From chemistry-request@ccl.net Fri Jan 30 03:21:38 2004
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From: Szieberth Denes <dino~at~iris.inc.bme.hu>
To: Eric Hu <yhu_2003~at~yahoo.com>
cc: chemistry~at~ccl.net
Subject: Re: CCL:g98 error
In-Reply-To: <20040130011228.81604.qmail~at~web60108.mail.yahoo.com>
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> b3lyp/6-31++g**. I got the following error message
> although I have plenty of disk space:
>
> Erroneous write during file extend. write 188415
> instead of 4096
> Probably out of disk space.
> Write error in NtrExt1
>

Hi,
If you are working on a 32bit platform, g98 has a file size limit of 2GB.
Try to split the rwf file into several parts (look for the %rwf option in
the manual).

cheers,
dino





From chemistry-request@ccl.net Fri Jan 30 00:17:09 2004
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From: Matthew Zwier <matthew.zwier~at~hope.edu>
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CC: chemistry~at~ccl.net
Subject: Re: CCL:g98 error
References: <20040130011228.81604.qmail~at~web60108.mail.yahoo.com>
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Dear Eric,

What architecture are you running G98 on?  If it's a 32-bit platform and 
not specially (and officially-unsupported-ly) compiled, your SCR, INT,  
RWF, and D2E files are each limited to 2GB.  The number given is 
probably wraparound error as G98 increments its file pointer past the 
~2*2^31  position.  You can work around this as follows with Link 0 command:

%rwf=rwf01,2047MB,rwf02,2047MB,rwf03,2047MB... and so on, just so you 
don't total more than 16GB for each of %rwf, %int, %d2e, and %chk.

You can also try adding MaxDisk keywords to your route line (# 
method/basis ... ... MaxDisk=2040MB).

I've been bitten by this before, and used both solutions successfully, 
though the most efficient thing to do would be find a friend at an 
institution with a 64-bit supercomputer ...

Good luck!

Matt Zwier
Hope College

Eric Hu wrote:

>Hi I am doing a frequency calculation with
>b3lyp/6-31++g**. I got the following error message
>although I have plenty of disk space:
>
>  99 vectors were produced by pass 10.
>  99 vectors were produced by pass 11.
>  99 vectors were produced by pass 12.
>  99 vectors were produced by pass 13.
>  99 vectors were produced by pass 14.
>  90 vectors were produced by pass 15.
>  49 vectors were produced by pass 16.
>Erroneous write during file extend. write 188415
>instead of 4096
>Probably out of disk space.
>Write error in NtrExt1
>
>Eric
>  
>




From chemistry-request@ccl.net Fri Jan 30 03:40:43 2004
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Date: Fri, 30 Jan 2004 03:42:40 -0500
From: "Jan K. Labanowski" <jlabanow{at}nd.edu>
To: chemistry{at}ccl.net, microelectronics{at}asdn.net
Cc: jlabanow{at}nd.edu
Subject: TMS Electronic Materials Conference, Notre Dame, June 23-25
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	servernd.ccl.net

Only few days are left until the deadline for abstract submissions to the
TMS Electronic Materials Conference, Notre Dame, Indiana, USA,
June 23-25

For details, please see the Web site of the Conference:

   http://www.tms.org/Meetings/Specialty/EMC04/EMC04.html

See you in Notre Dame.

> From the Conference Announcement:

TMS Electronic Materials Conference, Notre Dame, June 23-25

The 46th Electronic Materials Conference (EMC) sponsored by the
Electronic Materials Committee of TMS will be held at Notre Dame
University, Notre Dame, Indiana from June 23 through June 25, 2004.

The conference will provide a forum for topics of current interest and
significance in the areas related to the preparation and characterization
of electronic materials. Individuals actively engaged or interested in
electronic materials research and development are encouraged to attend
this meeting, and papers in this general subject are solicited.
EMC/DRC

The Device Research Conference (DRC) and the Electronic Materials
Conference (EMC) of TMS will again coordinate activities. The DRC will be
held on Monday, June 21 through Wednesday, June 23, 2004. The EMC will be
held on Wednesday, June 23 through Friday, June 25, 2004. Device-oriented
papers should be submitted to the DRC and materials-oriented papers to
the EMC.

