me that he has to rewrite his publications with Word or Word Perfect because ACS journals now require so (JPC in this case). Is this true? Any opinions? Hannes. -- Hannes Loeffler, Tel. +43-512-507-5166 Institute for General, Inorganic and Theoretical Chemistry University of Innsbruck/Austria From chemistry-request@server.ccl.net Wed Jan 10 08:50:10 2001 Received: from GOOFY1.UNI-MUENSTER.DE (GOOFY1.UNI-MUENSTER.DE [128.176.220.205]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f0ADo9p12364 for ; Wed, 10 Jan 2001 08:50:09 -0500 Received: from GOOFY1 (localhost.uni-muenster.de [127.0.0.1]) by GOOFY1.UNI-MUENSTER.DE (Postfix) with SMTP id D9A04757CD for ; Wed, 10 Jan 2001 14:50:03 +0100 (CET) From: Stefan Grimme Organization: Universitaet Muenster, Organisch-Chemisches Institut To: chemistry@ccl.net Subject: Re: CCL:document format for ACS journals? Date: Wed, 10 Jan 2001 14:37:19 +0100 X-Mailer: KMail [version 1.0.28] Content-Type: text/plain References: In-Reply-To: MIME-Version: 1.0 Message-Id: <01011014495809.08114@GOOFY1> Content-Transfer-Encoding: 8bit Dear CCl users, In my opinion we all should ignore the publishers requests for articles in special formats, mostly commercial (MS). I don't like to be forced to use this software and if they don't accept formats I'm using (LaTeX), I will not consider these journals anymore. Stefan _________________________________________________________ Prof. Dr. Stefan Grimme Organisch-Chemisches Institut (Abt. Theoretische Chemie) Westfaelische Wilhelms-Universitaet, Corrensstrasse 40 D-48149 Muenster, Tel (+49)-251-83 36512/33241/36515(Fax) Email:grimmes@uni-muenster.de http://www.uni-muenster.de/Chemie/OC/research/grimme/ _________________________________________________________ From chemistry-request@server.ccl.net Wed Jan 10 04:00:04 2001 Received: from mail.univ-reims.fr (mail.univ-reims.fr [193.50.208.6]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f0A903p11034 for ; Wed, 10 Jan 2001 04:00:03 -0500 Received: from univ-reims.fr (IDENT:henon@[193.50.208.246]) by mail.univ-reims.fr (8.11.2/8.11.1) with ESMTP id f0A8vbT18112 for ; Wed, 10 Jan 2001 09:57:37 +0100 (MET) Sender: henon@mail.univ-reims.fr Message-ID: <3A5C2E20.24E1DAD7@univ-reims.fr> Date: Wed, 10 Jan 2001 09:40:48 +0000 From: Eric HENON X-Mailer: Mozilla 4.5 [en] (X11; I; Linux 2.0.35 i586) X-Accept-Language: en MIME-Version: 1.0 To: CHEMISTRY@ccl.net Subject: PC/Linux-Workstation:Summary Content-Type: text/html; charset=us-ascii Content-Transfer-Encoding: 7bit Dear CCLers,

I would like to thank all people who replied to my question !
 

Original Question:

> Hello,
>
> We have a plan to get a workstation with 4 processors to do
> some ab initio calculations (g98, Molcas). The "Linux/xeon" platform
> seems to be an interesting alternative but, unfortunately, we have not
> found recent benchmarks for current xeon.
>
> Thus, I would be grateful if anyone could share his/her
> experience concerning the performance of Linux/current Xeon-PIII   vs
> Power 3-II  (IBM RS6000).
>
> Thank you in advance.

First of all, it is not easy to find very recent benchmarks for
the last CPU processors, concerning computational chemistry.
It seems however that the Xeon performances are pretty close to
its parents (PII/PII) ones, and it has a bad price/performance ratio.
That is the reason why we gave up the idea of buying such a configuration.

It was next difficult to decide without any doubt
from the answers what was the best
alternative : "Linux/PIII" (or "Linux/Athlon") platform
or Unix work station (such IBM Power 3-II) platform.
The reason is probably that PC machines are
faster and faster and their performances are now
relatively close to some Unix workstations. It seems from
recent benchmarks that Athlon is now faster that its
corresponding Pentium processor.
However,  the performance of computational chemistry programs
are not only determined  by the CPU,  and other criteria must be
taken into account:

- I/O system
- memory size
- cache memory size !
- Libraries and compiler choice !
...

PC has the best price/performance ratio but building PC
requires carefull choice of hardware
(e.g. SCSI configuration, good motherboard and
memory, etc.) and software (e.g. good compiler and optimized BLAS for G9X
compilation).

One has to consider also that
PC has limit on RAM and number of CPUs.
Moreover it was recently suggest that
that if you test LINUX boxes, you need a reasonable size problem,
as small test jobs run very fast, while real size problems may easyly be a
factor of 10 slower than the real UNIX machine
 
 

I present the following numbers.
These are timings from using Gaussian with a set of four jobs, using
either PC_Athlon/Linux or IBM Power III-2 (many thanks to D. Rinaldi
for CPU times facilities on the IBM machine !).

(Fortran 7.1, C++, IBM 44p-270,375MHz, one processor used, %MEM=90MB)

(the first number corresponds to Athlon 800MHz/Linux Mandrake release 7.1
Kernel 2.2.15-4, running G94)
(the last number corresponds to RISC Power3-II running G98
using Fortran 7.1, C++, IBM 44p-270,375MHz, one processor, %MEM=90MB)

*********************************************
SP B3LYP   33mn 42s ------> 17mn      (4mn21 with scf=incore)

    81 basis functions      451 primitive gaussians
    17 alpha electrons       16 beta electrons
*********************************************

*********************************************
FREQ  UHF    13mn 28s ------>  5mn30

    52 basis functions      298 primitive gaussians
    12 alpha electrons       11 beta electrons
*********************************************

*********************************************
H2S molecule CCSD(T)   2mn 26s ------>     32s

    62 basis functions      145 primitive gaussians
     9 alpha electrons        9 beta electrons
*********************************************

*********************************************
H2S molecule  CCSD(T)  42mn ------> 8mn

   119 basis functions      226 primitive gaussians
     9 alpha electrons        9 beta electrons
*********************************************
 

Here is a summary.

hi,

we have obtained verny good results by unsing a linux cluster with the
amd athlon processor. the new thunderbird core almost reaches the power3
processor of our sp. take a look at
"http://topas.chemie.uni-dortmund.de/mg98b.html" for benchmark results.
 

hope this will help

michael braunschweig
department of chemistry
university of dortmund
germany
 


Hi Eric,

We have some experience running Molcas on RS6000 model 270 workstations.
One thing that you should to bear in mind is that the performance of
Molcas is determined not so much by the CPU as by the I/O system.  A
modest sized CASPT2, for example, chokes even a uniprocessor machine: the
I/O system simply cannot feed the CPU quickly enough.  And if it can't
keep one satisified, having four CPUs would be pointless...

So your choice depends partly on how much you intend to use Molcas.  The
IBM is otherwise a very impressive beast and we are very happy with ours.
Certainly we have had no problems running other QM codes on them.  One
possibility you might want to consider is to buy a multiprocessor RS6K for
Gaussian, etc., and keep a cheap and cheerful Pentium (with a decent disk,
etc.) exclusively for Molcas.

Hope this helps, and good luck!

Chris Page
Università di Siena
 


From Stanislaw OldZiej

Hi all,

As usual all is about $$$$$.

First of all the g98 is not very well scalable on the multiprocesor
machines in my opinion is better (and cheaper) to buy four machines
(1CPU) than one 4xCPUs.
I'm not using g98 however and I do not have acess to Power-3-II IBM
machine but, I have some benchmark for GAMESS on PC-like processors
(single point MP2 energy calculations), the results are below (time in seconds):

DURON 600MHz                    -       1227.9
K-7 ATHLON 600MHz               -       1093.0
PIII CELERON 433MHz             -       2029.2 (app 600Mhz 1462.1)
PIII 650MHz                     -       1195.0 (app 600MHz 1294.2)
PIII XEON 700Mhz/1MB Cache      -       1081.1 (app 600MHz 1261.1)

I do not have access to the T-Bird AMD but I'm sure that T-Bird AMD will
be the best.

The second point is that Xeon is very expensive. If you want to have
4-way motherboard the XEON 700Mhz/1MB Cache will cost you 1349 USD,
XEON 550MHz/512K 975 USD. If you will buy 1-way motherboards you can
get XEON 933/256k for 670 USD.
The 4-way motherboard for Xeon is SC450NX and it cost c.a. 1800USD, or
S2QR6 c.a 2500 USD. It is mean that 4-way motherboards + 4 XEONs 700MHz
is ~7000 USD and you should add memory disks and all another stuff.

For comparison the 1000Mhz T-Bird + motherboard ASUSTek, 1GB RAM, 18 GB HD
SCSII cost ~1600 USD.

Have fun,

Stan
 

P.S. All prices are from: www.pricewatch.com.

===============================================================================
Dr Stanislaw Oldziej
Faculty of Chemistry,
University of Gdansk,           "Plucie to nie to samo co wolnosc wypowiedzi"
Molecular Modelling Group
Sobieskiego 18, 80-952 Gdansk
POLAND
tel:(048-58)-345-0361
fax:(048-58)-341-0357
===============================================================================


Hi,

Xeon .... I dont know. It would be better Athlon, in my mind. It runs Linux also,
but has better performance and is cheaper. But consider other answers.

A.Ziemys


From Frederick. P. Arnold, Jr

Hello:

First, try http://www.dl.ac.uk/CFS/benchmarks/compchem.html for a thorough
and well-balanced overview.

The basic take-home lesson is that the PowerIII is a nice chip, but an
Athlon 800 should be even with it for Hessian runs, and faster otherwise,
at a fraction of the price.  Xeon numbers I've seen in the past track the
parent PII/PIII pretty closely; i.e. even with the larger cache, their
performance doesn't jump by much, and their price is high.  If you're
willing to pay Xeon prices, you should probably be looking at Alphas.  Note
that Alpha near the top of the list is a generation and a half ago.  Newer
ones at 2-3 times faster for the same clock-frequency.
 
