From owner-chemistry@ccl.net Wed Feb 8 09:06:00 2006 From: "Gilles Marcou gilles.marcou .. pharma.u-strasbg.fr" To: CCL Subject: CCL: How to run AutoDock Message-Id: <-30818-060208061233-3333-uUTIwfHHz+mWAaeW8BGycg!A!server.ccl.net> X-Original-From: Gilles Marcou Content-Disposition: inline Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="iso-8859-15" Date: Wed, 8 Feb 2006 11:38:59 +0100 MIME-Version: 1.0 Sent to CCL by: Gilles Marcou [gilles.marcou=-=pharma.u-strasbg.fr] Hi, > Can any one tell me how to run AutoDock after unzipp the files? How to If you are using a Linux box, you should recompile autodock. I think that all of this is described in the file INSTALL of the distribution and is straightforward. I remember that effectively, once I had uncompressed the Autodock files, most of the scripts in the share directory did not worked properly because of improper paths (autodock/dist305). The problems were that the scripts in this directory were expecting to find autodock binaries and tools in a directory of the kind /usr/home/john/autodock/dist305... You should modify this part of the paths and put in place, a shell variable with a relevant variable name and then set it in your user profile. For example, my script called mol2topdbqs looks now like this: $AUTODOCK_UTI/mol2fftopdbq $1 | sort -n +4 | $AUTODOCK_UTI/rem-lp >! $1:r.pdbq $AUTODOCK_BIN/addsol $1:r.pdbq $1:r.pdbqs I have set $AUTODOCK_BIN as ~/autodock3/dist305/bin in my bash profile. I don't know if this problem was specific to me or not or if it was corrected. > set up the path and what command I have to use to execute AutoDock? Even I > dont know AutoDock is having GUI mode or only CLI mode. There is a GUI available. Just look at the SCRIPPS web site. Alternatively there is a funny web browser interface called GA_dpfgen.html in the share directory to generate the dpf file. > How do create the > protein/DNA/Ligand structures for AutoDock, I have to use some other > visualization (like gausview, cerius, maestro) software? Is it possible to > do all the calculations (receptor grid making, and docking) using GUI? I personally find the GUI is useless if not worse. The manual in html form in the doc directory is very good. Just read it. The Geting Started page is short and lets you make a first docking in five minutes. In general, informations you need are the center of the grid in which you make your docking and its extent. To get those informations, any molecular editor will do the job, so the best one is the one you best know... :-) In general I found the tools in the share directory are very usefull and efficient. Take a look on them. Just a short notice: always check your pdbqs because you do not always get a warning if something went wrong in your input data. Partial charges, for example, can be completely misunderstood. Those are not bugs, they are usually an input problem. > Looking forward for your reply. Thanks in advance. Sincerely, Good luck, -- Gilles Marcou Université Louis Pasteur de Strasbourg Faculté de Pharmacie Laboratoire de Pharmacochimie de la Communication Cellulaire, UMR7081 74, Route du Rhin, BP24 67401 Illkirch tel.:(0033)(0)3.90.24.42.21 eMail: marcou^^pharma.u-strasbg.fr From owner-chemistry@ccl.net Wed Feb 8 10:15:01 2006 From: "Elie Cohen elie[a]molecular-conceptor.com" To: CCL Subject: CCL: New release of Molecular Conceptor v2.5 Message-Id: <-30819-060208050856-25787-7f10ZblEHwpmmBHIzImROA*o*server.ccl.net> X-Original-From: "Elie Cohen" Sent to CCL by: "Elie Cohen" [elie : molecular-conceptor.com] Synergix Ltd. is pleased to announce the release of Molecular Conceptor v2.5 Molecular Conceptor is a computer-based course for teaching rational drug design, molecular modeling and cheminformatics. The course contains more than 3000 slides, 1500 3D molecules and is the fruit of 7 years of intensive development. Click here to review the NEW table of contents. http://www.molecular-conceptor.com/toc.html I invite you to get more details from our website: http://www.molecular-conceptor.com Elie Cohen elie,molecular-conceptor.com Project Leader Molecular Conceptor From owner-chemistry@ccl.net Wed Feb 8 13:37:00 2006 From: "Eric Scerri scerri],[chem.ucla.edu" To: CCL