From chemistry-request@server.ccl.net  Wed Feb  9 04:43:26 2000
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From: Daniel.Tunega@itc.univie.ac.at
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Date: Tue, 08 Feb 2000 20:36:36 +0000
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 Dear CCL users,

 I would like to summarize semiempirical codes (free, commercial, etc.) 
 proposed for periodic 2D/3D systems. 

 Thanks for each response.
-- 
 Daniel Tunega
 Institute for Theoretical Chemistry
 University of Vienna
 Waehringerstrasse 17
 A-1090 Vienna, Austria
 Phone: +43-1-4277-52754

From chemistry-request@server.ccl.net  Wed Feb  9 04:47:24 2000
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From: wlangen@vub.ac.be (Langenaeker W.)
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Subject: VCD spectra
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Dear all,
I'm doing some VCD calculations using Gaussian98. I've 
reproduced some examples from the literature, but now 
I want to start doing some original work.
I would like to know were I can have VCD spectra measured.
Thanks in advance.
Wilfried Langenaeker



From chemistry-request@server.ccl.net  Wed Feb  9 05:53:55 2000
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To: Computational Chemistry List <chemistry@ccl.net>
Subject: Meeting announcement: Modern software design ...
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        "Modern software design for scientific applications"

On Friday, March 31st, 2000, there will be a one day meeting held in the
Department of Nuclear Physics at Oxford University on the subject of
modern software design for scientific applications. Attendance of this
meeting is free. If you wish to attend please send an e-mail to Andrew
Horsfield at horsfield@fecit.co.uk in order to register.

The schedule of the meeting is:

10:00-10:55 Coffee

10:55-11:00 Andrew Horsfield (fecit)
            "Welcome"

11:00-12:00 Sven van den Bergh (fecit)
            "Java: an object oriented language"

12:00-12:30 Peter Chow (fecit)
            "Component approach to building an open software framework for
             mesh-based multi-physics simulations"

12:30-13:30 Lunch

14:00-15:00 Mike Rudgyard (Oxford Parallel)
            "Parallel Numerical Simulation and Integrated Problem Solving
             Environments"

15:00-15:30 David Bowler (Department of Physics and Astronomy, UCL)
            "Strategy for Linear Scaling Ab Initio Electronic Structure
             Calculations"

15:30-16:00 Tea

16:00-17:00 Terry Sloan (EPCC)
            "Integrated development environments and source code control."

  +----------------------------------------------------+
   Andrew Horsfield       e-mail: horsfield@fecit.co.uk 
     FECIT, 2 Longwalk Road, Stockley Park, Uxbridge,   
          Middlesex UB11 1AB, United Kingdom.           
   phone: +44-(0)181-606-4653  FAX: +44-(0)181-606-4422 
  +----------------------------------------------------+



From chemistry-request@server.ccl.net  Wed Feb  9 07:19:20 2000
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Message-ID: <01BF72F6.F2F691F0.jeanluc.verschelde@rug.ac.be>
From: Verschelde Jean-Luc <jeanluc.verschelde@rug.ac.be>
To: "'CCL'" <chemistry@ccl.net>
Subject: AMBER5.0 and MPICH
Date: Wed, 9 Feb 2000 12:12:27 +0100
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Dear all,

I installed and compiled AMBER5.0 and MPICH on a cluster of DEC alpha's with os Redhat linux 5.2.
When I start sander, I receive following message:

All processors started

     unknown flag: -p4wd                                                                           

     usage: sander  [-O] -i mdin -o mdout -p prmtop -c inpcrd -r restrt
                   [-ref refc -x mdcrd -v mdvel -e mden -inf mdinfo]
0 - MPI_ABORT : Null communicator
[0]  Aborting program !
[0] Aborting program!
p0_18892:  p4_error: : 197
bm_list_18893:  p4_error: interrupt SIGINT: 2
rm_l_3_3695:  p4_error: interrupt SIGINT: 2
rm_l_1_4471:  p4_error: interrupt SIGINT: 2
rm_l_2_4015:  p4_error: interrupt SIGINT: 2
p2_4014:  p4_error: interrupt SIGINT: 2
p3_3694:  p4_error: interrupt SIGINT: 2
p1_4470:  p4_error: interrupt SIGINT: 2


	I appreciate any help and would like to thank everybody who helped me before.


					Verschelde Jean-Luc



From chemistry-request@server.ccl.net  Wed Feb  9 12:58:07 2000
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Date: Wed, 9 Feb 2000 10:53:04 -0600
To: <chemistry@ccl.net>
From: "Robert E. Harris" <HarrisR@missouri.edu>
Subject: Re: Pseudorotation References So Far

I asked for information on pseudorotation in ring molecules, the motion
that moves the out-of-plane displacements around the ring without rotating
the ring.  I got some helpful references from those who responded to my
post.  Alas, I've lost their posts, so I can't thank them all.  (I'm
interested in the thermodynamics of large sulfur rings.  My remarks are of
course influences by my interest.)