Inquires about DRC should be forwarded to:

Pallab Bhattacharya
University of Michigan
Department of Electrical Engineering and Computer Science
1301 Beal Avenue
Ann Arbor, MI 48109-2122
Tel: (734)763-6678
Fax: (734)763-9324
Email: pkb{at}eecs.umich.edu

The major thrust areas of the 2004 Electronic Materials Conference
in Notre Dame, Indiana include:

    * Wide bandgap semiconductor materials and device applications
    * Nanoscale science and technology in materials
    * Organic, molecular and nanotube-based materials and devices
    * Epitaxial growth
    * Contacts
    * Materials integration
    * Materials issues in advanced silicon technology
    * Narrow-bandgap semiconductors
    * Spin-dependent electronic materials
    * Materials issues for sensors

The Electronic Materials Conference (EMC) aims to provide the premier
annual forum for presentations of current interest and significance to
the preparation, characterization and application of electronic
materials. Research on semiconductors, dielectrics, metals, and molecular
materials is included within the conference scope. Individuals actively
engaged or interested in electronic materials research and development
are encouraged to submit papers and attend the conference. The attended
audience includes students, professors, scientists, engineers,
researchers, technicians, R&D managers, and product managers

ABSTRACT DEADLINE: FEBRUARY 3, 2004
Contact:
Edward Yu
University of California, San Diego
9500 Gilman Drive
ECE Dept MC 0407
La Jolla, CA 92093-0407
Tel: (858)534-6619
Fax: (858)822-3425
Email: ety{at}ece.ucsd.edu

Sent by:

Jan K. Labanowski, Ph.D.                  tel. (574) 631-5465
Science Computing Facility                 FAX (574) 631-9293
University of Notre Dame
Notre Dame, IN 46556-5670




From chemistry-request@ccl.net Thu Jan 29 22:40:26 2004
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From: "Kadir Diri" <kadir_at_visual1.chem.pitt.edu>
To: "Eric Hu" <yhu_2003_at_yahoo.com>, <chemistry_at_ccl.net>
References: <20040130011228.81604.qmail_at_web60108.mail.yahoo.com>
Subject: Re: CCL:g98 error
Date: Thu, 29 Jan 2004 22:42:19 -0500
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Hi!
How big is the *.rwf file? If you are using the 32-bit g98, even if you have
lots of scratch space, you cannot have files bigger than 2GB. If that is the
problem, you can split the *.rwf file into several files. Gaussian98 will
allow you to create max 8 such files, which means you can run jobs that use
at most 8x2=16 GB of disk space on 32-bit systems.
kadir


----- Original Message ----- 
From: "Eric Hu" <yhu_2003_at_yahoo.com>
To: <chemistry_at_ccl.net>
Sent: Thursday, January 29, 2004 8:12 PM
Subject: CCL:g98 error


> Hi I am doing a frequency calculation with
> b3lyp/6-31++g**. I got the following error message
> although I have plenty of disk space:
>
>   99 vectors were produced by pass 10.
>   99 vectors were produced by pass 11.
>   99 vectors were produced by pass 12.
>   99 vectors were produced by pass 13.
>   99 vectors were produced by pass 14.
>   90 vectors were produced by pass 15.
>   49 vectors were produced by pass 16.
> Erroneous write during file extend. write 188415
> instead of 4096
> Probably out of disk space.
> Write error in NtrExt1
>
> Eric
>
> __________________________________
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> http://webhosting.yahoo.com/ps/sb/
>
>
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>
>
>
>
>




From chemistry-request@ccl.net Fri Jan 30 04:32:05 2004
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From: "Stefan Bromley" <S.T.Bromley<<at>>tnw.tudelft.nl>
Organization: Delft University of Technology (TNW-DCT)
To: chemistry<<at>>ccl.net
Date: Fri, 30 Jan 2004 10:33:52 +0100
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Subject: Summary: Computational drug discovery
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	servernd.ccl.net

Dear CCL,

many thanks to all of you who responded to my request. For those of 
you who also asked me for a forward of the summary please find it 
below.

