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From: meiselba <Heike.Meiselbach@organik.uni-erlangen.de>
Subject: free energy perturbation with Amber 5 
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Hello,

I test the Gibbs-Modul from Amber 5.0 with the valine to alanine FEP 
tutorial from the Amber website 
(http://www.amber.ucsf.edu/amber/tutorial/gibbs_box/HTML/xleap_edit_selected.html).
But I don't understand the perturbation charges.
Can you tell me, why the pert.charge in the tutorial for CB is 0.105 and 
not the charge for alanine (CB -0.1825)? Why are the other charges not 
changed as well?
My last question, what is the actual result (kcal/mol) for this simulation 
(valine to alanine)?

Thank you in advance,
Heike Meiselbach



Computer-Chemie-Centrum,
Friedrich-Alexander-Universitaet Erlangen-Nuernberg
Naegelsbachstraße 25
D-91052 Erlangen





From chemistry-request@server.ccl.net Fri Dec 13 09:27:09 2002
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From: "Liu, Zhanwu" <LiuxZx@anes.upmc.edu>
To: "'CHEMISTRY@ccl.net'" <CHEMISTRY@ccl.net>
Subject: Gaussian98 MP2 warning
Date: Fri, 13 Dec 2002 09:26:53 -0500
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Dear all, 

When I was running Gaussian98W to calculate MP2 energy, there is a warning:

**** Warning!!: The largest alpha MO coefficient is  0.49882375D+02

What does this warning mean? Will it affect the calculation results?
Thanks!

Yours Zhanwu
-----------------------------
Zhanwu Liu, Ph.D.
Department of Anesthesiology
University of Pittsburgh
Phone: 412-648-9137
Fax:   412-648-9587



From chemistry-request@server.ccl.net Fri Dec 13 04:42:27 2002
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To: gamercier@yahoo.com
Cc: pyquante-users@lists.sourceforge.net, pymol-users@lists.sourceforge.net,
   mmtk@python.net, chemistry@ccl.net
Subject: Re: [MMTK] [PyMOL] improving interoperability between python molecule toolkits (fwd)
References: <20021212183033.56193.qmail@web80301.mail.yahoo.com>
From: Konrad Hinsen <hinsen@cnrs-orleans.fr>
Date: 13 Dec 2002 10:41:30 +0100
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Gustavo Mercier <gamercier@yahoo.com> writes:

> to the chemistry of a problem. In advanced undergraduate course, an
> instructor may wish to breakthrough the "black box". The scripting

*Should* wish to do so. Understanding what one is doing is the
difference between a scientist and a lab technician.

> this effort. Unfortunately, the issue is one of leadership to
> initiate such a project. May be those who mantain MMTK, PyQuante,
> PyMol, etc. may be willing to take the initiative.

This issue has been addressed at a meeting on OpenSource software for
atomistic simulations (which includes physics and chemistry) this
year. The result is the formation of an informal organization called
"FSAtom": http://www.fsatom.org/ Among the goals of this organizations
is the design of common interfaces to ensure the interoperability of
OpenSource codes. There will be more meetings (not committee style,
but scientific workshops) as well as mailing list discussions.
Everybody is welcome to join.

> may go along way to make development not only easier but useful. It
> would be best not to rediscover the wheel.

And come up with a hexagon ;-)

> As a suggestion, let's consider the chemistry implementation of XML
> -- CML. Whatever the details of the object "molecule", it would be
> beneficial to input and output to/from CML. A specification of

I don't agree. I looked at CML a while ago, thought about implementing
it in MMTK, but quickly found out that almost none of the information
I needed to store about molecules could be represented in CML, except
by adding "conventions" of my own - but then I could just as well
define my own XML format. CML is based on the right intentions, but is
too weak as an implementation.

BTW, common file formats are another goal of the FSAtom organization.

Konrad.
-- 
-------------------------------------------------------------------------------
Konrad Hinsen                            | E-Mail: hinsen@cnrs-orleans.fr
Centre de Biophysique Moleculaire (CNRS) | Tel.: +33-2.38.25.56.24
Rue Charles Sadron                       | Fax:  +33-2.38.63.15.17
45071 Orleans Cedex 2                    | Deutsch/Esperanto/English/
France                                   | Nederlands/Francais
-------------------------------------------------------------------------------


From chemistry-request@server.ccl.net Fri Dec 13 12:21:42 2002
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Subject: Re: [Pyquante-users] Re: [MMTK] [PyMOL] improving interoperability between python molecule toolkits (fwd)
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To: Konrad Hinsen <hinsen@cnrs-orleans.fr>
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On Friday, December 13, 2002, at 01:41  AM, Konrad Hinsen wrote:
>
>> As a suggestion, let's consider the chemistry implementation of XML
>> -- CML. Whatever the details of the object "molecule", it would be
>> beneficial to input and output to/from CML. A specification of
>
> I don't agree. I looked at CML a while ago, thought about implementing
> it in MMTK, but quickly found out that almost none of the information
> I needed to store about molecules could be represented in CML, except
> by adding "conventions" of my own - but then I could just as well
> define my own XML format. CML is based on the right intentions, but is
> too weak as an implementation.
>
> BTW, common file formats are another goal of the FSAtom organization.


