From owner-chemistry@ccl.net Wed Sep 7 07:20:33 2005 From: "CCL" To: CCL Subject: CCL: W:GTO and STO Message-Id: <-29085-050907063915-6096-W+2w8DanHA1q/kw2MH4VTw^server.ccl.net> X-Original-From: Laurence Cuffe Content-disposition: inline Content-language: en Content-Transfer-Encoding: 8bit Content-type: text/plain; charset=windows-1252 Date: Wed, 07 Sep 2005 11:24:40 +0100 MIME-version: 1.0 Sent to CCL by: Laurence Cuffe [Laurence.Cuffe^ucd.ie] ----- Original Message ----- > From: CCL Date: Tuesday, September 6, 2005 6:31 pm Subject: CCL: W:GTO and STO > > Sent to CCL by: Serguei Patchkovskii [ps:+:ned.sims.nrc.ca] > > Sent to CCL by: Laurence Cuffe [Laurence.Cuffe]*[ucd.ie] >> The short answer is that calculating the overlap between two >> Gaussiantype -Orbitals can be done in closed form. That is given two >> GTO's A and B you can write an relatively simple algebraic expression >> for the size of the overlap between them. This is not possible with >> Slater type orbitals. >This statement, of course, is false. Closed-form expressions for >overlap integrals in terms of exponential integral-type functions >are very well known. For example:…(cut) >Dr. Serguei Patchkovskii A fair point Dr Patchkovskii. In hindsight I should, perhaps, have put more emphasis on “relatively simple” As Ahmed. Bouferguene wrote: The "flip side of the coin" is, multi-center integrals (which is the heart of ab initio calculations) over STOs is much much more difficult than with GTOs. I think I’d trust his judgment in this area, as its one where he’s published a number of papers e.g. Ahmed Bouferguene 2005 J. Phys. A: Math. Gen. 38 2899-2916 “Addition theorem of Slater type orbitals: a numerical evaluation of Barnett–Coulson/Löwdin functions” Historically evaluating GTO’s was faster, and while there are now claims that highly optimised STO codes can beat GTO codes, I remain to be convinced that highly optimised STO codes can beat highly optimised GTO codes. In the wider sense original question was about the popularity of Gaussian type orbital codes over STO based ones. Here I think the reason is also historical, and is based on the early popularity of the gaussian program as a collaborative venture among a number of theoretical chemists. The use of GTO’s was, I think, first suggested by S.F. Boys, in Proc. Roy. Soc. A200, 542 (1950) ADF (using STO’s) has been around for a long time, and I know that the Zeigler group has made many substantial contributions to it. It has not (yet) overtaken Gaussian in popularity, but maybe if( or when) it does we’ll be wondering what the advantages of GTO’s are. I’m not holding my breath. All the best Dr Laurence Cuffe From owner-chemistry@ccl.net Wed Sep 7 09:40:33 2005 From: "CCL" To: CCL Subject: CCL: W:Extended Abstract Deadlines/eCheminfo Autumn meetings & program Message-Id: <-29086-050907093712-31923-W+2w8DanHA1q/kw2MH4VTw]~[server.ccl.net> X-Original-From: "Barry Hardy" Sent to CCL by: "Barry Hardy" [barry.hardy]~[tiscalinet.ch] A copy of the Invited Program for our eCheminfo Autumn 2005 conference including the US Meeting (Philadelphia, October 11,12) and the European meeting (Basel, November 9,10) is now available as a downloadable pdf: http://barryhardy.blogs.com/cheminfostream/files/eCheminfo-ProgramAutumn05.pdf Abstracts and biographies are located in the Program area of the eCheminfo website at http://eCheminfo.com/ Between the summer break, vacations, and much recent chaos, disaster and flooding in our region and many others :(! I have extended the contributed abstract submission deadlines for the Autumn eCheminfo meetings: eCheminfo Autumn 2005 InterAction Meetings Applications of Cheminformatics & Chemical Modelling to Drug Discovery October 11-12, Bryn Mawr College, Philadelphia, USA November 9-10, Swissotel L'entre Conference Center, Basel, Switzerland http://echeminfo.com/ Extended Abstract Submission Deadlines: US meeting: September 16th Swiss meeting: September 30th Abstracts should be submitted to eCheminfo at douglasconnect.com Abstracts will be considered both for the meeting poster sessions and as