What I have found most helpful has been Herbert L. Strauss, Ann. Rev. Phys.
Chem. 1983, 34:301-28.  Pseudorotation: A Large Amplitude Molecular Motion.
(I thank H. Strauss for his help, but he did not point this one out to me!)
This is very useful and has lots of references.  It is mostly concerned
with the motion I am interested in, but it does have some discussion of the
"pseudorotation" of the PF5 type.

Kilpatrick, J. E.; Pitzer, K. S.; Spitzer, R.  J. Am. Chem. Soc. 69,
2483-88 (1947).  The grand-daddy pseudorotation motion paper, devoted to
cyclopentane (thermodynamic orientation).   See  also 80,697 (1958) for
correction of the symetry number of cyclopentane.

Cremer, D.; Pople, J. A.  J. Am. Chem Soc. 97, 1354-8 (1975).  They give a
generalized coordinate system for describing ring puckering, but not
directly applied to pseudorotation as a motion..  The coordinate system is
useful for defining the pseudorotation angle, so it is a useful paper for
the discussion of the motion.  One should also look at earlier papers by H.
M. Pickett and H. L. Strauss, J. Am. Chem. Soc. 92, 7281-90 (11970) and J.
Chem. Phys.55, 324-34 (1971).

Several articles in Conformational Behavior of Six-Membered Rings (E.
Juaristi, ed., VCH, 1995) also merit attention for discussions of motions
in six member rings, particularly "100+ Years of Conformational Analysis"
by E. L. Eliel (pp. 1-24) and  "Ab Initio Studies of Six-Membered Rings:
Present Status and Future Developments" by D.Cremer and K. J. Szabo (pp.
59-136).  There are a lot of references, as well as many nice illustrations
in these articles.  The other articles in this volume are interesting,
also.

Robert E. Harris  Phone: 573-882-3274  Fax:  573-882-2754
Department of Chemistry, University of Missouri-Columbia
Columbia, Missouri, USA 65211



From chemistry-request@server.ccl.net  Wed Feb  9 14:02:29 2000
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From: Bjoern Rabenstein <rabe@chemie.fu-berlin.de>
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Subject: Summary: Simple program for editing protein structure
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Dear CCLers!

A little bit late, but here it is:

I asked for simple and cheap programs for interactively editing protein
structure on a low level (e.g. modifying torsion angles, but not doing
mutations).

There are a lot of programs that do what I want. Of course, most of them
do a lot more. However, there is no ideal case (does what I need && free
&& open source && runs without problems or limitations)...

The free part:

- SWISS-PDBVIEWER: no source, binaries available for IRIX, Linux, 
  MacOS and "PC" (which probably means Windows :)
  http://www.expasy.ch/spdbv/
  (thanks to Osmar Norberto de Souza <osmarns@lnls.br> and Nick Rhodes
  <N.Rhodes@sheffield.ac.uk>)

- ICMLITE: only the "lite" version is free, no source, available for 
  IRIX, Win95/NT, Linux (Intel + PPC) Dec-Unix, Solaris
  I could not try the program since I got the following error message;
    can't resolve symbol '__register_frame_info' 
  (even if I preload a special libregframe.so supposed to fix this)
  http://www.molsoft.com/
  (thanks to Renxiao Wang <renxiao@chem.ucla.edu>)

- MODIFIED RASMOL: a enhanced version of RasMol based on the old
  version 2.6. No source, Binaries fo MacOS, "PC" (s.o.), Linux, DEC-Unix
  HP-UX, -->>Unix-versions for 8bit display only<<--
  http://mc2.CChem.Berkeley.EDU/Rasmol/
  (thanks to Rick Venable <rvenable@deimos.cber.nih.gov>)

- MOILVIEW:  with source, but it uses SGI-GL, so it will
  only compile on SGI machines and some IBM RS/6000.
  http://morita.chem.sunysb.edu/~carlos/moil-view.html
  (thanks to Carlos Simmerling <carlos.simmerling@sunysb.edu>)

- MOLDEN: This is more suitable for small molecules. With
  large molecules like proteins, it is very slow.
  http://www.cmbi.kun.nl/~schaft/molden/pdb3.html
  (thanks to Gijs Schaftenaar <schaft@cmbi.kun.nl>)

The expensive part:

- MIDAS: academic license $350.
  http://www.cgl.ucsf.edu/Outreach/midasplus/
  (thanks to Jeffrey P. Jones, jpj@wsu.edu)

