From chemistry-request@ccl.net Mon Apr  4 04:20:00 2005
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Subject: how to do the excited calculation with ADF package?
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hello,

Does someone know how to do the excited calculation in ADF package?
For example, i want to deal with the transition metal complex:[NH3)5Ru-
Pyrazine-Ru(NH3)5]5+, the ground state is calculated to be a single 
electron occupying in the Ru-dxz orbital, and zero electron occupying 
Ru-dz2 orbital, then i want to get the excited state with exciting the 
electron in Ru-dxz orbital to Ru-dz2 orbital? how to get the excited 
state? 

Thank you very much!

----------------------------------
HaiYan Wei
Ph. D.
College of Chemistry and Molecular Engineering
Peking University, Beijing 100871,
P. R. China
Tel: 86-10-6276-5703
Email: weihy !=! hpsv.pku.edu.cn


From chemistry-request@ccl.net Mon Apr  4 08:46:05 2005
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Hello

I am trying to generate an eletrostatic potential surface using Gaussian 03.
I have generated the formatted checkpionfile and, now I want to use the cubegen
funktion. My file lookes like this:

cubegen 0 density 4-HF-F-enamine.FChk 4-HF-F-enamine1_dens.cube 80 h

But it nevers starts and I get the message:

No route card found.

What am I doing wrong?

Anne





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From: Eric Hu <eric.y.hu /a\ gmail.com>
Reply-To: Eric Hu <eric.y.hu /a\ gmail.com>
To: chemistry /a\ ccl.net
Subject: Re: CCL:desolvation energy table for amino acids
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Thank you, Cheriff and Sandeep. Your comments are very helpful.