Konrad,

Thanks for the reminder about FSAtom. Maybe we should start a 
discussion somewhere about what needs to be included in either a common 
file format or a common interface.

R.

Rick Muller
rpm@wag.caltech.edu
http://wag.caltech.edu/home/rpm



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2002 Dec 13

A summary of three messages explaining the "WARNING!!: The largest alpha
MO coefficient..."
message should be in the CCL archives for 23 April 2002  08:56:51

E. Lewars
=============



From chemistry-request@server.ccl.net Fri Dec 13 11:20:10 2002
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From: "Jens Spanget-Larsen" <spanget@virgil.ruc.dk>
Organization: Roskilde Universitetscenter
To: Henrik Nilsson <henrikn@fy.chalmers.se>
Date: Fri, 13 Dec 2002 17:19:34 +0100
Subject: Re: CCL:HF/Sadlej calculations
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Henrik Nilsson :

> Has anyone experienced redicolous values of the mulliken charges
> calculated by ab initio quantum mechanical methods with
> HF/Sadlej-pvz basis set? Here is an example and corresponding data
> calculated with HF/6-31G*. The Lowdin charges are similar but the
> mulliken are totally off. 

Mulliken charges depend on the basis set and tend to diverge on 
increasing the number of functions. When diffuse functions are 
included, the Mulliken population analysis may give meaningless 
results. - See f.inst. Frank Jensen's book on computational 
chemistry.

Jens >--< 

=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=
JENS SPANGET-LARSEN         Office:         +45 4674 2710
Department of Chemistry     Fax:            +45 4674 3011
Roskilde University (RUC)   Mobile:         +45 2320 6246
P.O.Box 260                 E-Mail:        spanget@ruc.dk
DK-4000 Roskilde, Denmark   http://virgil.ruc.dk/~spanget
=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=


From chemistry-request@server.ccl.net Fri Dec 13 13:45:59 2002
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Date: Fri, 13 Dec 2002 13:45:51 -0500
From: Mihaly Mezei <mezei@inka.mssm.edu>
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Subject: Re: CCL:HF/Sadlej calculations
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> > Has anyone experienced redicolous values of the mulliken charges
> > calculated by ab initio quantum mechanical methods with

> Mulliken charges depend on the basis set and tend to diverge on

A good while ago E. Campbell and myself derived the equations and wrote
the program to partition charge densities by planes placed between pairs
of atoms. The paper (Theoret. Chim. Acta, Vol 43 pp 227-237 (1977) and the
program (MOMENTS) is available at

http://inka.mssm.edu/~mezei/maxwell

Mihaly Mezei,

Dept. of Physiology & Biophysics, Mount Sinai School of Medicine
           Voice: (212) 241-2186     Fax: (212) 860-3369|
                 WWW (MSSM home): http://
 adsr13.mssm.edu/domains/dept/facultyInfo.epl?objname=physbio&user=mezeim01
    WWW (Lab home - software, publications): http://inka.mssm.edu/~mezei


From chemistry-request@server.ccl.net Fri Dec 13 19:08:52 2002
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Date: Sat, 14 Dec 2002 09:39:19 +0930
From: Brian Salter-Duke <b_duke@octa4.net.au>
To: Comp Chem List <CHEMISTRY@ccl.net>
Subject: Strange G98 disk file error.
Message-ID: <20021214000802.GB2307@bsalterduke1>
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I have recently done two calculations (CCSD[T]) single point on the same
molecule with two different basis sets. The one with the large basis set
6-311G(3d2f,2p) worked using about 3GB for the rwf file. The smaller
6-311G(2d2f,p) fails eating up as much disk space (8 2GB files) as I can
give it. The diff output between the two logs files has nothing
exceptional until:-