 


Hi!
This doesn't answer your question, but have you considered using a beowulf
instead of a four-way smp machine?  It would be a far cheaper solution to
implement and works rather well for g98 (speaking from experience with both
dual-smp PIIs versus beowulfs).

Resepectfully,
Phillip Matz

matz@wsunix.wsu.edu


 

From Cédric Merlot:

Links to computational chemistry benchmarks:

http://www.emsl.pnl.gov:2080/docs/tms/abinitio-v4/cover.html
http://www.ccl.net/cgi-bin/ccl/message.cgi?1998+03+31+010
http://www.ccl.net/cgi-bin/ccl/message.cgi?1999+08+12+011
http://www.ccl.net/cgi-bin/ccl/message.cgi?1999+02+25+011
Cédric Merlot
ChemCAD - 120, rue du Général Gouraud - 67210 OBERNAI - France
Tel : 03 88 95 68 52 - Fax : 03 88 95 07 92

http://www.chemcad.fr
mailto:support@chemcad.fr

From Vincent KRIEF:

http://www.compaq.com/hpc/apps/app_chem.html
 
 
 

----------------------------------------------------------
Eric HENON - Maitre de Conférences
Groupe de Spectrometrie Moleculaire et Atmospherique (GSMA)
Equipe Associee au CNRS UMR 6089
UFR Sciences Exactes et Naturelles B.P. 1039
51687 REIMS Cedex 2
Tel  : 03 26 91 33 66
email: eric.henon@univ-reims.fr
----------------------------------------------------------
 
 
 
