From chemistry-request@server.ccl.net  Thu Dec  2 06:15:24 1999
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Date: Thu, 02 Dec 1999 12:32:28 +0200
From: Demetrios Xenides <qc2@chemistry.upatras.gr>
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Hi all!

Someone asked about VRML and if there is a patch or sth. (he called it
"add on") in order to work with molecules via Internet Explorer. Since
I'm not familiar with the matter I offered to ask the CCL community
(!!!!!!!!).

Any suggestion is very much wellcome...

DX

From chemistry-request@server.ccl.net  Thu Dec  2 07:15:15 1999
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The CAOS/CAMM Center, University of Nijmegen, The Netherlands,
announces a change of its name to CMBI: 
Centre for Molecular and Biomolecular Informatics.
New director is Prof. Gert Vriend, moving from EMBL Heidelberg.

As a consequence, our web address has also been changed, to
http://www.cmbi.kun.nl/
Similarly, cmbi becomes the domain name in our e-mail addresses.

People maintaining bookmarks or links to the Centre are
kindly asked to edit the URL, to reflect the new situation.

The former web site http://www.caos.kun.nl/ 
describes some translation rules for URL's, and examples of
new links for copying (MOLDEN, Mol4D, SRS, Bio-Toolkit, etc.).
In short:  
caos.kun.nl  -> cmbi.kun.nl
/caos/  -> /cheminf/
/camm/  -> /cheminf/
/cammsa/  -> /bioinf/
Example:
http://www.caos.kun.nl/tutorials/camm/mopac/comp.html
becomes
http://www.cmbi.kun.nl/tutorials/cheminf/mopac/comp.html

With apologies for multiple postings,
-- 

  *****    J.H. (Hens) Borkent, CMBI,
 *CMBI *   P.O. Box 9010, 6500 GL Nijmegen, The Netherlands
*   /   *  Tel 0031 24 36 52137  Fax 0031 24 36 52977
 * CMBI*   http://www.cmbi.kun.nl/   CAOS/CAMM Center is now 
  *****    Centre for Molecular and Biomolecular Informatics
From chemistry-request@server.ccl.net  Thu Dec  2 08:09:36 1999
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Date: Thu, 2 Dec 1999 13:00:12 +0100
From: mann@coch03.chm.tu-dresden.de (Matthias Mann)
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Dear all,

has anyone successfull installed the MOPAC97 source (distributed with
the WinMOPAC software) under IBM AIX and/or under Linux ?
The Makefile is pepared for use with DEC, SPARC and SGI only;
compilation under AIX and LINUX works, but results in binaries
which will crash for larger molecules. The message is:
    INSUFFICIENT MEMORY.  MEMORY NEEDED: 2067088  BYTES
The reason seems to be the "getmem" routine, which doesn't return   
correct values.
Any suggestions ?

Thanks,
Matthias

--

Dr. Matthias Mann 
Fachrichtung Chemie der TU Dresden
D-01069 Dresden, Mommsenstr. 13
Tel.: +49 (351) 463-4286 / Fax: -7030
Email: Matthias.Mann@chemie.tu-dresden.de

 
From chemistry-request@server.ccl.net  Thu Dec  2 08:50:19 1999
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>{*} Can anyone out there provide me a URL for the aforementioned
>{*} crystallography program? 3 different web searches have not proven
>{*} fruitful.

Have a look at :
http://shelx.uni-ac.gwdg.de/SHELX/index.html

Note that a "Crystallography Source Code Museum" is now open at :
    http://sdpd.univ-lemans.fr/museum/
This is only of some interest to programmers and does not
contain any executable, and few recent codes (certainly not
SHELX-97, only SHELX-76). Old codes are welcome !

Best,


Armel Le Bail - Universite du Maine, Laboratoire des Fluorures,
CNRS ESA 6010, Av. O. Messiaen, 72085 Le Mans Cedex 9, France
http://www.cristal.org/

From chemistry-request@server.ccl.net  Thu Dec  2 10:05:52 1999
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Date: Thu, 2 Dec 1999 14:58:33 +0100
From: "Dr. Peter Burger" <chburger@aci.unizh.ch>
To: CHEMISTRY@ccl.net
Subject: CCL: Comparative Linux quantum chemistry benchmark  
Message-ID: <Pine.SGI.4.21.9912021451450.8592-100000@rzusgi.unizh.ch>
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Dear netters,

just thought that there might be some interest for some comparative Linux
DFT benchmark data for a variety of programs. Note that this is
just a short test, i.e. your mileage may (will) vary for other systems.

The time required for one SCF-cycle was chosen as criterion.  Standard SCF-convergence
criteria implemented in the programs were used.

Peter
---------------------------------------------
Peter Burger
Anorg.-chem. Institut
University of Zuerich
chburger@aci.unizh.ch
---------------------------------------------

General Setup:

Hardware: ASUS P2BD, dual processor boards, 512 MB RAM memory, 
          fast EIDE HD's: 20.4 GB, 7'200 rpm, UDMA2 mode  
          CPU's PII/PIII, kernel: Linux 2.2.9-SMP, SuSE 6.1  
          parallel runs: mpich/MPI or pvm over 100 Mb Fast Ethernet network.