Best regards,
-Eric

On Apr 3, 2005 12:12 PM, SANDEEP KUMAR <skumar23 /a\ jhem.jhu.edu> wrote:
> Hi Cheriff,
> 
> I am sorry,  I  can't recall  specific references, but  its there in his papers /reviews with privalov in early 1990s.  I did a quick pubmed search and came up with the following:
> 
> Privalov PL, Makhatadze GI.
> Contribution of hydration to protein folding thermodynamics. II. The entropy and Gibbs energy of hydration.
> J Mol Biol. 1993 Jul 20;232(2):660-79.
> PMID: 8393941 [PubMed - indexed for MEDLINE]
> 
> Makhatadze GI, Privalov PL.
> Contribution of hydration to protein folding thermodynamics. I. The enthalpy of hydration.
> J Mol Biol. 1993 Jul 20;232(2):639-59.
> 
> But  I also remember reading more papers by him which deal with the effect of  substituting polar/non-polar amino acids on the heat capacity of Ubiquitin.  That work is more recent.   He also has a big table compiled in Biophyiscal Chemistry  on heat capacities of various polar and non-polar compounds. I guess the reference for that work is:
> 
> Makhatadze GI.
> Heat capacities of amino acids, peptides and proteins.
> Biophys Chem. 1998 Apr 20;71(2-3):133-56.
> 
> I think this is slightly off  from the original question on CCL but still quite useful.
> 
> Sincerely,
> Sandeep
> 
> -------------------------------------------------------------------
> Dr. Sandeep Kumar,
> Associate Research Scientist,
> Johns Hopkins University Department of Biology,
> 106 Mudd Hall, 3400 N. Charles Street,
> Baltimore, MD 21218,  USA.
> Phone: 410-516-8433,
> Email: kumarsan /a\ jhu.edu.
> URL:  http://myprofile.cos.com/Kumarsan.
> or      https://jshare.johnshopkins.edu/skumar23/public_html/
> 
> ----- Original Message -----
> From: Cherif Matta <Cherif.Matta /a\ Dal.Ca>
> Date: Saturday, April 2, 2005 8:58 pm
> Subject: Re: CCL:desolvation energy table for amino acids
> 
> > Hello Eric and Sandeep,
> >
> > Sandeep, do you have the ref to Makhatadze paper?
> >
> > Also have a look at the classic papers by Wolfenden:
> >
> > [1]  Wolfenden R, Andersson L, Cullis PM, Southgate CCB  (1981).
> > "Affinities of
> > amino acid side chains for solvent water". Biochem.; 20: 849-855.
> >
> > [2]  Radzicka A, Wolfenden R  (1988).  "Comparing the polarities of
> > the amino
> > acids: side-chain distribution coefficients between the vapor phase,
> > cyclohexane, 1-octanol, and neutral aqueous solutions". Biochem.; 27:
> > 1664-1670.
> >
> > Cheers,
> >
> > Cherif
> >
> > -------------------------------------------------------
> > Cherif F. Matta, Ph.D., MCIC
> > * Izaak Walton Killam Post Doctoral Fellow
> >  Department of Chemistry, Dalhousie University
> >  Halifax, NS, Canada.
> > * Adjunct Professor of Chemistry
> >  McMaster University, Hamilton, ON, Canada.
> > -------------------------------------------------------
> > * Web site:  http://chem.utoronto.ca/~cmatta/
> >  Tel: (902) 494 7021      Fax: (902) 494 1310
> > -------------------------------------------------------
> >
> >
> > Quoting SANDEEP KUMAR <skumar23 /a\ jhem.jhu.edu>:
> >
> > > Hi Erick ,
> > >
> > > Please see the work of  Makhatadze and co-workers. They have
> > compiled> hydration energies/enthalpies  for amino acids transfer
> > from Octanol to
> > > Water.
> > >
> > > Good luck,
> > > Sandeep
> > >
> > > ------------------------------------------------------------------
> > -
> > > Dr. Sandeep Kumar,
> > > Associate Research Scientist,
> > > Johns Hopkins University Department of Biology,
> > > 106 Mudd Hall, 3400 N. Charles Street,
> > > Baltimore, MD 21218,  USA.
> > > Phone: 410-516-8433,
> > > Email: kumarsan /a\ jhu.edu.
> > > URL:  http://myprofile.cos.com/Kumarsan.
> > > or      https://jshare.johnshopkins.edu/skumar23/public_html/
> > >
> > >
> > > ----- Original Message -----
> > > From: Eric Hu <eric.y.hu /a\ gmail.com>
> > > Date: Friday, April 1, 2005 6:45 pm
> > > Subject: CCL:desolvation energy table for amino acids
> > >
> > > > Hi, I wonder if anyone has knowledge of availability of a
> > desolvation> > energy table for each individual amino acid. Thanks.
> > > >
> > > > Eric
> > > >
> > > >
> > > > -= This is automatically added to each message by the mailing
> > > > script =-
> > > > To send e-mail to subscribers of CCL put the string CCL: on your
> > > > Subject: line
> > > >
> > > > Send your subscription/unsubscription requests to: CHEMISTRY-
> > > > REQUEST /a\ ccl.net
> > > > HOME Page: http://www.ccl.net   | Jobs Page:
> > > > http://www.ccl.net/jobs
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> > >
> > >
> > > -= This is automatically added to each message by the mailing
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> > Subject:> line
> > > and send your message to:  CHEMISTRY /a\ ccl.net
> > >
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>


From chemistry-request@ccl.net Mon Apr  4 13:44:20 2005
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We are organising a Web-based conference session for June 2005 on the eCheminfo Community of Practice (http://echeminfo.com/) on Applications of Web-based Services in Drug Design, chaired by Kirill Degtyarenko (European Bioinformatics Institute)

Invited speakers include Alexander Kel (BIOBASE GmbH), Joao Aires de Sousa (Universidade Nova de Lisboa), Andreas Bender (Cambridge University), Darren Flower (Edward Jenner Institute for Vaccine Research), Vladimir Poroikov (Institute of Biomedical Chemistry of Rus. Acad. Med. Sci.) and Adel Golovin (EBI)

The session will involve seminars and discussions with the invited speakers, a poster session and a Web-based and conference call discussion.  

Presentations will open on the eCheminfo Web site on the 6 June for a two week period of review and discussion and a conference call with the panel of presenters for Q&A. 

SignUp for eCheminfo and registration for this session and other eCheminfo meetings is available through http://echeminfo.com/

Posters

All meeting registrants are eligible to submit a Conference Poster. Attendees may view and discuss the Posters and leave messages for the authors on the Web site. Poster Abstracts (of ca. 300 words) with Title, Institution, Authors and Contact Information should be submitted for consideration to echeminfo at douglasconnect.com Abstracts should be submitted by 30 April 2005, and Posters submitted by 31 May 2005.  Conference Posters can be presented as HTML, pdf, Powerpoint or Word documents.