  From chemistry-request@server.ccl.net Wed Jan 10 04:53:07 2001 Received: from mx2.mr.netbig.com ([202.108.254.247]) by server.ccl.net (8.11.0/8.11.0) with SMTP id f0A9r6p11207 for ; Wed, 10 Jan 2001 04:53:07 -0500 Received: (qmail 11694 invoked by uid 99); 10 Jan 2001 09:57:37 -0000 Message-ID: <20010110095737.11693.qmail@mx2.mr.netbig.com> From: =?gb2312?B?Qm9va3dvcm0=?= To: chemistry@ccl.net Cc: amber@cgl.ucsf.edu Subject: =?gb2312?B?TUQgc2ltdWxhdGlvbiBvZiBwcm90ZWluLWluaGliaXRvcg==?= Date: Wed, 10 Jan 2001 17:57:37 +0800 MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=gb2312 Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from BASE64 to 8bit by server.ccl.net id f0A9r7p11208 Dear colleagues: I want to study the interactions of a protein-inhibitor complex by MD simulation. The protein is a serine protease and the inhibitor is: Methoxysuccinyl-Ala-Ala-Pro-NH-CH-B(OH)2 | CH3 I have following two questions: 1. There are not a atom type \"B\" and the buiding block of -NH-CH(CH3)B(OH)2 in the force field. Can anyone suggest a way to get the parameters of \"B\" and the building block. 2. There exists a covalent bond between protein and inhibitor (between \"o\" of Ser195 in the protein and \"B\" in the inhibitor). How to arrange this case? Thanks for your kind help in advance and all replies will be promptly summarized. Best wishes Zhiyong Zhang, Ph.D School of Life Science in USTC Hefei, Anhui, PRC ----------------------------------------------------- Free email by netbig.com: http://mail.netbig.com From chemistry-request@server.ccl.net Wed Jan 10 07:50:50 2001 Received: from matavnet.hu (mail.matavnet.hu [195.228.240.10]) by server.ccl.net (8.11.0/8.11.0) with SMTP id f0AConp12306 for ; Wed, 10 Jan 2001 07:50:50 -0500 Received: (qmail 29781 invoked from network); 10 Jan 2001 13:50:48 +0100 Received: from line-110-74.dial.matav.net (HELO chemaxon.com) (145.236.110.74) by mail.matavnet.hu with SMTP; 10 Jan 2001 13:50:48 +0100 Message-ID: <3A5C5BB0.F9E8936C@chemaxon.com> Date: Wed, 10 Jan 2001 13:55:12 +0100 From: Ferenc Csizmadia Organization: ChemAxon X-Mailer: Mozilla 4.51 [en] (WinNT; I) X-Accept-Language: en MIME-Version: 1.0 To: "Charlton, Michael" , CHEMISTRY@ccl.net Subject: Re: CCL:viewing SDfiles References: <5FD8C12EECBBD4119DD10002B3027B9A023578@GABRIELLE> Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Michael, ChemAxon's MarvinView application can display structure files (SDfiles, Molfiles, SMILES strings and files, etc..). It is free for academic users. If you go for a web based system consider - Marvin Applets for drawing and viewing structures (free for free web sites) - JChem, a chemical database tool that enables substructure/similarity searching. These systems are in Java, so they run under most operating systems, including SGI. Please follow this link if you would like to download some of the above software: http://www.chemaxon.com/products.html Regards, Ferenc -- Dr. Ferenc Csizmadia ChemAxon Ltd. http://www.chemaxon.com T:+3620 9570988 mailto:fcsiz@chemaxon.com "Charlton, Michael" wrote: > Hi, > does anyone know of a free/cheap tool for looking at MDL SDfiles ? It would > be good to be able to be able to rapidly examine the structures. > A web-based system would be ideal. > Alternatively, are there tools for turning a structure into a gif format ? > (It would bve good if it would run on an SGI machine.) > > Thanks in advance, > > Michael Charlton. > > -= This is automatically added to each message by mailing script =- > CHEMISTRY@ccl.net -- To Everybody | CHEMISTRY-REQUEST@ccl.net -- To Admins > MAILSERV@ccl.net -- HELP CHEMISTRY or HELP SEARCH > CHEMISTRY-SEARCH@ccl.net -- archive search | Gopher: gopher.ccl.net 70 > Ftp: ftp.ccl.net | WWW: http://www.ccl.net/chemistry/ | Jan: jkl@ccl.net From chemistry-request@server.ccl.net Wed Jan 10 09:08:28 2001 Received: from scsx01.sc.ehu.es (root@scsx01.sc.ehu.es [158.227.150.40]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f0AE8Rp12430 for ; Wed, 10 Jan 2001 09:08:28 -0500 Received: from sq.ehu.es (pobmelat@sqpx31.sq.ehu.es [158.227.108.131]) by scsx01.sc.ehu.es (8.9.3/8.9.1) with ESMTP id PAA12156 for ; Wed, 10 Jan 2001 15:08:25 +0100 (MET) Sender: pobmelat@sc.ehu.es Message-ID: <3A5C6DEA.157049A8@sq.ehu.es> Date: Wed, 10 Jan 2001 15:12:58 +0100 From: Txema Mercero Reply-To: pobmabej@sq.ehu.es To: chemistry@server.ccl.net Subject: [Fwd: II-VI materials] Txoni wrote: Hello! I'm interested on some information concerning II-VI materials, such as ZnO, ZnS and so on. I would like to know the values of cohesive energy of all combinatioins, along with the values of the atomic charges within the crystals. Thank you very much Txoni Matxain PhD Student From chemistry-request@server.ccl.net Wed Jan 10 10:05:39 2001 Received: from tc11.theochem.uni-stuttgart.de (teomgs@tc11.theochem.uni-stuttgart.de [129.69.55.131]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f0AF5cp12903 for ; Wed, 10 Jan 2001 10:05:38 -0500 Received: from localhost (teomgs@localhost) by tc11.theochem.uni-stuttgart.de (8.8.6 (PHNE_13947)/8.8.6) with ESMTP id QAA18561; Wed, 10 Jan 2001 16:05:35 +0100 (MET) X-Authentication-Warning: tc11.theochem.uni-stuttgart.de: teomgs owned process doing -bs Date: Wed, 10 Jan 2001 16:05:34 +0100 (MET) From: "Dr. Martin Schuetz" To: Stefan Grimme cc: chemistry@ccl.net Subject: Re: CCL:document format for ACS journals? In-Reply-To: <01011014495809.08114@GOOFY1> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII I agree totally. One might even consider to go one step further and to refuse any reviewing tasks for ACS journals... Martin ---------------------------------------------------------------------------- Dr. Martin G. Schuetz Phone: 0049 (0)711-685-4397 University of Stuttgart Fax: 0049 (0)711-685-4442 Institute for Theoretical Chemistry Pfaffenwaldring 55 Room Nr: 8.161 D-70569 Stuttgart Email: schuetz@theochem.uni-stuttgart.de WWW : http://www.theochem.uni-stuttgart.de/~schuetz/ ---------------------------------------------------------------------------- On Wed, 10 Jan 2001, Stefan Grimme wrote: > Dear CCl users, > In my opinion we all should ignore the publishers requests > for articles in special formats, mostly commercial (MS). I don't like to be > forced to use this software and if they don't accept formats I'm using (LaTeX), > I will not consider these journals anymore. > Stefan > _________________________________________________________ > Prof. Dr. Stefan Grimme > Organisch-Chemisches Institut (Abt. Theoretische Chemie) > Westfaelische Wilhelms-Universitaet, Corrensstrasse 40 > D-48149 Muenster, Tel (+49)-251-83 36512/33241/36515(Fax) > Email:grimmes@uni-muenster.de > http://www.uni-muenster.de/Chemie/OC/research/grimme/ > _________________________________________________________ > > -= This is automatically added to each message by mailing script =- > CHEMISTRY@ccl.net -- To Everybody | CHEMISTRY-REQUEST@ccl.net -- To Admins > MAILSERV@ccl.net -- HELP CHEMISTRY or HELP SEARCH > CHEMISTRY-SEARCH@ccl.net -- archive search | Gopher: gopher.ccl.net 70 > Ftp: ftp.ccl.net | WWW: http://www.ccl.net/chemistry/ | Jan: jkl@ccl.net > > > > > > From chemistry-request@server.ccl.net Wed Jan 10 10:01:58 2001 Received: from tucc-exchange.trinity.edu (Tucc15.Tucc.Trinity.Edu [131.194.151.15]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f0AF1wp12883 for ; Wed, 10 Jan 2001 10:01:58 -0500 Received: by Tucc15.Tucc.Trinity.Edu with Internet Mail Service (5.5.2653.19) id ; Wed, 10 Jan 2001 08:51:15 -0600 Message-ID: From: "Bachrach, Steven" To: "'Hannes Loeffler'" , chemistry@ccl.net Subject: RE: document format for ACS journals? Date: Wed, 10 Jan 2001 08:51:14 -0600 MIME-Version: 1.0 X-Mailer: Internet Mail Service (5.5.2653.19) Content-Type: text/plain; charset="iso-8859-1" Not often do I come to the defense of ACS pubs, I must chime in on this comment though in defense of ACS. I just received the referee reports for an article I submitted to JOC and the following is a direct quote: "Our Publication Division asks that your final copy be prepared with 12-point type and double-spaced through all parts of the manuscript. In addition, please supply the final version of your manuscript on computer disc. Complete the enclosed "Media Description Form" and return it to us along with the disc. MS Word and WordPerfect software have been used most frequently, but the Publications Division is willing to try any word processor on any disc from any computer as long as it is clearly identified." Now I don't think they intend to process a Wordstar file from a TRS-80 stored on an 8" floppy, but their willingness to deal with files other than the usual suspects is certainly reasonable and should be applauded. Steve -- Steven Bachrach ph: (210)999-7379 Department of Chemistry fax: (210)999-7569 Trinity University 715 Stadium Drive San Antonio, TX 78212 steven.bachrach@trinity.edu > -----Original Message----- > From: Hannes Loeffler [mailto:Hannes.Loeffler@uibk.ac.at] > Sent: Wednesday, January 10, 2001 4:38 AM > To: chemistry@ccl.net > Subject: CCL:document format for ACS journals? > > > Hello all, > > one of our co-workers just told me that he has to rewrite his > publications with > Word or Word Perfect because ACS journals now require so (JPC > in this case). > > Is this true? Any opinions? > > > Hannes. > > -- > Hannes Loeffler, Tel. +43-512-507-5166 > Institute for General, Inorganic and Theoretical Chemistry > University of Innsbruck/Austria > > > -= This is automatically added to each message by mailing script =- > CHEMISTRY@ccl.net -- To Everybody | > CHEMISTRY-REQUEST@ccl.net -- To Admins > MAILSERV@ccl.net -- HELP CHEMISTRY or HELP SEARCH > CHEMISTRY-SEARCH@ccl.net -- archive search | Gopher: > gopher.ccl.net 70 > Ftp: ftp.ccl.net | WWW: http://www.ccl.net/chemistry/ | > Jan: jkl@ccl.net > > > > > From chemistry-request@server.ccl.net Wed Jan 10 10:34:00 2001 Received: from xena.oai.co.uk ([195.172.92.249]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f0AFXvp12983 for ; Wed, 10 Jan 2001 10:33:58 -0500 Received: by XENA with Internet Mail Service (5.5.2650.21) id ; Wed, 10 Jan 2001 15:31:59 -0000 Message-ID: <5FD8C12EECBBD4119DD10002B3027B9A02357C@GABRIELLE> From: "Charlton, Michael" To: "'CHEMISTRY@ccl.net'" Subject: Re: viewing SDfiles Date: Wed, 10 Jan 2001 15:31:59 -0000 MIME-Version: 1.0 X-Mailer: Internet Mail Service (5.5.2650.21) Content-Type: text/plain; charset="iso-8859-1" Many thanks for all the replies (below) I received. I feel I ought to clarify what I want here. I can view structures in SDfiles already, using typical modelling packages (MOE, Cerius etc.), but I am after a program that will allow lots of chemists to browse them (hence the requirement for cheapness). The idea is to be able to flick up and down, one at a time, or perhaps several structures tiled on a page at a time. The pssmiles utility that comes with with ClogP does this kind of thing, except postscript output is not very convenient. A common proposed solution is MSI's weblab viewer. However, whenever I open an SDfile, I get all the structures overlaid on one another - 3000 structures looks like a pile of spaghetti!! I have yet to find a use for this - has anyone else ? ;-) The program I dream of could be stand-alone (for distribution around company PCs) or web-based (my intranet pages are on an SGI, so the clever bits would need to be on that). My preference would be for 2D Isis Draw/ ChemDraw style output rather than 3D, since most of the structures are only 2D. My (sadly lacking) web skills could probably patch in a "smiles-to-gif" utility to do what I want, if such a thing existed. Whilst I have been composing this, a message from Marc Nicklaus just came in, and this could be what I am after for the gif generation. Thanks again, Michael Charlton. Replies : Michael, On Wed, 10 Jan 2001, Charlton, Michael wrote: > does anyone know of a free/cheap tool for looking at MDL SDfiles ? It would > be good to be able