<  Estimate disk for full transformation  -129744316 words.
---
>  Estimate disk for full transformation  1059608561 words.
336,344c339,638
<  ModeAB=           4 MOrb=             1 LenV=      10967042
<  LASXX=    287208687 LTotXX=   417057574 LenRXX=   447333938
<  LTotAB=    30276364 MaxLAS=   448434000 LenRXY=           0
<  NonZer=   604693738 LenScr=   918007649 LnRSAI=     3986080
<  LnScr1=    16946162 MaxDsk=   786432000 Total=   1386273829
<  SrtSym=           T ITran=            5
<  No file to extend for IUnit=  1 -- out of disk space.
<  Error termination in NtrErr:
<  NtrErr called from NtrExt.
---
>  ModeAB=           4 MOrb=            11 LenV=      10733153
>  LASXX=     43752820 LTotXX=    43752820 LenRXX=    88016189
>  LTotAB=    44263369 MaxLAS=    60557156 LenRXY=           0
>  NonZer=   131769009 LenScr=   208386667 LnRSAI=    60557156
>  LnScr1=   101568887 MaxDsk=   786432000 Total=    458528899
>  SrtSym=           T ITran=            4
>  JobTyp=0 Pass  1:  I=   1 to  11.
>  Spin components of T(2) and E(2):
>      alpha-alpha T2 =       0.1774287359D-01 E2=     -0.4284075673D-01
>      alpha-beta  T2 =       0.1465056746D+00 E2=     -0.4085211273D+00
>      beta-beta   T2 =       0.1774287359D-01 E2=     -0.4284075673D-01
>  ANorm=    0.1087194289D+01
>  E2=       -0.4942026408D+00 EUMP2=       -0.10500304138370D+03
--- etc finishing the CCSD[T] run.

Note the -ve disk at the top in the failed run. Does anyone have any
idea what is going on? 

The system is linux G98-A-7 compliled with Portland Compiler on a
Pentium III machine but now running on a Pentium IV.

Regards, Brian.

-- 
            Brian Salter-Duke (Brian Duke) b_duke@octa4.net.au  
  Honorary Fellow in Chemistry, NT University, Darwin, NT 0909, Australia.
             Post: Box 1028, Humpty Doo, NT 0836, Australia.
Phone 08-89881600.  Fax 08-89881302.  http://www.octa4.net.au/linden/brian/

From chemistry-request@server.ccl.net Fri Dec 13 20:32:49 2002
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Date: Fri, 13 Dec 2002 20:32:49 -0500 (EST)
From: Jan Labanowski <jkl@ccl.net>
To: chemistry@ccl.net, mel@asdn.net
cc: Jan Labanowski <jkl@ccl.net>, alex.volinsky@motorola.com
Subject: 2003 ASME Summer Meeting of the Applied Mechanics and Material
 Division
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CALL FOR PAPERS

2003 ASME Summer Meeting of the Applied Mechanics and Material Division
June 17-20, 2003 Scottsdale, AZ.

Abstract due date: February 15, 2003
Conference website: www.eas.asu.edu/~cpd/conference.html

Symposium on Characterization and Mechanical Reliability of
     Advanced Electronic Materials at Nanoscale

Symposium organizers:
   Alex A. Volinsky, Motorola (alex.volinsky@motorola.com),
   Jun He, Intel (jun.he@intel.com), and
   Harley Johnson, University of Illinois at Urbana-Champaign,
           Department of Mechanical and Industrial Engineering (htj@uiuc.edu)

Rapid advances in microelectronics and MEMS pose great materials and
mechanical challenges. In microelectronic or MEMS devices materials are in the
form of nanoscale structures with a significant volume comprised of
interfaces, surfaces, and grain boundaries resulting in properties vastly
different from their bulk counterparts. Phenomena observed in these structures
include plasticity, fracture, adhesion failures and mass transport. The device
materials have to withstand multiple temperature cycles, as well as mechanical
stresses imposed during processing, packaging, and in operation. Phenomena
like electro and stress migration become extremely important as the features
get smaller.

Characterizing advanced materials in microelectronics and MEMS becomes
extremely challenging, as one has to operate almost on the angstrom scale.
Previously routine tasks such as film thickness measurement now require
development of novel characterization techniques. There is an objective need
to bring academia and industry together in solving these problems. Symposium
topics include, but are not limited to:

- Structure-properties relationship at the nanoscale

- Elasticity, plasticity, adhesion and fracture at nanoscale

- Stress-induced effects in thin films

- Electromigration and stress migration in metallic interconnects

- Mechanical stability and reliability of low-K dielectrics

- New methods of physical properties characterization at nanoscale

- Tribological properties of nanostructured materials

- Yield enhancement for advanced electronic devices

- Theoretical, computational and analytical modeling

- Relationships between processing, composition, structure, and mechanical
  properties








From chemistry-request@server.ccl.net Fri Dec 13 18:42:56 2002
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Date: Sat, 14 Dec 2002 01:42:50 +0200 (EET)
From: Arvydas Tamulis <tamulis@mserv.itpa.lt>
To: CHEMISTRY@ccl.net
Subject: Tree valence atoms with I= 0 or 1/2 
Message-ID: <20021214014212.I82548-100000@mserv.itpa.lt>
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Dear Netters,

I am looking for possibilities to replace C atom by three valent atom in
the benzene ring for the organizing stable radical. The nucleus spin of this
inserted three valent atom must be equal to 0 or 1/2.