- COSMOS: only available for Windows, academic about DM 1000 ($500).
  http://www.cosmos-software.de/
  (this we already knew by ourselves)

Two of you gave me the following hint, but I'm not sure, if this is what I
wanted:

- MMTK: I was already aware of this free and open source toolkit of Konrad
  Hinsen. But as far as I have understood, it is suitable to modify a
  molecular structure by scripts. Indeed, this is what I do usually,
  but this time I needed a tool to rotate a part of a molecule and watch
  it moving (to say "stop!" at the right moment). Perhaps such a tool 
  could easily be assembled using MMTK, but I don't know if anybody has
  already done it.
  http://dirac.cnrs-orleans.fr/MMTK/
  (thanks to Konrad Hinsen <hinsen@cnrs-orleans.fr> and Richard P. Muller
  <rpm@wag.caltech.edu>)

Thanks again for all the hints!
-- 
Bjoern Rabenstein * PhD student * Freie Universitaet Berlin * Fachbereich
Biologie/Chemie/Pharmazie * Inst. f. Chemie * Takustr. 6 * D-14195 Berlin
[email] rabe@chemie.fu-berlin.de                 [phone] +49-30-838-53484
[WWW] http://lie.chemie.fu-berlin.de/~rabe/        [fax] +49-30-838-53464


From chemistry-request@server.ccl.net  Wed Feb  9 14:51:32 2000
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Date: Wed, 09 Feb 2000 10:09:14 -0800
To: CHEMISTRY@ccl.net
From: "Jeffrey L. Nauss" <jnauss@msi.com>
Subject: Advanced Hypothesis and 3D Database Techniques Workshop
Cc: omoshile@msi.com
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Molecular Simulations Inc. will be holding a 2-day "Advanced Hypothesis and
3D Database Techniques Workshop."  The workshop will held March 23-24, 2000
at the San Diego Supercomputer Center, San Diego, CA.  This workshop is
designed to provide attendees with a better understanding of
structure-activity relationships and how to best exploit the most useful
features within Catalyst. Lectures presenting the methodologies and
examples of their application to solve real-world problems will be followed
by hands-on/discussion periods during which attendees can work though
tutorials or discuss their own work with experts from Molecular Simulations. 

Attendees should possess knowledge of basic UNIX commands and have a basic
understanding of QSAR theory.

Fees for the 2-day course are $1000 commercial, $500 government, and $400
academic.

Further detailed information about this and other MSI training workshops,
as well as on-line course registration, can be found at MSI's website
(http://www.msi.com/about/events/training).  Please do not hesitate to
contact me should you have any questions.

Thank you very much.

--
Jeffrey L. Nauss, PhD		Phone: (858) 799-5555
Customer Training Programs		Fax: (858) 458-0136
Molecular Simulations Inc.		E-mail: jnauss@msi.com
9685 Scranton Road			http://www.msi.com/about/events/training
San Diego, CA 92121



From chemistry-request@server.ccl.net  Wed Feb  9 14:51:35 2000
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Date: Wed, 09 Feb 2000 10:15:50 -0800
To: CHEMISTRY@ccl.net
From: "Jeffrey L. Nauss" <jnauss@msi.com>
Subject: MSI Life Science Workshops in New Jersey
Cc: tlyons@msi.com, rixin@msi.com
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Molecular Simulations Inc. will be holding a pair of 2-day workshops at
Rutgers University, New Brunswick, NJ. 

On March 14-15, the workshop "Life Science Modeling in Insight II" will be
offered.  This course provides an overview of molecular modeling techniques
for life sciences applications in the Insight II graphical user
environment.  Prior modeling experience is not assumed making this course a
great place to start molecular modeling. 

On March 16-17, the "Homology Based Protein Design" training will be
offered. This workshop is relevant to any of our customers who are
interested in predicting protein structure and who would like to make more
effective use of modeling in their work. During the two-day workshop, the
process of producing a three-dimensional model from a primary amino acid
sequence will be covered step-by-step.  Prerequisites for this course are
the "Life Science Modeling in Insight II" workshop or extensive experience
with Insight II.

Fees for each 2-day course are $1000 commercial, $500 government, and $400
academic.  However, register for both courses and receive a 50% discount
for the second course.

Further detailed information about this and other MSI training workshops,
as well as on-line course registration, can be found at MSI's website
(http://www.msi.com/about/events/training).  Please do not hesitate to
contact me should you have any questions.

Thank you very much.