Subject: CCL: International conference in august Message-Id: <-30820-060208121440-19018-sGUO2sZgdih+gQ+9RbyHhg]=[server.ccl.net> X-Original-From: Eric Scerri Content-Type: multipart/alternative; boundary=Apple-Mail-35-50386530 Date: Wed, 8 Feb 2006 09:14:20 -0800 Mime-Version: 1.0 (Apple Message framework v746.2) Sent to CCL by: Eric Scerri [scerri]=[chem.ucla.edu] --Apple-Mail-35-50386530 Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=US-ASCII; delsp=yes; format=flowed ISPC Summer Symposium 2006 International Society for the Philosophy of Chemistry Tenth Summer Symposium August 6 - 10, 2006 Split, Croatia Organizers: Hrvoj Vancik, Professor of Chemistry (Zagreb) Ante Graovac, Professor of Chemistry (Split) Department of Chemistry Faculty of Science University of Zagreb Horvatovac 102 A 10000 Zagreb, Croatia Phone +385 1 4819 280 Fax +385 1 4819 288 vancik^irb.hr The Departments of Chemistry at University of Zagreb, and University of Split invite you kindly to participate the ISPC 10 Symposium that will be organized in Split, Croatia, from 6 till 10 August 2006. Tentative schedule Sunday afternoon: Registration and opening reception Monday: Opening plenary session, contributed papers Tuesday: Plenary session, contributed papers Wednesday: Plenary session, contributed papers, conference banquet Thursday: Closing session, executive committee meeting, departure Sightseeing and social events include tours of the museums and galleries (Archeology museum, Museum of old Croatian monuments, etc.) in Split, visits to the old Roman center as well as boat excursion on the Adriatic. Facilities Symposium sessions will be held in the Student Center - Spinut - of the University of Split. On the same place are also dormitories. Photographs of this place are attached to this Invitation. Lecturing hall contains auditorium with seating capacity ranging from 100 to 150. All the conventional audiovisual equipment including computer projection is available. There is also coffee bar and restaurant for refreshments. Housing will be arranged in the University dormitories at Spinut campus (street Sinjska 6) and at local hotels, which are within walking distance of campus. Campus prices for single room is 150 Kn per person, double room 1s 130 Kn per person. (Note that 1 USD = 6 Kn, or 1EURO = 7.35 Kn) Inexpensive meals are available in on-campus dining facilities. There is also a broad range of restaurants within walking distance because Campus is very close to the center of Split. Location and Transportation After Zagreb, Split is the largest city in Croatia. It is located in the most attractive region of Croatia, in central Dalmatia on the Adriatic coast. Transportation to Split is simple because there is international airport. There are also many fast inter-city train connections with Zagreb, and people coming by car can use the highway A-1, E-71 (nearly 400 km from Zagreb). Croatia Airlines flights daily on the line Zagreb - Split. Another possibility is to use Dubrovnik international airport, which is 200 kilometers away from Split. Registration fee Following the tradition of the ISPC symposia, on the Conference is only the voluntary registration fee of $20. Publication of Symposium Papers Several recent symposia have resulted in published volumes. Every effort will be made to provide an appropriate venue for publication of the papers presented at this symposium. A special issue of Foundations of Chemistry is an excellent option, but others may appear as the time approaches. ------------------------------------------------------------------------ --------------------------- Dr. Eric Scerri Department of Chemistry & Biochemistry, Charles Young Drive, Los Angeles, CA 90095. 310 206 7443 fax: 310 206 2061 UCLA faculty web page: http://www.chem.ucla.edu/dept/Faculty/scerri/ Editor of Foundations of Chemistry, http://www.springer.com/sgw/cda/frontpage/0,11855,4-40399-70-35545882- detailsPage%253Djournal%257CmostViewedArticles%257CmostViewedArticles, 00.html International Society for the Philosophy of Chemistry, http://ispc.sas.upenn.edu/ --Apple-Mail-35-50386530 Content-Transfer-Encoding: quoted-printable Content-Type: text/html; charset=ISO-8859-1
ISPC Summer Symposium 2006