to be able to rapidly examine the structures. > A web-based system would be ideal. > Alternatively, are there tools for turning a structure into a gif format ? > (It would bve good if it would run on an SGI machine.) If 2D GIF drawings are what you want, try our web-based tool http://cactus.nci.nih.gov/services/gifcreator/. Maybe that's what you're looking for. Please let us how it works out for you. Marc ------------------------------------------------------------------------ Marc C. Nicklaus National Institutes of Health E-mail: mn1@helix.nih.gov Bldg 376, Rm 207 Phone: (301) 846-5903 376 Boyles Street Fax: (301) 846-6033 FREDERICK, MD 21702 USA http://rex.nci.nih.gov/RESEARCH/basic/medchem/mcnbio.htm Laboratory of Medicinal Chemistry, National Cancer Institute, FCRDC ------------------------------------------------------------------------ > Hi, > does anyone know of a free/cheap tool for looking at MDL SDfiles ? It would > be good to be able to be able to rapidly examine the structures. > A web-based system would be ideal. > Alternatively, are there tools for turning a structure into a gif format ? > (It would bve good if it would run on an SGI machine.) > > Thanks in advance, > > Michael Charlton. Hi Michael, You can browse an SD file with Mol2mol 3.5. The current structure can be transformed into several other formats, or copied to the clipboard as bmp image. It has no bmp-to-gif module, but there are a great number of image converters out there to convert it into gif in a second. Mol2mol is not free, anyway, not very expensive. Look at http://www.compuchem.com/mol2mol.htm Tamas Dr Tamas E. Gunda Research Group for Antibiotics of the Hungarian Acad. Sci. University of Debrecen, POBox 36 H-4010 Debrecen, Hungary tel.: (+36-52) 512 900/2472 fax: (+36-52) 512 914 e-mail: tamasgunda@tigris.klte.hu home-page: www.klte.hu/~gundat/gunda.htm Check out JMol at http://www.openscience.org/jmol/ - Jack -=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=- Jack A. Smith || Union Carbide || Phone: (304) 747-5797 Catalyst Skill Center || FAX: (304) 747-4672 P.O. Box 8361 || S. Charleston, WV 25303 || smithja@ucarb.com -=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=- > ---------- > From: Charlton, Michael[SMTP:mcharlto@oai.co.uk] > Sent: Wednesday, January 10, 2001 5:09 AM > To: 'CHEMISTRY@ccl.net' > Subject: CCL:viewing SDfiles > > Hi, > does anyone know of a free/cheap tool for looking at MDL SDfiles ? It > would > be good to be able to be able to rapidly examine the structures. > A web-based system would be ideal. > Alternatively, are there tools for turning a structure into a gif format ? > (It would bve good if it would run on an SGI machine.) > > Thanks in advance, > > Michael Charlton. > > > -= This is automatically added to each message by mailing script =- > CHEMISTRY@ccl.net -- To Everybody | CHEMISTRY-REQUEST@ccl.net -- To > Admins > MAILSERV@ccl.net -- HELP CHEMISTRY or HELP SEARCH > CHEMISTRY-SEARCH@ccl.net -- archive search | Gopher: gopher.ccl.net > 70 > Ftp: ftp.ccl.net | WWW: http://www.ccl.net/chemistry/ | Jan: > jkl@ccl.net > > > > > Hi Michael, How about web lab view lite, MSI's freebie, which will read an sd file and render all the structures; not sure how easy it is to go through them one by one. Or parse an SD file server-side, strip out all the mol components, save them separately and construct a web page table that references each, and get Chime (MDL's plugin, also free) to view each one; you could go through an SD file in blocks of whatever fits on a page. "All" you have to do is write the script or scripts to parse etc and build the web pages. Regards, Graham Graham Mullier Chemistry Design Group & AI Discovery Informatics Project Syngenta, Jealott's Hill direct line: +44 (0) 1344 414163 mailto:Graham.Mullier@syngenta.com -----Original Message----- From: Charlton, Michael [mailto:mcharlto@oai.co.uk] Sent: 10 January 2001 10:10 To: 'CHEMISTRY@ccl.net' Subject: CCL:viewing SDfiles Hi, does anyone know of a free/cheap tool for looking at MDL SDfiles ? It would be good to be able to be able to rapidly examine the structures. A web-based system would be ideal. Alternatively, are there tools for turning a structure into a gif format ? (It would bve good if it would run on an SGI machine.) Thanks in advance, Michael Charlton. -= This is automatically added to each message by mailing script =- CHEMISTRY@ccl.net -- To Everybody | CHEMISTRY-REQUEST@ccl.net -- To Admins MAILSERV@ccl.net -- HELP CHEMISTRY or HELP SEARCH CHEMISTRY-SEARCH@ccl.net -- archive search | Gopher: gopher.ccl.net 70 Ftp: ftp.ccl.net | WWW: http://www.ccl.net/chemistry/ | Jan: jkl@ccl.net Michael, ChemAxon's MarvinView application can display structure files (SDfiles, Molfiles, SMILES strings and files, etc..). It is free for academic users. If you go for a web based system consider - Marvin Applets for drawing and viewing structures (free for free web sites) - JChem, a chemical database tool that enables substructure/similarity searching. These systems are in Java, so they run under most operating systems, including SGI. Please follow this link if you would like to download some of the above software: http://www.chemaxon.com/products.html Regards, Ferenc -- Dr. Ferenc Csizmadia ChemAxon Ltd. http://www.chemaxon.com T:+3620 9570988 mailto:fcsiz@chemaxon.com "Charlton, Michael" wrote: > Hi, > does anyone know of a free/cheap tool for looking at MDL SDfiles ? It would > be good to be able to be able to rapidly examine the structures. > A web-based system would be ideal. > Alternatively, are there tools for turning a structure into a gif format ? > (It would bve good if it would run on an SGI machine.) > > Thanks in advance, > > Michael Charlton. > > -= This is automatically added to each message by mailing script =- > CHEMISTRY@ccl.net -- To Everybody | CHEMISTRY-REQUEST@ccl.net -- To Admins > MAILSERV@ccl.net -- HELP CHEMISTRY or HELP SEARCH > CHEMISTRY-SEARCH@ccl.net -- archive search | Gopher: gopher.ccl.net 70 > Ftp: ftp.ccl.net | WWW: http://www.ccl.net/chemistry/ | Jan: jkl@ccl.net On 10 Jan 01, at 10:09, Charlton, Michael wrote in his immortal words: > Hi, > does anyone know of a free/cheap tool for looking at MDL SDfiles ? It would > be good to be able to be able to rapidly examine the structures. > A web-based system would be ideal. Not web based: ACD Chemsketch with 3D extension look at: www.acdlabs.com > Alternatively, are there tools for turning a structure into a gif format ? > (It would bve good if it would run on an SGI machine.) On SGI IRIX Systems there are some tools to capture the screen: snapshot or capture convert the resulting rgb files into gif with xv or imagemagick. Wolfgang > > Michael Charlton. > > > -= This is automatically added to each message by mailing script =- > CHEMISTRY@ccl.net -- To Everybody | CHEMISTRY-REQUEST@ccl.net -- To Admins > MAILSERV@ccl.net -- HELP CHEMISTRY or HELP SEARCH > CHEMISTRY-SEARCH@ccl.net -- archive search | Gopher: gopher.ccl.net 70 > Ftp: ftp.ccl.net | WWW: http://www.ccl.net/chemistry/ | Jan: jkl@ccl.net > > > > > *********************************************************************** Dr. Wolfgang Utz Department of Medicinal Chemistry Emil Fischer Center Friedrich-Alexander University Schuhstr. 19 D-91052 Erlangen Germany Tel. 09131/8524100 Fax 09131/8522585 E-mail:utz@pharmazie.uni-erlangen.de http://www.medchem.uni-erlangen.de/personel/utz.htm *********************************************************************** Dear Michael I believe that MSI's weblab viewer lite (ugly spelling) has MDL .sd files has one of its input formats. This will also save a GIF of JPG file for your website. Its free but for a PC not an SGI. Hope this helps. Mark Charlton, Michael wrote: > Hi, > does anyone know of a free/cheap tool for looking at MDL SDfiles ? It would > be good to be able to be able to rapidly examine the structures. > A web-based system would be ideal. > Alternatively, are there tools for turning a structure into a gif format ? > (It would bve good if it would run on an SGI machine.) > > Thanks in advance, > > Michael Charlton. > > -= This is automatically added to each message by mailing script =- > CHEMISTRY@ccl.net -- To Everybody | CHEMISTRY-REQUEST@ccl.net -- To Admins > MAILSERV@ccl.net -- HELP CHEMISTRY or HELP SEARCH > CHEMISTRY-SEARCH@ccl.net -- archive search | Gopher: gopher.ccl.net 70 > Ftp: ftp.ccl.net | WWW: http://www.ccl.net/chemistry/ | Jan: jkl@ccl.net -- Dr Mark J Forster Ph.D. Principal Scientist Informatics Laboratory National Institute for Biological Standards and Control Blanche Lane, South Mimms, Hertfordshire EN6 3QG, United Kingdom. Tel +44 (0)1707 654753 FAX +44 (0)1707 646730 E-mail mforster@nibsc.ac.uk JChemPaint (http://jchempaint.sourceforge.net/) can read SDF files and also export GIF pictures. There is also an applet version available for integration with web pages. The program is OpenSource. Bugs and requests can be posted on the website at SourceForge: http://sourceforge.net/projects/jchempaint Please report any problems with the software so we can correct it. (Though i do not expect problems, considering your demands...) greetings, Egon Willighagen Plus a 'phone call from Peter Bladon : http://www.interprobe.co.uk/inter/interprobe.html From chemistry-request@server.ccl.net Wed Jan 10 10:56:53 2001 Received: from sol.cc.u-szeged.hu (root@sol.cc.u-szeged.hu [160.114.8.24]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f0AFuqp13031 for ; Wed, 10 Jan 2001 10:56:52 -0500 Received: from fk01 by sol.cc.u-szeged.hu (8.9.3+Sun/SMI-SVR4) id QAA05692; Wed, 10 Jan 2001 16:56:51 +0100 (MET) From: "Zoltan A. Fekete" Organization: University of Szeged To: chemistry@ccl.net Date: Wed, 10 Jan 2001 16:56:05 +0100 MIME-Version: 1.0 Content-type: text/plain; charset=US-ASCII Content-transfer-encoding: 7BIT Subject: Re: CCL:document format for ACS journals? CC: Stefan Grimme Message-ID: <3A5C9425.25364.119FF7A@localhost> X-Confirm-Reading-To: "Zoltan A. Fekete" X-pmrqc: 1 Priority: normal References: In-reply-to: <01011014495809.08114@GOOFY1> X-mailer: Pegasus Mail for Win32 (v3.12c) On 10 Jan 2001, at 14:37, Stefan Grimme wrote: > In my opinion we all should ignore the publishers requests > for articles in special formats, mostly commercial (MS). I agree with the sentiment in general, however "MS format" can simply be the (essentially) open-source RTF - to which most other formats, including (La)TeX can be converted without too much hassle. Having one agreed-upon common format is preferable, IMHO, to everyone sticking to their own preferred format... Dr. Zoltan A. Fekete SZTE University of Szeged, Department of Physical Chemistry Szeged, Rerrich ter 1, POB 105, H-6701 Hungary, FAX 36-62-544652 From chemistry-request@server.ccl.net Wed Jan 10 09:51:50 2001 Received: from tigris.klte.hu (tigris.klte.hu [193.6.138.33]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f0AEpnp12843 for ; Wed, 10 Jan 2001 09:51:49 -0500 Received: from anti07 (193.6.133.59) by tigris.klte.hu (MX V5.1-A Vn6f) with SMTP; Wed, 10 Jan 2001 15:48:35 +0100 Message-ID: <001501c07b14$cfbce780$3b8506c1@chem.klte.hu> From: "Tamas E. Gunda" To: "Charlton, Michael" , References: <5FD8C12EECBBD4119DD10002B3027B9A023578@GABRIELLE> Subject: Re: CCL:viewing SDfiles Date: Wed, 10 Jan 2001 15:51:26 +0100 MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-2" X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 5.00.2615.200 X-MimeOLE: Produced By Microsoft MimeOLE V5.00.2615.200 Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id f0AEpop12844 > Hi, > does anyone know of a free/cheap tool for looking at MDL SDfiles ? It would > be good to be able to be able to rapidly examine the structures. > A web-based system would be ideal. > Alternatively, are there tools for turning a structure into a gif format ? > (It would bve good if it would run on an SGI machine.) > > Thanks in advance, > > Michael Charlton. Hi Michael, You can browse an SD