The Web Services program will be continued at our Autumn eCheminfo meeting in Philadelphia in October and at our European meeting in Switzerland in November; exceptional contributions will be considered for inclusion in these meetings.  

best regards
Barry Hardy
eCheminfo Community of Practice Coordinator

eCheminfo Blog: http://barryhardy.blogs.com/cheminfostream/

Barry Hardy, PhD
Douglas Connect
Baermeggenweg 14, Zeiningen
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We are organising a Web-based conference session for May 2005 on the eCheminfo Community of Practice (http://echeminfo.com/) on Protein Folding & Misfolding: Applications to Drug Discovery, chaired by Nikolay V. Dokholyan (University of North Carolina) and Marc Fasnacht (Columbia University)

Invited speakers include Vijay Pande, Stanford University; Ruhong Zhou, IBM; Guido Tiana, University of Milan; Joan-Emma Shea, University of California, Santa Barbara; Sergey Buldyrev, Yeshiva University; and Yong Duan, University of California, Davis

The session will involve seminars and discussions with the invited speakers, a poster session and a Web-based and conference call discussion.  

Presentations will open on the eCheminfo Web site on the 9 May for a two week period of review and discussion and a conference call with the panel of presenters for Q&A. 

SignUp for eCheminfo and registration for this session and other eCheminfo meetings is available through http://echeminfo.com/ 


Posters

All meeting registrants are eligible to submit a Conference Poster. Attendees may view and discuss the Posters and leave messages for the authors on the Web site. Poster Abstracts (of ca. 300 words) with Title, Institution, Authors and Contact Information should be submitted for consideration to echeminfo at douglasconnect.com Abstracts should be submitted for consideration by 15 April 2005, and Posters submitted by 30 April 2005.  Conference Posters can be presented as HTML, pdf, Powerpoint or Word documents.

The protein folding & misfolding program will be continued at our Autumn eCheminfo meeting in Philadelphia in October; exceptional contributions will be considered for inclusion in the meeting program.  

best regards
Barry Hardy
eCheminfo Community of Practice Coordinator

eCheminfo Blog: http://barryhardy.blogs.com/cheminfostream/


Barry Hardy, PhD
Douglas Connect, 
Baermeggenweg 14, Zeiningen
CH-4314, Switzerland
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barry.hardy () tiscalinet.ch
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From chemistry-request@ccl.net Mon Apr  4 13:26:05 2005
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To: <CHEMISTRY %a% ccl.net>
Subject: CCL: Call for paper for the Fall ACS symposium on "Chemical Information and Open Access"
Date: Mon, 4 Apr 2005 10:05:49 -0400
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Dear Colleagues,
=20
We invite you to submit papers for the symposium on "Chemical =
Information
and Open Access." This symposium will take place as part of the CINF =
section
at the 230th American Chemical Society National Meeting, August =
28-September
1 in Washington, DC.
=20
We are organizing a symposium to discuss chemical information and open
access. We all know scientific literature from broad areas of chemistry =
and
biology represents a rich source of knowledge for the scientists in the
medical sciences field.  Journal abstracts, full-text scientific =
articles,
and chemical patents are readily available in electronic form and =
accessible
through a variety of mechanisms.   Scientists needing to identify =
efficient
reactions, new and/or novel lead compounds, compounds for SAR analyses,
understand in vivo behavior of molecules, will use the prior art to
facilitate their efforts.  The volume of electronic information has been
rapidly increasing and will continue to do so; therefore computational
techniques for automatically identifying and extracting chemical names,
chemical and biological properties, and chemical reactions from =
scientific
documents will become ever more essential.=20
=20
In the biological sciences field a large body work has been carried out =
by a
broad array of computational techniques to mine biological data both in =
the
academia and in the industry. This has largely been possible due to the
availability of open access to the data.  Such open access to chemical
information, were it to ever happen, would greatly increase the level of
research activity in the chemical sciences field and lead to greater =
benefit
to the medicinal sciences community at large.
=20
Given the scope of the topic, the idea of the symposium is to bring
scientists together from diverse backgrounds to discuss novel techniques =
and
resources developed to address the issues outlined above. This session =
is
sponsored by:
=20
The Chemical Information Division (CINF) and the Division of Medicinal
Chemistry (MEDI).
=20
All are invited to participate and submit abstracts for this session.
Please use the OASYS to submit your abstract. You can access the CINF
symposia at OASYS via
http://oasys.acs.org/acs/230nm/cinf/papers/index.cgi.=20
=20
The deadline for submitting abstracts is May 03, 2005. =20
=20
=20
Symposium organizers:
=20
Suresh B. Singh           &          Richard Hull
Vitae Pharmaceuticals               Axontologic, Inc.
502 West Office Center Drive      12565 Research Parkway, Suite 300
Fort Washington, PA 19034        Orlando, FL 32826
V:215-461-2048                         V:407-737-7772
F:215-461-2006                          F:407-737-2512
ssingh %a% vitaerx.com                   hull %a% axontologic.com=20
=20