=A0

=A0

International = Society for the Philosophy of Chemistry
 Tenth Summer = Symposium
August 6 - 10, 2006
 Split, = Croatia

Organizers:
Hrvoj Vancik, Professor of = Chemistry (Zagreb)
Ante Graovac, Professor of = Chemistry (Split)

Department of Chemistry
Faculty of Science
University of = Zagreb
Horvatovac 102 = A
10000 Zagreb, Croatia
Phone +385 1 4819 280
Fax +385 1 4819 = 288

The Departments of Chemistry at = University of Zagreb, and University of Split invite you kindly to = participate the ISPC 10 Symposium that will be organized in Split, = Croatia, from 6 till 10 August 2006.

=A0

Tentative = schedule

Sunday afternoon:=A0=A0=A0=A0=A0=A0=A0 = Registration and opening reception
Monday:=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0 =A0=A0=A0=A0=A0=A0=A0=A0=A0= =A0=A0=A0 Opening plenary session, contributed papers

Tuesday:=A0=A0=A0=A0=A0=A0=A0=A0=A0 = =A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0 Plenary session, contributed = papers

Wednesday:=A0=A0=A0=A0 =A0=A0=A0=A0=A0=A0= =A0=A0=A0=A0=A0=A0=A0 Plenary session, contributed papers, conference = banquet

Thursday:=A0=A0=A0=A0=A0=A0=A0 =A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0= =A0 Closing session, executive committee meeting, departure

=A0

Sightseeing = and social events include tours of the museums and galleries (Archeology = museum, Museum of old Croatian monuments, etc.) in Split, visits to the = old Roman center as well as boat excursion on the Adriatic.

=A0

Facilities
Symposium sessions will be held in the Student Center - = Spinut - of the University of Split. On the same place are also = dormitories. Photographs of this place are attached to this Invitation. = Lecturing hall contains auditorium with seating capacity ranging from = 100 to 150. All the conventional audiovisual equipment including = computer projection is available. There is also coffee bar and = restaurant for refreshments.

Housing will be arranged in the = University dormitories at Spinut campus (street Sinjska 6) and at local = hotels, which are within walking distance of campus.

=A0

Campus prices for single room = is 150 Kn per person, double room 1s 130 Kn per person.

(Note that 1 USD =3D=A0 6 Kn, = or 1EURO =3D 7.35 Kn)

Inexpensive meals are available in on-campus dining = facilities.
There is also a broad range of = restaurants within walking distance because Campus is very close to the = center of Split.



Location and Transportation

After Zagreb, Split is the = largest city in Croatia. It is located in the most attractive region of = Croatia, in central Dalmatia on the Adriatic coast. Transportation to = Split is simple because there is international airport. There are also = many fast inter-city train connections with Zagreb, and people coming by = car can use the highway A-1, E-71 (nearly 400 km from Zagreb). Croatia = Airlines = flights daily on the line Zagreb - Split. Another possibility is to use = Dubrovnik international airport, which is 200 kilometers away from = Split.

Registration fee

Following the tradition of the = ISPC symposia, on the Conference is only the voluntary registration fee = of $20.

Publication of Symposium = Papers

Several recent symposia have = resulted in published volumes. Every effort
will = be made to provide an appropriate venue for publication of the = papers
presented at this symposium.=A0 A special issue of = Foundations of Chemistry is
an excellent option, but = others may appear as the time approaches.