file with Mol2mol 3.5. The current structure can be transformed into several other formats, or copied to the clipboard as bmp image. It has no bmp-to-gif module, but there are a great number of image converters out there to convert it into gif in a second. Mol2mol is not free, anyway, not very expensive. Look at http://www.compuchem.com/mol2mol.htm Tamas Dr Tamas E. Gunda Research Group for Antibiotics of the Hungarian Acad. Sci. University of Debrecen, POBox 36 H-4010 Debrecen, Hungary tel.: (+36-52) 512 900/2472 fax: (+36-52) 512 914 e-mail: tamasgunda@tigris.klte.hu home-page: www.klte.hu/~gundat/gunda.htm From chemistry-request@server.ccl.net Wed Jan 10 11:49:36 2001 Received: from unomail.unomaha.edu (unomail.unomaha.edu [137.48.1.6]) by server.ccl.net (8.11.0/8.11.0) with SMTP id f0AGnZp13440 for ; Wed, 10 Jan 2001 11:49:35 -0500 Received: by unomail.unomaha.edu(Lotus SMTP MTA v4.6.4 (830.2 3-23-1999)) id 862569D0.005BEAA0 ; Wed, 10 Jan 2001 10:43:58 -0600 X-Lotus-FromDomain: UNIVERSITY OF NEBRASKA From: Douglas_Stack/CAS/UNO/UNEBR@unomail.unomaha.edu To: "Phillip D. Matz" cc: chemistry@ccl.net, jolsenho@cosmos.dsc.unomaha.edu Message-ID: <862569D0.005BE894.00@unomail.unomaha.edu> Date: Wed, 10 Jan 2001 10:43:51 -0600 Subject: Re: CCL:Quick question on G98 Mime-Version: 1.0 Content-type: text/plain; charset=us-ascii Content-Disposition: inline Dear Phillip, Thanks again for your clear insight. Is there another issue to consider, namely the shmem variable. Isn't a Unix kernel compiled to set the maximum amount of memory one processor can use. I refer specifically to an SGI Orgin 2000 running IRIX 6.5. How does one change this value (I think many default to 512 MB). Thanks again! Douglas E. Stack Assistant Professor Department of Chemistry University of Nebraska at Omaha Omaha, NE 68182-0109 (402) 554-3647 (402) 554-3888 (fax) destack@unomaha.edu From chemistry-request@server.ccl.net Wed Jan 10 10:38:40 2001 Received: from rzumail2.unizh.ch (rzumail2.unizh.ch [130.60.128.10]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f0AFcep12993 for ; Wed, 10 Jan 2001 10:38:40 -0500 Received: from toukie.zzmk.unizh.ch (zzmkfw.unizh.ch [130.60.67.4]) by rzumail2.unizh.ch (8.9.3/8.9.3/08) with ESMTP id QAA09950; Wed, 10 Jan 2001 16:38:38 +0100 (MET) Message-Id: <4.3.2.7.0.20010110164705.00aa6a70@ziaix-imap.unizh.ch> X-Sender: toukie@ziaix-imap.unizh.ch X-Mailer: QUALCOMM Windows Eudora Version 4.3.2 Date: Wed, 10 Jan 2001 16:47:34 +0100 To: chemistry@server.ccl.net From: "Hr. Dr. S. Shapiro" Subject: Two books Cc: toukie@zui.unizh.ch Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii"; format=flowed Dear Colleagues, If anyone out there has copies of either Ter Haar, "The Old Quantum Mechanics" and/or M. Jammer, "The Conceptual Development of Quantum Mechanics" that they no longer need and would like to donate to a good cause (i.e. myself), kindly contact me _directly_ at toukie@zui.unizh.ch Thanks in advance to all responders, S. Shapiro Baechlerstrasse 45 CH-8802 Kilchberg (ZH) Switzerland toukie@zui.unizh.ch From chemistry-request@server.ccl.net Wed Jan 10 13:19:41 2001 Received: from canario.iqm.unicamp.br (canario.iqm.unicamp.br [143.106.51.212]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f0AIJep13996 for ; Wed, 10 Jan 2001 13:19:40 -0500 Received: (from morgon@localhost) by canario.iqm.unicamp.br (8.9.3/8.9.3) id QAA40785 for CHEMISTRY@ccl.net; Wed, 10 Jan 2001 16:19:39 -0200 (EDT) (envelope-from morgon) From: Nelson Henrique Morgon Message-Id: <200101101819.QAA40785@canario.iqm.unicamp.br> Subject: Re: CCL:document format for ACS journals? In-Reply-To: from "Dr. Martin Schuetz" at "Jan 10, 2001 04:05:34 pm" To: CHEMISTRY@ccl.net Date: Wed, 10 Jan 2001 16:19:39 -0200 (EDT) HP: http://canario.iqm.unicamp.br - DFQ-IQ/UNICAMP. SP,Brasil X-Mailer: ELM [version 2.4ME+ PL54 (25)] MIME-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit I agree, too. Nelson NELSON HENRIQUE MORGON Department of Physical-Chemistry Institute of Chemistry State University of Campinas (UNICAMP) Postal Box: 6154 Zip Code: 13083-970 CAMPINAS - SP - BRAZIL. Telephone: 55 (19) 3788-3157 Fax: 55 (19) 3788-3023 e-mail: morgon@iqm.unicamp.br HP: http://canario.iqm.unicamp.br > > I agree totally. One might even consider to go one step further and to > refuse any reviewing tasks for ACS journals... > > Martin > > ---------------------------------------------------------------------------- > Dr. Martin G. Schuetz Phone: 0049 (0)711-685-4397 > University of Stuttgart Fax: 0049 (0)711-685-4442 > Institute for Theoretical Chemistry > Pfaffenwaldring 55 Room Nr: 8.161 > D-70569 Stuttgart > Email: schuetz@theochem.uni-stuttgart.de > WWW : http://www.theochem.uni-stuttgart.de/~schuetz/ > ---------------------------------------------------------------------------- > > > > On Wed, 10 Jan 2001, Stefan Grimme wrote: > > > Dear CCl users, > > In my opinion we all should ignore the publishers requests > > for articles in special formats, mostly commercial (MS). I don't like to be > > forced to use this software and if they don't accept formats I'm using (LaTeX), > > I will not consider these journals anymore. > > Stefan > > _________________________________________________________ > > Prof. Dr. Stefan Grimme > > Organisch-Chemisches Institut (Abt. Theoretische Chemie) > > Westfaelische Wilhelms-Universitaet, Corrensstrasse 40 > > D-48149 Muenster, Tel (+49)-251-83 36512/33241/36515(Fax) > > Email:grimmes@uni-muenster.de > > http://www.uni-muenster.de/Chemie/OC/research/grimme/ > > _________________________________________________________ > > > > > > > > > > > > > > > > > -= This is automatically added to each message by mailing script =- > CHEMISTRY@ccl.net -- To Everybody | CHEMISTRY-REQUEST@ccl.net -- To Admins > MAILSERV@ccl.net -- HELP CHEMISTRY or HELP SEARCH > CHEMISTRY-SEARCH@ccl.net -- archive search | Gopher: gopher.ccl.net 70 > Ftp: ftp.ccl.net | WWW: http://www.ccl.net/chemistry/ | Jan: jkl@ccl.net > > > > > > From chemistry-request@server.ccl.net Wed Jan 10 14:13:15 2001 Received: from postoffice.mail.cornell.edu (postoffice.mail.cornell.edu [132.236.56.7]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f0AJDFp14295 for ; Wed, 10 Jan 2001 14:13:15 -0500 Received: from cornell.edu (carbo2.foodsci.cornell.edu [132.236.147.61]) by postoffice.mail.cornell.edu (8.9.3/8.9.3) with ESMTP id OAA18838 for ; Wed, 10 Jan 2001 14:13:16 -0500 (EST) Sender: dwood@cornell.edu Message-ID: <3A5CB37B.303B30D9@cornell.edu> Date: Wed, 10 Jan 2001 14:09:47 -0500 From: "Dr. Richard Wood" Organization: Cornell University X-Mailer: Mozilla 4.7C-SGI [en] (X11; I; IRIX 6.5 IP32) X-Accept-Language: en MIME-Version: 1.0 To: chemistry@ccl.net Subject: Re: CCL:document format for ACS journals? References: Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit I would think that given the wide availability of such programs, it wouldn't matter that a journal required such a thing. It's not like the ACS is asking you to use a program that no one uses. Richard "Dr. Martin Schuetz" wrote: > I agree totally. One might even consider to go one step further and to > refuse any reviewing tasks for ACS journals... > > Martin > > ---------------------------------------------------------------------------- > Dr. Martin G. Schuetz Phone: 0049 (0)711-685-4397 > University of Stuttgart Fax: 0049 (0)711-685-4442 > Institute for Theoretical Chemistry > Pfaffenwaldring 55 Room Nr: 8.161 > D-70569 Stuttgart > Email: schuetz@theochem.uni-stuttgart.de > WWW : http://www.theochem.uni-stuttgart.de/~schuetz/ > ---------------------------------------------------------------------------- > > On Wed, 10 Jan 2001, Stefan Grimme wrote: > > > Dear CCl users, > > In my opinion we all should ignore the publishers requests > > for articles in special formats, mostly commercial (MS). I don't like to be > > forced to use this software and if they don't accept formats I'm using (LaTeX), > > I will not consider these journals anymore. > > Stefan > > _________________________________________________________ > > Prof. Dr. Stefan Grimme > > Organisch-Chemisches Institut (Abt. Theoretische Chemie) > > Westfaelische Wilhelms-Universitaet, Corrensstrasse 40 > > D-48149 Muenster, Tel (+49)-251-83 36512/33241/36515(Fax) > > Email:grimmes@uni-muenster.de > > http://www.uni-muenster.de/Chemie/OC/research/grimme/ > > _________________________________________________________ > > > > > > > > > > > > > > > > -= This is automatically added to each message by mailing script =- > CHEMISTRY@ccl.net -- To Everybody | CHEMISTRY-REQUEST@ccl.net -- To Admins > MAILSERV@ccl.net -- HELP CHEMISTRY or HELP SEARCH > CHEMISTRY-SEARCH@ccl.net -- archive search | Gopher: gopher.ccl.net 70 > Ftp: ftp.ccl.net | WWW: http://www.ccl.net/chemistry/ | Jan: jkl@ccl.net -- Richard L. Wood, Ph. D. Physical/Computational Chemist Post-doctoral Associate Cornell University, Ithaca, NY 14853 From chemistry-request@server.ccl.net Wed Jan 10 11:36:58 2001 Received: from usc.edu (root@usc.edu [128.125.253.136]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f0AGawp13336 for ; Wed, 10 Jan 2001 11:36:58 -0500 Received: from rcf-fs.usc.edu (root@rcf-fs.usc.edu [128.125.253.166]) by usc.edu (8.9.3.1/8.9.3/usc) with ESMTP id IAA22093; Wed, 10 Jan 2001 08:36:57 -0800 (PST) Received: from usc.edu (IDENT:jorgevil@futura.usc.edu [128.125.14.59]) by rcf-fs.usc.edu (8.9.3.1/8.9.3/usc) with ESMTP id IAA14339; Wed, 10 Jan 2001 08:36:57 -0800 (PST) Sender: jorgevil@rcf-fs.usc.edu Message-ID: <3A5C9178.1F426113@usc.edu> Date: Wed, 10 Jan 2001 08:44:40 -0800 From: Jordi Villa X-Mailer: Mozilla 4.61 [en] (X11; I; Linux 2.2.12-20 i686) X-Accept-Language: en MIME-Version: 1.0 To: Stefan Grimme CC: chemistry@ccl.net Subject: Re: CCL:document format for ACS journals? References: <01011014495809.08114@GOOFY1> Content-Type: multipart/alternative; boundary="------------789A0537801231E0D500BC55" --------------789A0537801231E0D500BC55 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit I also prefer to write my papers in LaTeX, and it would be nice to show the ACS editors that the choice of the word processor is not only a question of taste. I think that the choice of word processor should be done by the author, as long as it is understandable by the editors. Jordi Stefan Grimme wrote: > Dear CCl users, > In my opinion we all should ignore the publishers requests > for articles in special formats, mostly commercial (MS). I don't like to be > forced to use this software and if they don't accept formats I'm using (LaTeX), > I will not consider these journals anymore. > Stefan > _________________________________________________________ > Prof. Dr. Stefan Grimme > Organisch-Chemisches Institut (Abt. Theoretische Chemie) > Westfaelische Wilhelms-Universitaet, Corrensstrasse 40 > D-48149 Muenster, Tel (+49)-251-83 36512/33241/36515(Fax) > Email:grimmes@uni-muenster.de > http://www.uni-muenster.de/Chemie/OC/research/grimme/ > _________________________________________________________ > > -= This is automatically added to each message by mailing script =- > CHEMISTRY@ccl.net -- To Everybody | CHEMISTRY-REQUEST@ccl.net -- To Admins > MAILSERV@ccl.net -- HELP CHEMISTRY or HELP SEARCH > CHEMISTRY-SEARCH@ccl.net -- archive search | Gopher: gopher.ccl.net 70 > Ftp: ftp.ccl.net | WWW: http://www.ccl.net/chemistry/ | Jan: jkl@ccl.net -- Jordi Villa i Freixa jorgevil@usc.edu http://laetro.usc.edu/wgroup/people/jorgevil Department of Chemistry, University of Southern California Los Angeles, CA, USA, 90089-1062 Tlf: 1-(213)-740 7671 Fax: 1-(213)-740 2701 --------------789A0537801231E0D500BC55 Content-Type: text/html; charset=us-ascii Content-Transfer-Encoding: 7bit I also prefer to write my papers in LaTeX, and it would be nice to show the ACS editors that the choice of the word processor is not only a question of taste. I think that the choice of word processor should be done by the author, as long as it is understandable by the editors.