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<DIV><SPAN style=3D"FONT-SIZE: 10pt; FONT-FAMILY: Arial"><o:p><SPAN=20
class=3D803273016-23032005>Dear Colleagues,</SPAN></o:p></SPAN></DIV>
<DIV><SPAN style=3D"FONT-SIZE: 10pt; FONT-FAMILY: Arial"><o:p><SPAN=20
class=3D803273016-23032005><SPAN=20
class=3D803273016-23032005></SPAN></SPAN></o:p></SPAN>&nbsp;</DIV>
<DIV><SPAN style=3D"FONT-SIZE: 10pt; FONT-FAMILY: Arial"><o:p><SPAN=20
class=3D803273016-23032005><SPAN class=3D803273016-23032005>We invite =
you=20
to&nbsp;</SPAN>submit papers for the symposiu<SPAN=20
class=3D803273016-23032005><FONT color=3D#0000ff><FONT color=3D#000000>m =
on "Chemical=20
Information and Open Access." This symposium will take place as part of =
the CINF=20
section at </FONT></FONT></SPAN>the 230th American Chemical Society =
National=20
Meeting, August 28-September 1 in Washington, =
DC.</SPAN></o:p></SPAN></DIV>
<DIV><SPAN style=3D"FONT-SIZE: 10pt; FONT-FAMILY: Arial"><o:p><SPAN=20
class=3D803273016-23032005></SPAN></o:p></SPAN>&nbsp;</DIV>
<DIV class=3DSection1>
<P class=3DMsoNormal style=3D"mso-layout-grid-align: none"><FONT =
face=3DArial=20
size=3D2><SPAN style=3D"FONT-SIZE: 10pt; FONT-FAMILY: Arial">We are =
organizing a=20
symposium to discuss chemical information and open access. We all know=20
scientific literature from broad areas of chemistry and biology =
represents a=20
rich source of knowledge for the scientists in the medical sciences =
field.<SPAN=20
style=3D"mso-spacerun: yes">&nbsp; </SPAN>Journal abstracts, full-text =
scientific=20
articles, and chemical patents are readily available in electronic form =
and=20
accessible through a variety of mechanisms.<SPAN=20
style=3D"mso-spacerun: yes">&nbsp;&nbsp; </SPAN>Scientists needing to =
identify=20
efficient reactions, new and/or novel lead compounds, compounds for SAR=20
analyses, understand in vivo behavior of molecules, will use the prior =
art to=20
facilitate their efforts.<SPAN style=3D"mso-spacerun: yes">&nbsp; =
</SPAN>The=20
volume of electronic information has been rapidly increasing and will =
continue=20
to do so; therefore computational techniques for automatically =
identifying and=20
extracting chemical names, chemical and biological properties, and =
chemical=20
reactions from scientific documents will become ever more essential.=20
<o:p></o:p></SPAN></FONT></P>
<P class=3DMsoNormal style=3D"mso-layout-grid-align: none"><FONT =
face=3DArial=20
size=3D2><SPAN=20
style=3D"FONT-SIZE: 10pt; FONT-FAMILY: =
Arial"><o:p>&nbsp;</o:p></SPAN></FONT></P>
<P class=3DMsoNormal style=3D"mso-layout-grid-align: none"><FONT =
face=3DArial=20
size=3D2><SPAN style=3D"FONT-SIZE: 10pt; FONT-FAMILY: Arial">In the =
biological=20
sciences field a large body work has been carried out by a broad array =
of=20
computational techniques to mine biological data both in the academia =
and in the=20
industry. This has largely been possible due to the availability of open =
access=20
to the data.<SPAN style=3D"mso-spacerun: yes">&nbsp; </SPAN>Such open =
access to=20
chemical information, were it to ever happen, would greatly increase the =
level=20
of research activity in the chemical sciences field and lead to greater =
benefit=20
to the medicinal sciences community at =
large.<o:p></o:p></SPAN></FONT></P>
<P class=3DMsoNormal style=3D"mso-layout-grid-align: none"><FONT =
face=3DArial=20
size=3D2><SPAN=20
style=3D"FONT-SIZE: 10pt; FONT-FAMILY: =
Arial"><o:p>&nbsp;</o:p></SPAN></FONT></P>
<P class=3DMsoNormal style=3D"mso-layout-grid-align: none"><FONT =
face=3DArial=20
size=3D2><SPAN style=3D"FONT-SIZE: 10pt; FONT-FAMILY: Arial">Given the =
scope of the=20
topic, the idea of the symposium is to bring scientists together from =
diverse=20
backgrounds to discuss novel techniques and resources developed to =
address the=20
issues outlined above. This session is sponsored=20
by:<o:p></o:p></SPAN></FONT></P>