=A0

=A0--------------------------------------------------------= -------------------------------------------

Dr. Eric = Scerri
Department of Chemistry & = Biochemistry,
Charles Young Drive,
Los = Angeles,
CA 90095.

310 206 7443
fax: = 310 206 2061

UCLA faculty web page:=A0=A0=A0=




= --Apple-Mail-35-50386530-- From owner-chemistry@ccl.net Wed Feb 8 16:24:00 2006 From: "omar Deeb deeb2000il%yahoo.com" To: CCL Subject: CCL: stability of a salt Message-Id: <-30821-060208161444-2942-9HGAgNGX9ipmoLHTCIgmKw]![server.ccl.net> X-Original-From: omar Deeb Content-Transfer-Encoding: 8bit Content-Type: multipart/alternative; boundary="0-822454774-1139429680=:25831" Date: Wed, 8 Feb 2006 12:14:40 -0800 (PST) MIME-Version: 1.0 Sent to CCL by: omar Deeb [deeb2000il(0)yahoo.com] --0-822454774-1139429680=:25831 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit Dear CCl, I would like to ask about a way or method to calculate theoretically the stability of a salt as well as the solubility of it.. Any suggestions. Best wishes Omar Dr. Omar Deeb Assistant Professor , PhD Theoretical/computational chemist Chemistry and chemical technology department Faculty of science and technology Alquds University Abu-deis, Jerusalem e-mail : deeb2000il*|*yahoo.com --------------------------------- Brings words and photos together (easily) with PhotoMail - it's free and works with Yahoo! Mail. --0-822454774-1139429680=:25831 Content-Type: text/html; charset=iso-8859-1 Content-Transfer-Encoding: 8bit
Dear CCl,
I would like to ask about a way or method to calculate theoretically the stability of a salt as well as the solubility of it..
Any suggestions.
Best wishes
Omar


Dr. Omar Deeb
Assistant Professor , PhD
Theoretical/computational chemist
Chemistry and chemical technology department
Faculty of science and technology
Alquds University
Abu-deis, Jerusalem
e-mail : deeb2000il*|*yahoo.com

Brings words and photos together (easily) with
PhotoMail - it's free and works with Yahoo! Mail. --0-822454774-1139429680=:25831-- From owner-chemistry@ccl.net Wed Feb 8 17:51:00 2006 From: "David Sherrill sherrill.:.chemistry.gatech.edu" To: CCL Subject: CCL: Georgia Tech Summer Theory REU Message-Id: <-30822-060208174701-29800-5CbJghTY59lLI2EKBWp8YQ#server.ccl.net> X-Original-From: David Sherrill Content-Type: TEXT/PLAIN; charset=US-ASCII; format=flowed Date: Wed, 8 Feb 2006 17:02:38 -0500 (EST) MIME-Version: 1.0 Sent to CCL by: David Sherrill [sherrill]~[chemistry.gatech.edu] Georgia Tech will host its annual Summer Theory Program as part of its NSF-sponsored Research Experiences for Undergraduates (REU) program in chemistry and biochemistry. The ten-week program runs from May 22 to July 28 and is open to students who will be in their junior or senior years during the 2005-2006 academic year. Theory students will work with Professors David Sherrill, Rigoberto Hernandez, or Jean-Luc Bredas in the areas of electronic structure theory, nonequilibrium dynamics, or the electronic properties of organic materials. The research experience is supplemented by an introductory lecture series in theoretical chemistry. Successful applicants will receive a stipend of $4000, a travel allowance, and housing. Further details are available at http://vergil.chemistry.gatech.edu/opp/summer.html The deadline for applications is February 15, 2006. -- C. David Sherrill, Ph.D. sherrill|a|gatech.edu Associate Professor of Chemistry Phone: (404) 894-4037 School of Chemistry and Biochemistry Fax: (404) 894-7452 Georgia Institute of Technology http://www.chemistry.gatech.edu/faculty/sherrill/