--
Jeffrey L. Nauss, PhD		Phone: (858) 799-5555
Customer Training Programs		Fax: (858) 458-0136
Molecular Simulations Inc.		E-mail: jnauss@msi.com
9685 Scranton Road			http://www.msi.com/about/events/training
San Diego, CA 92121



From chemistry-request@server.ccl.net  Wed Feb  9 18:16:06 2000
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Date: Wed, 09 Feb 2000 14:07:01 -0800
To: chemistry@ccl.net
From: "Jeffrey L. Nauss" <jnauss@msi.com>
Subject: MSI Material Science Workshop in North Carolina
Cc: Stephen Todd <stodd@msi-eu.com>
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Molecular Simulations Inc. will be holding a 3-day "Materials Science
Applications using Cerius2" workshop on March 8th-10th, 2000 at the North
Carolina Supercomputing Center, Research Triangle Park, North Carolina.
This workshop is relevant to any of our customers who are interested in an
introduction to materials science applications using Cerius2. During the
three-day workshop, we will be covering the basics of molecular modeling
including molecular mechanics and dynamics, polymer modeling applications
and quantum mechanics applications. The course will be split into one day
on each of the above areas.

Fees for the 3-day course are $1500 commercial, $750 government, and $600
academic.

Further detailed information about this and other MSI training workshops,
as well as on-line course registration, can be found at MSI's website
(http://www.msi.com/about/events/training).  Please do not hesitate to
contact me should you have any questions.

Thank you very much.

				- Stephen Todd
				  MSI Training Programs

				  (+44) 1223 507568


--
Jeffrey L. Nauss, PhD		Phone: (858) 799-5555
Customer Training Programs		Fax: (858) 458-0136
Molecular Simulations Inc.		E-mail: jnauss@msi.com
9685 Scranton Road			http://www.msi.com/about/events/training
San Diego, CA 92121



From chemistry-request@server.ccl.net  Wed Feb  9 19:41:10 2000
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Date: Wed, 9 Feb 2000 15:43:05 -0800 (PST)
From: Renxiao Wang <renxiao@chem.ucla.edu>
Reply-To: Renxiao Wang <renxiao@chem.ucla.edu>
To: Computational Chemistry List <chemistry@ccl.net>
Subject: Anybody agrees with me?
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Dear CCLers,

Have you got tired of learning how to use a new molecular modeling
software? I have. 

Of course if a certain software can cover all the aspects of your research
and you always stick to it, you will not complain like me. If so, you are
lucky! But if you have to apply multiple softwares to your work, you will
always waste time on something rather than science. For instance, if you
want to rotate a bond of your molecule in a certain way by using a
software that you are not familiar with, you probably have to search all
the menus and buttons, or even worse, go through piles of manuals to
finally make it. 

Maybe you will argue that every software has its own advantages and
disadvantages. I agree. But this should not be the reason why those
softwares are so different in interface! I have experience in using quite
many molecular modeling softwares, such as QUANTA, Cerius2, InsightII,
Sybyl, Spartan, and MacroModel, no speaking of other "simpler" programs,
such as RasMol, Molgen, and etc. In my personal view, Spartan is the most
user-friendly, Biosym's products are generally very complicated, while
MacroModel is the worst in worst.

Actually these softwares overlap each other considerably. I just cannot
help wondering why the guys who develop these molecular modeling softwares
have not met together and defined a "standard". This standard could be a
uniformed but expandable interface or framework, which at least covers all
the "basic" elements of molecular modeling that have already been
well-established (such as how to manipulate the molecule, how to color and
display the molecule, how to perform minimization, MC and MD, and etc). I
am sure there is no technical problem to do so. 

Take the computer industry as an example. If they had not had such a
standard at the very beginning (proposed by IBM, right?), maybe today we
are using dozens of different style computers. That would be a chao! Take
MicroSoft as another example. Although they make too much money, :-) they
have done an excellent job to help "unifying" the interface of most
current softwares. Therefore a software seems less confusing when we try
to use it for the first time. 

So if such a "standard" for molecular modeling programs does exist, it is
good for the users, because they will complain less; it is also good for
the programmers, because they will be able to concentrate on developing
new algorithms rather than re-inventing the wheel; and I believe it is
also good for the sellers, because the molecular modeling softwares can
become more popular in this way.

Any comment?

Best wishes,

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| Dr. Renxiao Wang                                                     | 
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| Department of Chemistry and Biochemistry | 3281 Sawtelle Blvd. #104  | 
| University of California Los Angeles     | Los Angeles, CA90066      | 
| Los Angeles, CA 90024                    | U.S.A                     | 
| Phone: 310-8250269 (Lab)                 | Phone: 310-3904638 (Home) | 
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| E-mail: renxiao@chem.ucla.edu                                        | 
| WWW: http://zimbu.chem.ucla.edu/~arthur/                             |
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