Jordi

Stefan Grimme wrote:

Dear CCl users,
In my opinion we all should ignore the publishers requests
for articles in special formats, mostly commercial (MS). I don't like to be
forced to use this software and if they don't accept formats I'm using (LaTeX),
I will not consider these journals anymore.
Stefan
_________________________________________________________
Prof. Dr. Stefan Grimme
Organisch-Chemisches Institut (Abt. Theoretische Chemie)
Westfaelische Wilhelms-Universitaet, Corrensstrasse 40
D-48149 Muenster, Tel (+49)-251-83 36512/33241/36515(Fax)
Email:grimmes@uni-muenster.de
http://www.uni-muenster.de/Chemie/OC/research/grimme/
_________________________________________________________

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Jordi Villa i Freixa                  
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Department of Chemistry, University of Southern California
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  --------------789A0537801231E0D500BC55-- From chemistry-request@server.ccl.net Wed Jan 10 14:39:45 2001 Received: from mail2.panix.com (mail2.panix.com [166.84.0.213]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f0AJdjp14483 for ; Wed, 10 Jan 2001 14:39:45 -0500 Received: from panix3.panix.com (panix3.panix.com [166.84.0.228]) by mail2.panix.com (Postfix) with ESMTP id CF0A191A8 for ; Wed, 10 Jan 2001 14:39:46 -0500 (EST) Received: (from kynn@localhost) by panix3.panix.com (8.8.8/8.7.1/PanixN1.0) id OAA28978; Wed, 10 Jan 2001 14:39:46 -0500 (EST) Date: Wed, 10 Jan 2001 14:39:46 -0500 (EST) Message-Id: <200101101939.OAA28978@panix3.panix.com> X-Authentication-Warning: panix3.panix.com: kynn set sender to kynn@panix.com using -f From: To: "chemistry@ccl.net" Subject: Polymer animations? Hi. I've written a program to simulate the behavior of short, linear polymer under the influence of a specialized force field I developed. The program can easily produce a list of coordinates for all the monomers along the chain at periodic time intervals during a simulation. I would like this information to make a movie of the polymer in action under this force field. Therefore, I'm looking for a simple, public-domain piece of software that I can feed these coordinates to, and will generate the corresponding graphics and play them back as a movie. Any suggestions? Thanks! Kevin From chemistry-request@server.ccl.net Wed Jan 10 10:02:47 2001 Received: from narnia1.rutgers.edu (narnia1.rutgers.edu [165.230.180.157]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f0AF2lp12890 for ; Wed, 10 Jan 2001 10:02:47 -0500 Received: from eden.rutgers.edu (molly.envsci.rutgers.edu [165.230.5.148]) by narnia1.rutgers.edu (8.8.8/8.8.8) with ESMTP id KAA25653 for ; Wed, 10 Jan 2001 10:02:53 -0500 (EST) Message-ID: <3A5C7B29.DF2D9B8F@eden.rutgers.edu> Date: Wed, 10 Jan 2001 10:09:29 -0500 From: "Mary O'Connor" X-Mailer: Mozilla 4.08 [en] (Win98; I) MIME-Version: 1.0 To: chemistry@ccl.net Subject: Summary of replies regarding PES Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Thank-you to everyone who responded to my inquiry about good introductions to Potential Energy Surfaces: Mark Thompson suggested: The latest version of Szabo and Ostlund "Advanced Electronic Structure Methods". Kirk Peterson gave: J.N. Murrell et al "Molecular Potential Energy Functions" 1984 Wiley and Sons Dr. Boyd suggested McKee and Page in Vol 4 in Reviews in Computational Chemistry "Computing Reaction Pathways on Molecular Potential Energy Surfaces". Guosheng Wu supplied: A.F. Sax "Potential Energy Surfaces" in Lecture Notes in Chemistry (71) Springer 1999 and G.C. Schatz: Rev. Mod, Phys. 61 (1989) 669. Michael Jakusch gave me a title [ublished by Springer ISBN # 3-540-65106-3 T.Veszpremi suggested Quantum Chemistry, Fundamentals to Application. Kluwer, 1999.pp. 69-76. Thank you to everyone who responded. I will read these publications. Happy New Year to everyone. Mary O'Connor Doctoral Candidate Rutgers University New Brunswick, NJ From chemistry-request@server.ccl.net Wed Jan 10 15:04:53 2001 Received: from toronto.acdlabs.com (toronto.acdlabs.com [207.176.233.2]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f0AK4qp14641 for ; Wed, 10 Jan 2001 15:04:52 -0500 Received: from gavin (gavin.acdlabs.com [207.176.233.80]) by toronto.acdlabs.com (8.9.0/8.9.0) with SMTP id PAA07356; Wed, 10 Jan 2001 15:04:54 -0500 (EST) From: "Gavin Shear" To: , "Charlton, Michael" Subject: viewing SDfiles Date: Wed, 10 Jan 2001 15:12:00 -0500 Message-ID: MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 7bit X-Priority: 3 (Normal) X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook IMO, Build 9.0.2416 (9.0.2910.0) X-MimeOLE: Produced By Microsoft MimeOLE V5.00.2314.1300 Importance: Normal In-reply-To: <3A5C5BB0.F9E8936C@chemaxon.com> Dear Michael, ChemSketch 4.5 will suit your needs, and it is available for free at www.acdlabs.com/download With the addition of ChemBasic Goodies, you can import AND export structures from SDFiles using this popular chemical drawing software. GIF (and many other formats) export is supported, and OLE linking will allow the easy update and editing of chemical structures embedded in your MS Office documents. With the inexpensive integration of ChemFolder 4.5(trial available for download), you can turn your drawing software into a powerful SDFile friendly database engine. All fields from SDFiles are carried along with the import, and may also be exported unchanged. Structure/Substructure searching, list management, user notes, attachment of files and URL's are just a few of the features of ChemFolder 4.5 We have provided some sample databases on our website for free download. Please feel free to contact us should you have any questions. Best wishes, Gavin Shear > > "Charlton, Michael" wrote: > > > Hi, > > does anyone know of a free/cheap tool for looking at MDL > SDfiles ? It would > > be good to be able to be able to rapidly examine the structures. > > A web-based system would be ideal. > > Alternatively, are there tools for turning a structure into a > gif format ? > > (It would bve good if it would run on an SGI machine.) > > > > Thanks in advance, > > > > Michael Charlton. > > > > > > > -= This is automatically added to each message by mailing script =- > CHEMISTRY@ccl.net -- To Everybody | CHEMISTRY-REQUEST@ccl.net -- > To Admins > MAILSERV@ccl.net -- HELP CHEMISTRY or HELP SEARCH > CHEMISTRY-SEARCH@ccl.net -- archive search | Gopher: > gopher.ccl.net 70 > Ftp: ftp.ccl.net | WWW: http://www.ccl.net/chemistry/ | Jan: > jkl@ccl.net > > > > > > From chemistry-request@server.ccl.net Wed Jan 10 15:39:28 2001 Received: from markov.chem.rochester.edu (markov.chem.rochester.edu [128.151.176.16]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f0AKdSp14879 for ; Wed, 10 Jan 2001 15:39:28 -0500 Received: (from serg@localhost) by markov.chem.rochester.edu (8.10.1/8.10.1) id f0BKdSI14368; Wed, 11 Jan 2001 15:39:28 -0500 (EST) Date: Wed, 11 Jan 2001 15:39:28 -0500 (EST) From: Sergei Tretiak To: kynn@panix.com cc: "chemistry@ccl.net" Subject: Re: CCL:Polymer animations? In-Reply-To: <200101101939.OAA28978@panix3.panix.com> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Kevin, MOLDEN (http://www.cmbi.kun.nl/~schaft/molden/molden.html) will do the job for you. It can generate graphics GIF files for each step and play it like a movie, but to merge all GIFs into a single movie file you have to use another software. Best, Sergei .-----------------------------------------------------------------------. |\ / \ | Sergei Tretiak | / \ /| |.\/...\|.......................................................|/...\/.| | Theoretical Division | Voice: (505) 667-8351 | | Mail stop B262 | Fax: (505) 665-4063 | | Los Alamos National Lab | E-mail: serg@markov.chem.rochester.edu | | Los Alamos, NM 87545 | serg@wigner.chem.rochester.edu | | Homepage: http://markov.chem.rochester.edu/serg/welcome.html | |_______________________________________________________________________| On Wed, 10 Jan 2001 kynn@panix.com wrote: > > > > > Hi. I've written a program to simulate the behavior of short, linear > polymer under the influence of a specialized force field I developed. > The program can easily produce a list of coordinates for all the > monomers along the chain at periodic time intervals during a > simulation. I would like this information to make a movie of the > polymer in action under this force field. Therefore, I'm looking for > a simple, public-domain piece of software that I can feed these > coordinates to, and will generate the corresponding graphics and play > them back as a movie. > > Any suggestions? > > Thanks! > > Kevin > > -= This is automatically added to each message by mailing script =- > CHEMISTRY@ccl.net -- To Everybody | CHEMISTRY-REQUEST@ccl.net -- To Admins > MAILSERV@ccl.net -- HELP CHEMISTRY or HELP SEARCH > CHEMISTRY-SEARCH@ccl.net -- archive search | Gopher: gopher.ccl.net 70 > Ftp: ftp.ccl.net | WWW: http://www.ccl.net/chemistry/ | Jan: jkl@ccl.net > > > > > From chemistry-request@server.ccl.net Wed Jan 10 12:45:12 2001 Received: from ns.chemie.uni-hamburg.de (ns.chemie.uni-hamburg.de [134.100.212.5]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f0AHjBp13840 for ; Wed, 10 Jan 2001 12:45:12 -0500 Received: from blubber.chemie.uni-hamburg.de (blubber.chemie.uni-hamburg.de [134.100.212.9]) by ns.chemie.uni-hamburg.de (8.11.1/8.11.1) with ESMTP id f0AHjBQ23805; Wed, 10 Jan 2001 18:45:11 +0100 (MET) Received: from localhost (lankau@localhost) by blubber.chemie.uni-hamburg.de (AIX4.3/UCB 8.8.8/8.8.8) with ESMTP id SAA39924; Wed, 10 Jan 2001 18:42:01 +0100 Date: Wed, 10 Jan 2001 18:42:00 +0100 (NFT) From: Timm Lankau To: "Dr. Martin Schuetz" cc: Stefan Grimme , chemistry@ccl.net Subject: Re: CCL:document format for ACS journals? In-Reply-To: Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hello, please stop this off topic discussion before it becomes to hot. As far as I know, ACS journals accept LaTeX and TeX documents. I recently submitted my manusscript to J. Phys. Chem. and got in return a leaflet on different document forms. This leaflet states that both LaTeX and TeX documents are accepted by ACS journals. Best wishes, Timm ========================================================================== Timm Lankau phone (+)40 42838 3686 Institut fuer Physikalische Chemie fax (+)40 42838 3452 Universitaet Hamburg e-mail lankau@chemie.uni-hamburg.de Bundesstr. 