Cheers,

Stefan

> 
> Hi, CCLers!
> 
> Last week I posted a question asking for references of marketed 
drugs
> whose invention were largely aided by structure-based design 
methods.
> Most of the replies point to the following review article:
> 
> Larry Hardy & Antony Malikayil, The impact of structure-guided drug
> design on clinical agents, Current Drug Discovery, 2003, December,
> 15-20.
> http://www.currentdrugdiscovery.com/2003/december.html
> This paper discussed ~40 compounds developed with SBDD, seven of 
them
> are marketed drugs.
> 
> Here are some addtional examples: Crixivan (1,2), Viracept (3), 
Trusopt
> (4), Zanamivir (5,6)
> 
> 1. BD Dorsey, RB Levin, SL McDaniel, JP Vacca, JP Guare, PL Darke, 
JA
> Zugay, EA Emini, WA Schleif, JC. Quintero, JH Lin, I-W Chen, MK
> Holloway,
> PMD Fitzgerald, MG. Axel, D Ostovic, PS Anderson, JR Huff. L-
735,524:
> The
> Design of a Potent and Orally Bioavailable HIV Protease Inhibitor. 
J
> Med
> Chem 37:3443-3451, 1994.
> 
> 2. Holloway, M. K. et al. In Computer-Aided Molecular Design,
> Reynolds, C. H. et al., Eds. ACS Symp. Series 589:36-50, 1995.
> 
> 3. SW Kaldor, VJ Kalish, JF Davies, II, BV Shetty, JE Fritz, K
> Appelt, JA Burgess, KM Campanale, NY Chirgadze, DK Clawson, BA
> Dressman,
> SD Hatch, DA Khalil, MB Kosa, PP Lubbehusen, MA Muesing, AK Patick, 
SH
> 
> Reich, KS Su, JH Tatlock. Viracept (Nelfinavir Mesylate, AG1343): A
> Potent, Orally Bioavailable Inhibitor of HIV-1 Protease. J Med Chem
> 40:3979-3985, 1997.
> 
> 4. J Greer, JW Erickson, JJ Baldwin, MD Varney. Application of the
> Three-Dimensional Structures of Protein Target Molecules in
> Structure-Based Drug Design J Med Chem 37:1035-1054; 1994.
> 
> 5. von Itzstein, M.; Wu, W. Y.; Kok, G. B.; Pegg, M. S.; Dyason, J. 
C.;
> Jin,
> B.; Van Phan, T.; Smythe, M.; White, H. F.; Oliver, S. W.; Colman, 
P.
> M.;
> Varghese, J. N.; Ryan, D. M.; Woods, J. M.; Bethell, R. C.; Hotham, 
V.
> J.;
> Cameron, J. M.; Penn, C. R. Rational Design of Potent Sialidase-
based
> Inhibitors of Influenza Virus Replication. Nature, 363, 418-423 
(1993).
> 
> 6. M. von Itzstein, Jeffrey C. Dyason, Stuart W. Oliver, Hume F. 
White,
> 
> Wen-Yang Wu, Gaik B. Kok and Michael S. Pegg, A Study of the Active
> Site
> of Influenza Sialidase: An Approach to the Rational Design of Novel
> Anti-Influenza Drugs. J. Med. Chem., 39, 388-391, (1995).
> 
> Again, thanks for all of the responses!
> 
> With best regards,
> 
> Renxiao________________________________________________________

Dr Stefan T. Bromley
Laboratory of Applied Organic Chemistry and Catalysis
DelftChemTech, Delft University of Technology
Julianalaan 136, 2628 BL Delft
The Netherlands

Phone  : + 31 1527 89418
 
e-mail  : S.T.Bromley<<at>>tnw.tudelft.nl
________________________________________________________




From chemistry-request@ccl.net Fri Jan 30 09:23:11 2004
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Date: Fri, 30 Jan 2004 15:11:07 +0100 (MET)
From: Marcin Krol <mykrol~at~cyf-kr.edu.pl>
To: chemistry~at~ccl.net
Subject: CHARMM res number overflow
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	servernd.ccl.net

Dear CCL'ers

I tried to perform energy minimization of a protein molecule immersed in a
rectangular box of water molecules. The structure is after 1ns of MD.
After SD started I got the message RESIDUE NUMBER OVERFLOW, even though I
know it is impossible (I performed 1ns MD on exactly the same system and I
minimized the structure at the begininnig of MD). The command coor orient
helps a bit - I got this overflow message after a couple of minimization
steps. There must be a problem with orienting water with respect to
protein and/or image atoms. If you know how I could perform minimzation
and what the problem actually is, please let me know.