<P class=3DMsoNormal style=3D"mso-layout-grid-align: none"><FONT =
face=3DArial=20
size=3D2><SPAN=20
style=3D"FONT-SIZE: 10pt; FONT-FAMILY: =
Arial"><o:p>&nbsp;</o:p></SPAN></FONT></P>
<P class=3DMsoNormal style=3D"mso-layout-grid-align: none"><SPAN =
class=3DGramE><FONT=20
face=3DArial size=3D2><SPAN style=3D"FONT-SIZE: 10pt; FONT-FAMILY: =
Arial">The Chemical=20
Information Division (CINF) and the Division of Medicinal Chemistry=20
(MEDI).</SPAN></FONT></SPAN><FONT face=3DArial size=3D2><SPAN=20
style=3D"FONT-SIZE: 10pt; FONT-FAMILY: =
Arial"><o:p></o:p></SPAN></FONT></P>
<P class=3DMsoNormal style=3D"mso-layout-grid-align: none"><FONT =
face=3DArial=20
size=3D2><SPAN=20
style=3D"FONT-SIZE: 10pt; FONT-FAMILY: =
Arial"><o:p>&nbsp;</o:p></SPAN></FONT></P>
<P class=3DMsoNormal style=3D"mso-layout-grid-align: none"><SPAN=20
style=3D"FONT-SIZE: 10pt; FONT-FAMILY: Arial">All are invited to =
participate and=20
submit abstracts for this session.<SPAN style=3D"mso-spacerun: =
yes">&nbsp;=20
</SPAN>Please use the OASYS to submit <SPAN class=3DGramE>your</SPAN> =
abstract.=20
You can access the CINF symposia at OASYS via&nbsp;<SPAN=20
class=3D140424516-28032005><FONT =
color=3D#0000ff>&nbsp;</FONT></SPAN></SPAN><SPAN=20
style=3D"FONT-SIZE: 10pt; FONT-FAMILY: Arial"><SPAN=20
class=3D140424516-28032005>&nbsp;</SPAN><A=20
href=3D"http://oasys.acs.org/acs/230nm/cinf/papers/index.cgi">http://oasy=
s.acs.org/acs/230nm/cinf/papers/index.cgi</A><SPAN=20
class=3D140424516-28032005><FONT =
color=3D#0000ff>.&nbsp;</FONT></SPAN></SPAN></P>
<P class=3DMsoNormal style=3D"mso-layout-grid-align: none"><FONT =
face=3DArial=20
size=3D2><SPAN=20
style=3D"FONT-SIZE: 10pt; FONT-FAMILY: =
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<P class=3DMsoNormal style=3D"mso-layout-grid-align: none"><FONT =
face=3DArial=20
size=3D2><SPAN style=3D"FONT-SIZE: 10pt; FONT-FAMILY: Arial">The =
deadline for=20
submitting abstracts is May 03, 2005.<SPAN style=3D"mso-spacerun: =
yes">&nbsp;=20
</SPAN></SPAN></FONT></P>
<P class=3DMsoNormal style=3D"mso-layout-grid-align: none"><FONT =
face=3DArial=20
size=3D2><SPAN=20
style=3D"FONT-SIZE: 10pt; FONT-FAMILY: =
Arial"><o:p>&nbsp;</o:p></SPAN></FONT></P>
<P class=3DMsoNormal style=3D"mso-layout-grid-align: none"><FONT =
face=3DArial=20
size=3D2><SPAN=20
style=3D"FONT-SIZE: 10pt; FONT-FAMILY: =
Arial"><o:p></o:p></SPAN></FONT></P>
<P class=3DMsoNormal style=3D"mso-layout-grid-align: none"><FONT =
face=3DArial=20
size=3D2><SPAN=20
style=3D"FONT-SIZE: 10pt; FONT-FAMILY: =
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<P class=3DMsoNormal style=3D"mso-layout-grid-align: none"><FONT =
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size=3D2><SPAN style=3D"FONT-SIZE: 10pt; FONT-FAMILY: Arial">Symposium=20
organizers:<o:p></o:p></SPAN></FONT></P>
<P class=3DMsoNormal style=3D"mso-layout-grid-align: none"><FONT =
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size=3D2><SPAN=20
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B.=20
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1">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;=20
</SPAN><B><SPAN style=3D"FONT-WEIGHT: bold">Richard=20
Hull<o:p></o:p></SPAN></B></SPAN></FONT></P>
<P class=3DMsoNormal style=3D"mso-layout-grid-align: none"><FONT =
face=3DArial=20
size=3D2><SPAN style=3D"FONT-SIZE: 10pt; FONT-FAMILY: Arial">Vitae=20
Pharmaceuticals<SPAN=20
style=3D"mso-spacerun: =
yes">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&n=
bsp;&nbsp;&nbsp;=20
</SPAN>Axontologic, Inc.<o:p></o:p></SPAN></FONT></P>
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From chemistry-request@ccl.net Mon Apr  4 13:40:05 2005
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Date: Mon, 4 Apr 2005 21:31:28 +0800 (CST)
From: <chenzhz * sohu.com>
To: <CHEMISTRY * ccl.net>
Subject: CCL:how to get a sample routine of correlate in Tinker
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Dear CCLer:

  I want to compute time correlation functions using the correlate routine in Tinker package. the routine requires a user supplied function  property that  computes the value  of the property.but i don't know how to do the job.Do you know where i can obtain samples of user supplied function  property
thanks in advance.

chen
chenzhz * sohu.com



From chemistry-request@ccl.net Mon Apr  4 15:36:51 2005
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From: "David Danovich" <david.danovich|at|huji.ac.il>
To: <chemistry|at|ccl.net>
Subject: CCL:G03
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Hello,


I would like to know if somebody has successfully used G03 on opteron 
under RH enterprise linux WS 4.
I have opteron 250 with two sata disk and 8 GB  400 MHz memory. Jaguar 
5.5 and Turbomole 5.71 work fine on this system
but with G03 I have problems.  When I tried to use 32 bit PC version of 
G03 which I have compiled on Intel PC with  RHEL WS 4 and
Intel fortran compiler 8.1 it just stopped the computer completely and I 
had to reboot it ( it  is not kernel panic it just completely stopped 
it).
I have downloaded Portland group compiler and tried to compile Gaussian 
with it but it again stopped the computer even during compilation 
process.
I think that it is a hardware problem, probably with memory but I would 
like to know if somebody has used G03 with RHEL WS 4. On the other
hand if it is hardware problem why does it work with jaguar and 
turbomole?

Thank you  David

________________________________________________________________
Dr. David Danovich, Department of Organic Chemistry, The Hebrew 
University,
Edmond J. Safra Campus - Givat Ram, 91904 Jerusalem, Israel
http://yfaat.ch.huji.ac.il/david.html, David.Danovich|at|huji.ac.il
FAX:(+972)-2-6586934, Phone:(+972)-2-6586934(w), 
(+972)-54-4768669(mobile)