45 20146 Hamburg Germany http://www.chemie.uni-hamburg.de/pc/AKs/Nagorny/nago.html From chemistry-request@server.ccl.net Wed Jan 10 13:14:48 2001 Received: from sdnt1.Acadia-SD (mail.acadia-pharm.com [209.77.18.3]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f0AIElp13976 for ; Wed, 10 Jan 2001 13:14:47 -0500 Received: by sdnt1 with Internet Mail Service (5.5.2650.21) id ; Wed, 10 Jan 2001 10:13:11 -0800 Message-ID: <15189A4705A8D31189B700805F85410B41436C@sdnt1> From: Daniel Severance To: "CCL (E-mail)" Cc: Daniel Severance Subject: Viewing multiple structure files Date: Wed, 10 Jan 2001 10:13:01 -0800 MIME-Version: 1.0 X-Mailer: Internet Mail Service (5.5.2650.21) Content-Type: text/plain; charset="iso-8859-1" Greetings CClers, I've generated a set of conformations of a molecule and want to send it to some chemists at a remote site. Is there a simple application (Windows NT) for simply scrolling through the set of conformations one at a time (visually, with 3D rotation ability) so they can see the results? It needs to do nothing else, although it might be nice to be able to dump out the current conformation into a new file, it wouldn't be required. Is there anything available to do this (either academic or commercial is fine)? Thanks! Dan ____________________________________________________ Daniel L. Severance Ph.D. Computational Chemistry ACADIA Pharmaceuticals 3911 Sorrento Valley Boulevard San Diego CA 92121-1402 USA phone (858) 558 2871 fax (858) 558 2872 dseverance@acadia-pharm.com www.acadia-pharm.com From chemistry-request@server.ccl.net Wed Jan 10 14:06:59 2001 Received: from hermes.bmc.uu.se (hermes.bmc.uu.se [130.238.39.159]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f0AJ6xp14166 for ; Wed, 10 Jan 2001 14:06:59 -0500 Received: from alpha2.bmc.uu.se ([130.238.37.65]) by hermes.bmc.uu.se (Post.Office MTA v3.5.3 release 223 ID# 0-62649U1500L1000S0V35) with SMTP id se; Wed, 10 Jan 2001 20:08:15 +0100 Received: from zorn.bmc.uu.se by alpha2.bmc.uu.se (5.65v3.2/1.1.10.5/07Jan00-1145AM) id AA30849; Wed, 10 Jan 2001 20:06:52 +0100 Date: Wed, 10 Jan 2001 17:55:12 +0100 (CET) From: David van der Spoel X-Sender: spoel@zorn.bmc.uu.se To: "Dr. Martin Schuetz" Cc: Stefan Grimme , chemistry@ccl.net Subject: Re: CCL:document format for ACS journals? In-Reply-To: Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII On Wed, 10 Jan 2001, Dr. Martin Schuetz wrote: > >I agree totally. One might even consider to go one step further and to >refuse any reviewing tasks for ACS journals... Not so fast... According to the JPC website one can send in papers in a stripped down Latex, i.e., things like bold, math etc. are preserved, which is what counts. But a boycot of Nature would be in place... They can't even print an EPS file. Groeten, David. ________________________________________________________________________ Dr. David van der Spoel Biomedical center, Dept. of Biochemistry s-mail: Husargatan 3, Box 576, 75123 Uppsala, Sweden e-mail: spoel@xray.bmc.uu.se www: http://zorn.bmc.uu.se/~spoel phone: 46 18 471 4205 fax: 46 18 511 755 ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ From chemistry-request@server.ccl.net Wed Jan 10 13:39:17 2001 Received: from postoffice.igalaxy.net (postoffice.igalaxy.net [64.160.104.184]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f0AIdGp14069 for ; Wed, 10 Jan 2001 13:39:16 -0500 Received: from hpotter.vaughan.home [64.160.106.30] by postoffice.igalaxy.net with ESMTP (SMTPD32-6.04) id A040E80210; Wed, 10 Jan 2001 10:56:00 -0800 Received: from daddy by hpotter.vaughan.home with local (Exim 3.20 #1 (Debian)) id 14GO3V-0000Ba-00 for ; Wed, 10 Jan 2001 08:24:57 -0800 Date: Wed, 10 Jan 2001 08:24:57 -0800 From: Kenward Vaughan To: chemistry@ccl.net Subject: Re: CCL:document format for ACS journals? Message-ID: <20010110082456.A695@hpotter.vaughan.home> References: Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Disposition: inline User-Agent: Mutt/1.2.5i In-Reply-To: ; from Hannes.Loeffler@uibk.ac.at on Wed, Jan 10, 2001 at 11:38:29AM +0100 Sender: Daddy Vaughan On Wed, Jan 10, 2001 at 11:38:29AM +0100, Hannes Loeffler wrote: > Hello all, > > one of our co-workers just told me that he has to rewrite his publications > with Word or Word Perfect because ACS journals now require so (JPC in this > case). > > Is this true? Any opinions? Personally I would be very troubled if an organization such as the ACS decreed that submissions were dependent on specific software rather than styles. Certainly that group knows the great strengths which lie in other, well-established software available to the academic community, especially since it is (literally) free _and_ created in the spirit of the academic world? Perhaps they need to revamp their "document-handlers" pool... Kenward Vaughan Bakerfield College kvaughan@bc.cc.ca.us (work) -- It is not so very important for a person to learn facts. For that he doesn't really need a college education, for he can learn them from books. The value of an education in a liberal arts college is not the learning of many facts but the training of the mind to thinking--something that cannot be learned from books. Albert Einstein From chemistry-request@server.ccl.net Wed Jan 10 12:55:07 2001 Received: from chala.q1.fcen.uba.ar (chala.q1.fcen.uba.ar [157.92.31.25]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f0AHt5p13874 for ; Wed, 10 Jan 2001 12:55:05 -0500 Received: from localhost (damian@localhost) by chala.q1.fcen.uba.ar (8.9.3/8.9.3) with ESMTP id QAA05314 for ; Wed, 10 Jan 2001 16:42:53 +0100 Date: Wed, 10 Jan 2001 16:42:53 +0100 (MET) From: =?X-UNKNOWN?Q?Dami=E1n_Scherlis?= To: chemistry@ccl.net Subject: Summary: ONIOM/AMBER in Gaussian Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=X-UNKNOWN Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from QUOTED-PRINTABLE to 8bit by server.ccl.net id f0AHt7p13875 I want to thank Stefan Fau, Nicolas Ferre, Ivan Rossi and Douglas Fox, their answers have been of help. Following are the original question and the answers: Hi, I have done some test calculations using the ONIOM method (Gaussian98) to combine DFT with either AM1 or AMBER. I assumed that the ONIOM procedure will solve the High and Low regions of the system in a self consistent way, so that the electron density of one part is affected by the density of the other. Instead I noticed that the energy of the High and Low layers did not depend on each other, as if each subsystem were isolated. As you see, I have probably a wrong idea of what ONIOM is, or I can't manage to interpret the results. I will appreciate any comment to clarify this question. Let me ask another question: when I try to run AMBER the computation is interrupted with the following message, though I included all atom types in the input: Stretching parameters undefined for 1 (O ) - 2 (O ) Stretching parameters undefined for 3 (HC) - 6 (CC) Stretching parameters undefined for 4 (CW) - 10 (HC) Stretching parameters undefined for 5 (CR) - 11 (HC) Bending parameters undefined for 3 (HC) - 6 (CC) - 4 (CW) Bending parameters undefined for 3 (HC) - 6 (CC) - 7 (NA) Bending parameters undefined for 6 (CC) - 4 (CW) - 10 (HC) Bending parameters undefined for 7 (NA) - 5 (CR) - 11 (HC) Bending parameters undefined for 8 (NA) - 4 (CW) - 10 (HC) Bending parameters undefined for 8 (NA) - 5 (CR) - 11 (HC) Not enough parameters to run AMBER Error termination via Lnk1e in /usr/bin/g98/l402.exe. Should I provide all these parameters in an additional file? How is this done? Thanks in advance -- Hi Damian, ONIOM works by calculating the whole molecule at the low level. Then the high-level zone is saturated with hydrogens and calculated at both the high and the low level. The final energy is: E(low,all) - E(low,part) + E(high,part) There is a paper by Stefan Dapprich et al explaining all this in detail. It is about three or four years old. Yours, Stefan ______________________________________________________________________ Dr. Stefan Fau | fau@qtp.ufl.edu Quantum Theory Project | (352) 392-6714 University of Florida Gainesville, FL 32611-8435 _______________________________________________________________________ Hi, In your case, the energy of the whole system is given by : E = E(DFT in High) + E(AM1 or Amber in Low) - E(AM1 or Amber in Low) The DFT calculation is performed on a cluster builded from the High region saturated with hydrogens. So the electronic density is not affected by the environment. However, this effect is taken into account at the low level with a calculation on the whole system (only with AM1 as Amber is not a polarizable forcefield). Double counting of interactions is avoided by substracting the energy of the whole system at the low level of theory. Second part of the question (about AMBER): You can't do this. Maybe you have to modify the Gaussian code to include those cases. But before doing this, did you check the connectivity of your system ?If you let G98 generating the connectivity in an automatic way, maybe it can be wrong. You can define this connectivity in the input file. Use the IOP(1/57=2). Then, after the geometry specifications, you can write the connectivity as following. For every