          (Exemplary tests show that the codes seem to scale very nicely
          with clock frequency).
   


All times are walltimes: Machines have been performing
no jobs otherwise. 23 heavy atoms (C,N,O), 18 H atoms.
basis sets varying from  358-389 basis functions.
DFT: BP86 functional, default (medium) grid: 

-------------------------------------------------------------------------
reference-98 (6-31G*)

On PIII-550 

 1 CPU, 381 basis function   235 min/15 cycle   =     940 sec/cycle

 2 CPU's, shared mem   129 min/15 SCF cycle     =     516 sec/cycle
-------------------------------------------------------------------------
QCHEM ver 1.2:

On PII-450

standard grid, basis (381) 169 min/12 SCF     =    844 sec/cycle
                                (extrapolated to 550 MHz, 680 sec/cycle)        
-------------------------------------------------------------------------
Jaguar v 3.5 rel 50:
 
On PIII-550

      (quick accuracy for pseudospectral method)
   
      381 SCF basis functions:   64 min/11 SCF cycl. =    349 sec/cycle 
-------------------------------------------------------------------------
ADF-99

ON PII-400

                   
 1 CPU:      389 SCF basis functions:                
                  191 min, 17 SCF cycles      =    674 sec/cycle
(including setup/analysis)
                 (127 min for 17 SCF cycles)  =   (448 sec/cycle)
                                (extrapolated to 550 MHz, 326 sec/cycle)

 10 CPUs, parallel (PVM) latest version:  8 x PII 400, 2x PII-450
             389 SCF basis functions:  

                 30 min, 17 SCF cycles        =    106 sec/cycle
(including setup/analysis)
                (20 min for 17 SCF cyc.)      =                  (71
sec/cycle)
-------------------------------------------------------------------------
DMOL 3.5

On PIII-550

1 CPU  358 SCF basis functions    49 min/18 SCF cycl. =    163 sec/cycle
 
8 CPU's parallel MPI (mpich), 2x PIII 550, 6 x PII 400

       358 SCF basis fucntions    10 min/16 SCF cycl. =     38 sec/cycle

-------------------------------------------------------------------------
Turbomole, RIDFT method,

On PIII-550

1 CPU ver. 5.1

      389 SCF basis functions    20 min/12 SCF cycles  =   100 sec/cycle 


6 CPU's parallel, (ver 4.9), 2x PIII-550, 2x PII-450,2x PII 400 

                                  6 min/12 SCF cycles =     30 sec/cycle

12 CPU's, 2x PIII-550, 2x PII-450, 8x PII 400 

                                  4 min/12 SCF cycles =      20 sec/cycle

Turbomole, DFT method
-------------------------

1 CPU, 1 PIII-550 (last cycle with large grid) (rel 5.1)

                                102 min, 10 SCF cycles =     610 sec/cycle

12 CPUs  (rel. 4.9) 12 CPU's, 2x PIII-550, 2x PII-450, 8x PII 400

                               11 sec 30 min, 10 SCF cycles = 68 sec/cycle

-------------------------------------------------------------------------



From chemistry-request@server.ccl.net  Thu Dec  2 10:52:03 1999
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Date: Thu, 2 Dec 1999 09:44:46 -0500 (EST)
From: WeiQuan Tian <wtian@uoguelph.ca>
X-Sender: wtian@ccshst01
To: chemistry@ccl.net
Subject: Re: CCL:Gaussian on Clusters
In-Reply-To: <Pine.HPP.3.95.991201184131.472A-100000@ccshst01>
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 I should be more specific about my question. The clusters mean the
clusters of computer connected together doing computations.


 Wei Quan Tian


On Wed, 1 Dec 1999, WeiQuan Tian wrote:

> 
>  Dear Lister:
> 
>   Does anyone know anygroup running Gaussian 98 or 94 on clusters? What
> are the operating system and hardware?
> 
>   I will summarize the responces.
> 
>  Wei Quan Tian
> 
> 
> 
> 
> -= 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  Thu Dec  2 11:09:07 1999
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From: "Kline, Richard (NIDA)" <rkline@nida.nih.gov>
To: "'CHEMISTRY@ccl.net'" <CHEMISTRY@ccl.net>
Subject: Browser Question
Date: Thu, 2 Dec 1999 10:01:36 -0500 
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Dear netters,

We at NIDA are in the development phase of a web based chemical database of CNS
compounds.  A question has arisen as to which browser(s) we should be developing
our web application for.  The question for the CCL is, except for the obvious
browsers (Netscape and IE) are there any other browsers (e.g., Opera, etc) being
used by a significant number of researchers?  Your response is appreciated.