Thank you in advance
marcin

Dr Marcin Krol
Zaklad Biostatystyki Collegium Medicum UJ
Kopernika 7E
31-501 Krakow
tel/fax (012) 422-77-64


From chemistry-request@ccl.net Fri Jan 30 09:55:19 2004
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From: Jonathan Tennyson <j.tennyson|at|ucl.ac.uk>
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To: chemistry|at|ccl.net
Subject: CCP6 Booklet on "High Accuracy Potentials for Quantum Dynamics"
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	servernd.ccl.net

We recently organised a CCP1/CCP6/ChemReact Workshop at UCL on
"High Accuracy Potentials for Quantum Dynamics"
We have now produced a booklet containing short reviews by the
Workshop participants, and single copies of this are available
free of charge to interested researchers (until we run out).

The booklet is intended as an "introductory guide" rather than as
conference proceedings. Each invited speaker was asked to write a
brief summary of their work in the field and to set in context, in
a style that would be useful for researchers in related areas.

Copies have already been sent out automatically to the Workshop
participants and to everyone on the CCP6 Newsletter mailing list.

If you are not in either of the above groups and you would like a
copy, please email

Christine Johnston <christine.johnston|at|ucl.ac.uk>

Your email should include your _postal_ address in a format that
can easily be cut-and-pasted onto an address label.

-----------------------------------------------------------------------
High Accuracy Potentials for Quantum Dynamics"
edited by Andrea Miani, Jonathan Tennyson and Tanja van Mourik
published by CCP6, Daresbury, 2003.
107 pages

ISBN 0-9545289-0-5

Contents:

Ground-State Potential Energy Surfaces at the Focal Point
Attila G. Cs`sz`r

The Explicitly Correlated Coupled-Cluster
Models CC2-R12 and CCSD(R12)
Wim Klopper

Exploiting Systematic Basis Set Convergence for Accurate Potential Energy Surfaces
Kirk A. Peterson

Relativistic, Quantum Electrodynamic and Electroweak Effects in Molecules
H. M. Quiney

The Role of Born-Oppenheimer Breakdown Terms in the Prediction of Accurate
Transition Frequencies for Ordinary Molecules
David~W. Schwenke

The Asymptotic Regions of the Potential Energy Surfaces Relevant
for the O(3P) + O2(X3Sigmag-) -O3 and
O(3P) + OH(X2Pi) -O2(X3Sigmag-) + H(2S) Reactions
Claire Gillery and Pavel Rosmus

Two Exothermic Reactions in the {}``Lithium Chemistry'' Network:
LiH+H -Li+H2 and LiH+ + H -Li+ +H2. A Comparison of Computed
Potential Energy Surfaces.
E. Bodo, R. Martinazzo and F. A. Gianturco

Spectroscopic Determination of Ground and Excited State Potential Energy Surfaces.
K. Ahmed, G. G. Balint-Kurti and C. M. Western

> From Single- to Multi-Sheeted Potential Energy Surfaces: a
Dual Strategy for Accurate Global Forms
A. J. C. Varandas

Adiabatic and Diabatic Intermolecular Potentials
for Open-Shell Complexes and Their Applications.
J. Klos, W. Zeimen, V. Lotrich, G. C. Groenenboom and A. van der Avoird

Intermolecular Interaction Potentials
Krzysztof Szalewicz


Accurate Coupled-Cluster Potential Energy Surfaces:
Large Calculations on Cyclopropenylidene Anharmonicities
Timothy J. Lee and Christopher E. Dateo

Vibrational Effects on Molecular Properties:
the Dalton Approach
Trygve Helgaker and Torgeir A. Ruden, Dan Jonsson,
Kenneth Ruud, Peter R. Taylor and Per-Olof Astrand

Subwavenumber Accuracy for the Ab Initio Rotation-Vibration
Transitions of Water.
Oleg Polyansky

Analytical Energy Gradients for Internally Contracted Second-Order
Multi-reference Perturbation Theory (CASPT2)
Hans-Joachim Werner and Paolo Celani

Model Hamiltonians for Accelerating Orbital Basis Convergence
Peter J. Knowles

-----------------------
Jonathan Tennyson,
Department of Physics & Astronomy,       mailto:   j.tennyson|at|ucl.ac.uk
University College London,               Tel (work): +(44) 20 7679 7809
Gower Street,                            Tel (home): +(44) 20 8340 9225
London   WC1E 6BT, UK                    Fax (if you must): +(44) 20 7679 7145
http://www.tampa.phys.ucl.ac.uk/jonny