atom: "Bonded atom number 1" "Type of bond 1" "Bonded atom number 2" "Type of bond 2" ... and so on The atom number is an integer, the type of bond is a real (1.00 for a single bond, 2.00 for a double bond ...). Hope this helps. Nicolas -- ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Nicolas FERRE Tel : (33)3.83.91.20.00. poste 35.52. Fax : (33)3.83.91.25.30. Laboratoire de Chimie Theorique Universite Henri Poincare - Nancy 1 BP 239 mailto:ferre@lctn.uhp-nancy.fr 54506 VANDOEUVRE-LES-NANCY Cedex FRANCE http://www.lctn.uhp-nancy.fr/Etudiants/Nicolas.Ferre.html/ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ From chemistry-request@server.ccl.net Wed Jan 10 13:09:48 2001 Received: from potsdam.edu (potsdam.edu [137.143.110.101]) by server.ccl.net (8.11.0/8.11.0) with SMTP id f0AI9lp13940 for ; Wed, 10 Jan 2001 13:09:47 -0500 Received: (qmail 23096 invoked by alias); 10 Jan 2001 18:10:07 -0000 Received: (qmail 23082 invoked by uid 0); 10 Jan 2001 18:10:06 -0000 Received: from comp10205.potsdam.edu (HELO comp10205) (137.143.109.46) by potsdam.edu with SMTP; 10 Jan 2001 18:10:06 -0000 Message-Id: <3.0.6.32.20010110132158.0080fd70@potsdam.edu> X-Sender: marteljm@potsdam.edu X-Mailer: QUALCOMM Windows Eudora Light Version 3.0.6 (32) Date: Wed, 10 Jan 2001 13:21:58 -0500 To: "Bachrach, Steven" , chemistry@ccl.net From: Jaime Martell Subject: Re: CCL:document format for ACS journals? In-Reply-To: Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" At 08:51 AM 1/10/01 -0600, Bachrach, Steven wrote: >Not often do I come to the defense of ACS pubs, I must chime in on this >comment though in defense of ACS. > >I just received the referee reports for an article I submitted to JOC and >the following is a direct quote: > >"Our Publication Division asks that your final copy be prepared with >12-point type and double-spaced through all parts of the manuscript. In >addition, please supply the final version of your manuscript on computer >disc. Complete the enclosed "Media Description Form" and return it to us >along with the disc. MS Word and WordPerfect software have been used most >frequently, but the Publications Division is willing to try any word >processor on any disc from any computer as long as it is clearly >identified." > >Now I don't think they intend to process a Wordstar file from a TRS-80 >stored on an 8" floppy, but their willingness to deal with files other than >the usual suspects is certainly reasonable and should be applauded. > Bravo, Steve! Thanks for supplying the complete story to clear this up. Apparently the Word or WordPerfect only rumour was just that; jumping to conclusions is not the hallmark of a good scientist. Those who choose to not submit to or do referee work for ACS should consider that the reason for the requested word processor documents is for more rapid publication, something these journals have been doing a great job at and for which they should be applauded. I for one will continue to use JPC as my journal of choice for publication. Respectfully yours, Jaime Jaime Martell, Ph.D. Assistant Professor Department of Chemistry SUNY Potsdam Potsdam, NY 13676 Phone: 315-267-2268 Fax: 315-267-3170 e-mail: marteljm@potsdam.edu WWW: http://www2.potsdam.edu/marteljm/ From chemistry-request@server.ccl.net Wed Jan 10 16:23:56 2001 Received: from blackadder.cis.McMaster.CA (blackadder.CIS.McMaster.CA [130.113.128.1]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f0ALNup15134 for ; Wed, 10 Jan 2001 16:23:56 -0500 Received: from mcmaster.ca (joule.Chemistry.McMaster.CA [130.113.108.215]) by blackadder.cis.McMaster.CA with ESMTP id QAA13410 for ; Wed, 10 Jan 2001 16:23:56 -0500 (EST) Sender: jenkins@blackadder.cis.McMaster.CA Message-ID: <3A5CE2B9.B09726E1@mcmaster.ca> Date: Wed, 10 Jan 2001 17:31:21 -0500 From: Samantha Jenkins Organization: McMaster University X-Mailer: Mozilla 4.75 [en] (X11; U; Linux 2.2.14-5.0 i686) X-Accept-Language: en MIME-Version: 1.0 To: CHEMISTRY@ccl.net Subject: basis set optimiser in solid X-Priority: 1 (Highest) References: Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Sergei Tretiak wrote: > > Kevin, > > MOLDEN (http://www.cmbi.kun.nl/~schaft/molden/molden.html) will do the > job for you. It can generate graphics GIF files for each step and play it > like a movie, but to merge all GIFs into a single movie file you have to > use another software. > > Best, > > Sergei > > >.-----------------------------------------------------------------------. > |\ / \ | Sergei Tretiak | / \ /| > |.\/...\|.......................................................|/...\/.| > | Theoretical Division | Voice: (505) 667-8351 | > | Mail stop B262 | Fax: (505) 665-4063 | > | Los Alamos National Lab | E-mail: serg@markov.chem.rochester.edu | > | Los Alamos, NM 87545 | serg@wigner.chem.rochester.edu | > | Homepage: http://markov.chem.rochester.edu/serg/welcome.html | > |_______________________________________________________________________| Hello. I am trying to optimise basis sets using LOPTCG within crytsal98 and I am having little success. Does anyone have a working set of input files for LOPTCG, which optimse the basis set. The code seem to work OK for geometries and comes with example files for the geometries, but not the basis sets. Any simple solid would do, diamond etc. Thanks, Samantha Jenkins From chemistry-request@server.ccl.net Wed Jan 10 12:55:07 2001 Received: from chala.q1.fcen.uba.ar (chala.q1.fcen.uba.ar [157.92.31.25]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f0AHt5p13874 for ; Wed, 10 Jan 2001 12:55:05 -0500 Received: from localhost (damian@localhost) by chala.q1.fcen.uba.ar (8.9.3/8.9.3) with ESMTP id QAA05314 for ; Wed, 10 Jan 2001 16:42:53 +0100 Date: Wed, 10 Jan 2001 16:42:53 +0100 (MET) From: =?X-UNKNOWN?Q?Dami=E1n_Scherlis?= To: chemistry@ccl.net Subject: Summary: ONIOM/AMBER in Gaussian Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=X-UNKNOWN Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from QUOTED-PRINTABLE to 8bit by server.ccl.net id f0AHt7p13875 ONIOM answers continued... [chopped in two pieces by Jan Labanowski] > From ivan@biocomp.unibo.it Tue Jan 9 20:34:06 2001 Date: Tue, 9 Jan 2001 11:15:38 +0100 (CET) From: Ivan Rossi To: "[X-UNKNOWN] Damián Scherlis" Subject: Re: CCL:ONIOM/AMBER in Gaussian [ The following text is in the "X-UNKNOWN" character set. ] [ Your display is set for the "US-ASCII" character set. ] [ Some characters may be displayed incorrectly. ] On Mon, 8 Jan 2001, [X-UNKNOWN] Damián Scherlis wrote: > I have done some test calculations using the ONIOM method (Gaussian98) > to combine DFT with either AM1 or AMBER. I assumed that the ONIOM > procedure will solve the High and Low regions of the system in a self > consistent way, so that the electron density of one part is affected by > the density of the other. Instead I noticed that the energy of the High > and Low layers did not depend on each other, as if each subsystem were > isolated. As you see, I have probably a wrong idea of what ONIOM is, or I > can't manage to interpret the results. I will appreciate It is exactly as you noticed. E(ONIOM) = E( low-level/whole molecule) - E(low-level/High layer) + + E( high-level/high layer) The advantage is the simplicity and the reduced problem in the treatment of boundaries. drawbacks: the influence of the low layer on the high layer is only indirect through geometric distortion of the high layre from its optimal geometry. This means that the interaction between your low and high layer have to be described reliably at the lowest level used, since no correction is applied to it. you need to be able to calculate the WHOLE MOLECULE at the lowest level of theory: if you are missing MM or semiemiprical parameters you simply cannot do the calculation. I use ONIOM a lot, but i found it most useful when it can be used with HF as the lowest level, and not very useful as a qm/mm method, at least for my applications. -- Dr. Ivan Rossi - PNACoS Consulting & CIRB Biocomputing Unit PNACoS, Via della Grada 4/F, I-40122 Bologna, ITALY e-mail: ivan@biocomp.unibo.it Web: http://www.biocomp.unibo.it/ivan > From gaussian.com!csd@gaussian.com Tue Jan 9 20:34:15 2001 Date: Tue, 9 Jan 2001 14:54:59 -0300 From: Cust. Service Doug Reply-To: gaussian.com!help%gaussian.com@gaussian.com To: "[X-UNKNOWN] Damián Scherlis" Subject: Re: CCL:ONIOM/AMBER in Gaussian Dr. Scherlis, The ONIOM method, as currently implemented, does not include the ability for the results of the layers to interact. There are a number of different models you could imagine for this and we continue to investigate ways to make ONIOM more effective. These will be incorporated into future releases of the Gaussian software but are not currently available. The question you ask about AMBER is a common mis-understanding. AMBER does not rely on just atom type but the stretch, bend and dihedral parameters are defined for each combination of atom types. The defined parameters in the literature are limited and are defined with biological systems, amino acids and proteins, in mind. Thus even some simple systems like a peroxide bond cannot be handled with the standard parameter set. At present G98 implements the standard AMBER parameters but does not have a mechanism for defining and incorporating novel parameters. Similarly you need to supply atom charges for each center, see test432.com in g98/tests/com, in order to get realistic results. For most systems involving metals or general organic systems that you want to treat with a molecular mechanics low level ONIOM calculation I end up recommending UFF. This does not treat biological systems nearly as well but it does allow all common chemically bonded systems to be treated. Let me know if you have additional questions. -- Douglas J. Fox Technical Support Gaussian, Inc. help@gaussian.com