Rik Kline

Richard Kline, Ph.D.
DTR&D/NIDA/NIH
6001 Executive Blvd, Room 4123, MSC 9551
Bethesda, MD 20892-9551
Phone:  301-443-8293
Fax:      301-443-2599
mailto:   rik@nih.gov
From chemistry-request@server.ccl.net  Thu Dec  2 10:16:32 1999
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Date: Thu, 2 Dec 1999 15:09:14 +0100
From: "Dr. Peter Burger" <chburger@aci.unizh.ch>
To: CHEMISTRY@ccl.net
Subject: CCL:Linux DFT benchmarks
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Dear netters,

forgot to mention: The default grids of the programs were chosen.

Peter


From chemistry-request@server.ccl.net  Thu Dec  2 13:02:47 1999
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Date: Thu, 02 Dec 1999 18:55:18 +0200
From: Tzvika Aviv <tzvika_a@md2.huji.ac.il>
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Hi all

I'm trying to dock a peptide to an enzyme, since I know the binding site
I want to use autodock3 to search for the best conformotion of the
ligand in it's place (not using the random initation). I tried to use
this parametrs at the .dpf file:


# Initial Translation, Quaternion and Torsions
tran0 0.0 0.0 0.0  # initial coordinates/A or "random"
quat0 1.0 0.0 0.0 0.0  # initial quaternion or "random"
ndihe 30  # number of initial torsions
dihe0 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0.

but the peptide moves out of the binding site. (when I use the peptide
as a rigid molecule, It is not moving out).

Does anybody know how to set the parametrs for this kind of runs? (a
conformation search on a ligand at a binding site)

tzvika

tzvika aviv
e-mail: tzvika_a@md2.huji.ac.il
pharmacy school
hebrew university
jerusalem

From chemistry-request@server.ccl.net  Thu Dec  2 15:38:36 1999
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Date: Thu, 2 Dec 1999 13:28:31 -0600 (CST)
From: "Konstantin N. Kudin" <knk@castor.rice.edu>
To: Computational Chemistry List <chemistry@ccl.net>
Subject: Re: CCL:Comparative Linux quantum chemistry benchmark
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On Thu, 2 Dec 1999, Dr. Peter Burger wrote:

> Dear netters,
> 
> just thought that there might be some interest for some comparative Linux
> DFT benchmark data for a variety of programs. Note that this is
> just a short test, i.e. your mileage may (will) vary for other systems.
> 
> The time required for one SCF-cycle was chosen as criterion.  Standard SCF-convergence
> criteria implemented in the programs were used.
> 
> Peter
> ---------------------------------------------
> Peter Burger
> Anorg.-chem. Institut
> University of Zuerich
> chburger@aci.unizh.ch
> ---------------------------------------------
> 

 
 Dear Dr. Burger

 Could you enlighten the general public what the "default" grids were,
convergence of the density matrix, accuracy of the final energy, etc?
Otherwise your results appear to be somewhat meaningless.

 Sincerely, 
 Konstantin Kudin




 


From chemistry-request@server.ccl.net  Thu Dec  2 16:33:36 1999
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The Student Stipends for The 2000 Charleston Conferences have awarded and
the names of the winners are posted at http://www.netsci.org

The awards are made possible by Network Science, Cambridge Crystallographic
Data Centre and Chemical Computing Group.  The sponsors would like to thank
the numerous students and post doctoral fellows who participated.


From chemistry-request@server.ccl.net  Thu Dec  2 16:33:59 1999
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From: Jordi Villa <jorgevil@usc.edu>
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Dear cclers,

I wonder if there is some way to add external charges in GAMESS. Any
hint will be very welcome.

Jordi

--
Jordi Villa i Freixa
Department of Chemistry, University of Southern California
3620 S McClintock Av. #418; Los Angeles, CA, USA, 90089-1062
Tlf: 1-(213)-740 7671 Fax: 1-(213)-740 2701
jorgevil@usc.edu      http://futura.usc.edu/~jorgevil



From chemistry-request@server.ccl.net  Thu Dec  2 17:43:18 1999
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Jordi Villa wrote:
> 
> Dear cclers,
> 
> I wonder if there is some way to add external charges in GAMESS. Any
> hint will be very welcome.
> 
> Jordi
> 

Last time I checked there wasn't a standard way to do it. Some time ago
(Jordi -- my code may still be on Warshel's computers) I hacked up
GAMESS and added a common block that contained point charges, which
could then be piped through the nuclear attraction integrals in GAMESS.
This was an inelegant solution, but it got the job done.

Let me know if I can be of more help--I might be able to flip through
the GAMESS code and figure out a bit more if this is important to you. 
-- 
Richard P. Muller, Ph.D. 
rpm@wag.caltech.edu 
http://www.wag.caltech.edu/home/rpm
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Date: Thu, 02 Dec 1999 22:32:37 -0500
From: "Amadeu K. Sum" <sum@che.udel.edu>
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Subject: MOLSIM
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I have been searched unsuccessfully for some information
about MOLSIM (a molecular modelling program by P. Linse and
A. Wallqvist) in the web. Would anyone know of a pointer for
information about this program? 

Amadeu Sum
sum@udel.edu