Unfortunately I did not found nucleus spin of S(32 isotope) in the
WEBsite:  http://www.chimorg.unifi.it/~chimichi/O.html

Maybe you know the nucleus spins of S(32 isotope) and S(34 isotope)?

Other possibility exist to replace C atom by P(31 isotope) with nucleus
Spin=1/2, but I do not know how stable should be such the readical with P
atom in the carbon ring (I am not expert in chemistry and never saw the P
atms in the carbon rings). Maybe you can confirm that such a radical should
exist?

Maybe you know other possibilities to replace C atom by other three
valence atoms in the benzene ring wich possess nucleus spins = 0 or 1/2 ?

Thanking your in advance.
With best regards, Arvydas Tamulis
*******************************************************************
                  Arvydas Tamulis

Doctor of Natural Sciences, senior research fellow

Temporal address until 28 February 2003:
Los Alamos National Laboratory
Center for Nonlinear Studies
P.O. Box 1663, Mail Stop B258
Los Alamos, New Mexico 87545
Work Phone: (505) 667-7278
Fax: (505) 665-2659
e-mail: tamulis@cnls.lanl.gov
*******************************************************************





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From: "Carsten Detering" <detering@u.washington.edu>
To: <chemistry@ccl.net>
Subject: AutoDock Linux Problem
Date: Sat, 14 Dec 2002 01:02:48 +0100
Organization: University of Washington
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Hi all,

I am currently busy compiling Autodock on Redhat Linux 8. Everything =
worked fine. Only the mol2fftopdbq is giving me (again) a hard time. I =
know that this problem has been posted before, however, I couldnt find a =
satisfying answer. Changing from gawk to awk or nawk didnt solve the =
problem, neither did gawk --traditional (like in the answers I fouund).
by executing, I get the following error message:

mol2fftopdbq.awk:90: fatal: expression for =B4<' redirection has null =
string value.

I looked in the awk file, but couldnt find anything suspicious.
Anybody any idea how to fix that???

Thanks in advance,

Carsten
~~~~~~~~~~~~~~~~~~~~~~~~~~~
Carsten Detering, Ph.D.
University of Washington
Seattle, WA 98195
Phone 206-543-5081
Fax 206-685-8665
email detering@u.washington.edu
~~~~~~~~~~~~~~~~~~~~~~~~~~~

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<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN">
<HTML><HEAD>
<META http-equiv=3DContent-Type content=3D"text/html; =
charset=3Diso-8859-1">
<META content=3D"MSHTML 6.00.2715.400" name=3DGENERATOR>
<STYLE></STYLE>
</HEAD>
<BODY bgColor=3D#ffffff>
<DIV>Hi all,</DIV>
<DIV>&nbsp;</DIV>
<DIV>I am currently busy compiling Autodock on Redhat Linux 8. =
Everything worked=20
fine. Only the mol2fftopdbq is giving me (again) a hard time. I know =
that this=20
problem has been posted before, however, I couldnt find a satisfying =
answer.=20
Changing from gawk to awk or nawk didnt solve the problem, neither did =
gawk=20
--traditional (like in the answers I fouund).</DIV>
<DIV>by executing, I get the following error message:</DIV>
<DIV>&nbsp;</DIV>
<DIV>mol2fftopdbq.awk:90: fatal: expression for =B4&lt;' redirection has =
null=20
string value.</DIV>
<DIV>&nbsp;</DIV>
<DIV>I looked in the awk file, but couldnt find anything =
suspicious.</DIV>
<DIV>Anybody any idea how to fix that???</DIV>
<DIV>&nbsp;</DIV>
<DIV>Thanks in advance,</DIV>
<DIV>&nbsp;</DIV>
<DIV>Carsten</DIV>
<DIV>~~~~~~~~~~~~~~~~~~~~~~~~~~~<BR>Carsten Detering, =
Ph.D.<BR>University of=20
Washington<BR>Seattle, WA 98195<BR>Phone 206-543-5081<BR>Fax=20
206-685-8665<BR>email <A=20
href=3D"mailto:detering@u.washington.edu">detering@u.washington.edu</A><B=
R>~~~~~~~~~~~~~~~~~~~~~~~~~~~</DIV></BODY></HTML>

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