contributed talks. All papers submitted for the meeting and passing refereeing will be published by Taylor & Francis in 2006 in a special drug discovery issue of Molecular Simulation. We are also very pleased to acknowledge our new eCheminfo project sponsors: Johnson & Johnson Pharmaceutical Research & Development, LLC, and Merck Research Laboratories. best regards Barry Hardy Community of Practice Manager Barry Hardy, PhD Douglas Connect, Switzerland +41 61 851 0170 (office) www.douglasconnect.com From owner-chemistry@ccl.net Wed Sep 7 10:27:55 2005 From: "CCL" To: CCL Subject: CCL: W:GTO and STO Message-Id: <-29087-050907101849-12617-W+2w8DanHA1q/kw2MH4VTw;;server.ccl.net> X-Original-From: John McKelvey Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=windows-1252; format=flowed Date: Wed, 07 Sep 2005 09:17:16 -0500 MIME-Version: 1.0 Sent to CCL by: John McKelvey [jmmckel;;attglobal.net] All, I have not seen any timing benchmarks of ADF and Slater functions versus a gaussian based code. With intent to compare accuracy I suppose one could start by comparing a D-Z Slater calculation in ADF with an equivalent D-Z/STO-6G basis in a gaussian based code. The cusp conditions and hence energies would be off some, but I would guess that geometries might be very similar.... Not sure of codes that have STO-NG for d functions.. I have to say that after sitting through the ADF seminar at the recent ACS meeting I am quite impressed with it's capabilities. CPU times may not be the only issue; after all understanding chemistry is the main point. :-) Best regards, John McKelvey CCL wrote: >Sent to CCL by: Laurence Cuffe [Laurence.Cuffe^ucd.ie] > > >----- Original Message ----- > > >>From: CCL >> >> >Date: Tuesday, September 6, 2005 6:31 pm >Subject: CCL: W:GTO and STO > > > >>Sent to CCL by: Serguei Patchkovskii [ps:+:ned.sims.nrc.ca] >> >> >>>Sent to CCL by: Laurence Cuffe [Laurence.Cuffe]*[ucd.ie] >>>The short answer is that calculating the overlap between two >>>Gaussiantype -Orbitals can be done in closed form. That is given two >>>GTO's A and B you can write an relatively simple algebraic expression >>>for the size of the overlap between them. This is not possible with >>>Slater type orbitals. >>> >>> >>This statement, of course, is false. Closed-form expressions for >>overlap integrals in terms of exponential integral-type functions >>are very well known. For example:…(cut) >>Dr. Serguei Patchkovskii >> >> >A fair point Dr Patchkovskii. In hindsight I should, perhaps, have put >more emphasis on “relatively simple” As Ahmed. Bouferguene wrote: >The "flip side of the coin" is, multi-center integrals (which is the heart >of ab initio calculations) over STOs is much much more difficult than with >GTOs. I think I’d trust his judgment in this area, as its one where he’s >published a number of papers e.g. >Ahmed Bouferguene 2005 J. Phys. A: Math. Gen. 38 2899-2916 “Addition >theorem of Slater type orbitals: a numerical evaluation of >Barnett–Coulson/Löwdin functions” >Historically evaluating GTO’s was faster, and while there are now claims >that highly optimised STO codes can beat GTO codes, I remain to be >convinced that highly optimised STO codes can beat highly optimised GTO >codes. >In the wider sense original question was about the popularity of >Gaussian type orbital codes over STO based ones. Here I think the reason >is also historical, and is based on the early popularity of the gaussian >program as a collaborative venture among a number of theoretical chemists. >The use of GTO’s was, I think, first suggested by S.F. Boys, in Proc. >Roy. Soc. A200, 542 (1950) > >ADF (using STO’s) has been around for a long time, and I know that the >Zeigler group has made many substantial contributions to it. It has not >(yet) overtaken Gaussian in popularity, but maybe if( or when) it does >we’ll be wondering what the advantages of GTO’s are. I’m not holding my >breath. >All the best >Dr Laurence Cuffe> > > > > > > From owner-chemistry@ccl.net Wed Sep 7 11:02:01 2005 From: "CCL" To: CCL Subject: CCL: Compile DL_POLY 3.02 on SGI Altix Message-Id: <-29088-050907104240-27562-W+2w8DanHA1q/kw2MH4VTw ~~ server.ccl.net> X-Original-From: XIAOFENG FRANK DUAN Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Wed, 07 Sep 2005 10:06:45 -0400 MIME-Version: 1.0 Sent to CCL by: XIAOFENG FRANK DUAN [duanx ~~ asc.hpc.mil] Hi, Has anyone installed DL_POLY 3.02 or earlier version on SGI Altix or IA64 Linux machine? If yes, can you supply me the Makefile? We are having some problems to install it, especially in the C preprocessor parts. Thanks! Frank -- Xiaofeng Frank Duan, Ph.D | Phone: 937-904-8307 Sr. Application Analyst | Fax: 937-656-9538 ASC MSRC | Email: duanx ~~ asc.hpc.mil Wright-Patterson AFB | URL: www.asc.hpc.mil From owner-chemistry@ccl.net Wed Sep 7 11:02:01 2005 From: "CCL" To: CCL Subject: CCL: W:GTO and STO Message-Id: <-29090-050907102824-17382-W+2w8DanHA1q/kw2MH4VTw^server.ccl.net> X-Original-From: "Ahmed" Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="iso-8859-1" Date: Wed, 7 Sep 2005 08:38:40 -0600 MIME-Version: 1.0 Sent to CCL by: "Ahmed" [ahmed.bouferguene^ualberta.ca] -----Original Message----- > From: owner-chemistry^ccl.net [mailto:owner-chemistry^ccl.net] Sent: Wednesday, September 07, 2005 4:25 AM To: Bouferguene, Ahmed Subject: CCL: W:GTO and STO Sent to CCL by: Laurence Cuffe [Laurence.Cuffe^ucd.ie] ----- Original Message ----- > From: CCL Date: Tuesday, September 6, 2005 6:31 pm Subject: CCL: W:GTO and STO > > Sent to CCL by: Serguei Patchkovskii [ps:+:ned.sims.nrc.ca] > > Sent to CCL by: Laurence Cuffe [Laurence.Cuffe]*[ucd.ie] >> The short answer is that calculating the overlap between two >> Gaussiantype -Orbitals can be done in closed form. That is given two >> GTO's A and B you can write an relatively simple algebraic expression >> for the size of the overlap between them. This is not possible with >> Slater type orbitals. >This statement, of course, is false. Closed-form expressions for >overlap integrals in terms of exponential integral-type functions >are very well known. For example:…(cut) >Dr. Serguei Patchkovskii A fair point Dr Patchkovskii. In hindsight I should, perhaps, have put more emphasis on “relatively simple” As Ahmed. Bouferguene wrote: The "flip side of the coin" is, multi-center integrals (which is the heart of ab initio calculations) over STOs is much much more difficult than with GTOs. I think I’d trust his judgment in this area, as its one where he’s published a number of papers e.g. Ahmed Bouferguene 2005 J. Phys. A: Math. Gen. 38 2899-2916 “Addition theorem of Slater type orbitals: a numerical evaluation of Barnett–Coulson/Löwdin functions” Historically evaluating GTO’s was faster, and while there are now claims that highly optimised STO codes can beat GTO codes, I remain to be convinced that highly optimised STO codes can beat highly optimised GTO codes. ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ ^^^^^^ I beg to disagree on this very aspect. At the SCF level, I do not believe that there is any chance the STOs would beat the GTOs. However, and that was the pitch that was made for very long time: "The STOs would gain whatever ground they lost (and probably more!!) for investigations beyond the SCF level as, [1] The configuration space would be smaller (given the accuracy of the STOs) [2] No transformation would be needed to generate the approximate STOs from GTOs" Now, to the best of my knowledge the above statement was the "marketing slogan" for selling STOs but it is yet to be proved that this is true as one needs (first) to find the algorithm that can squeeze as much as one can from the evaluation of multi-center integrals. Cheers In the wider sense original question was about the popularity of Gaussian type orbital codes over STO based ones. Here I think the reason is also historical, and is based on the early popularity of the gaussian program as a collaborative venture among a number of theoretical chemists. The use of GTO’s was, I think, first suggested by S.F. Boys, in Proc. Roy. Soc. A200, 542 (1950) ADF (using STO’s) has been around for a long time, and I know that the Zeigler group has made many substantial contributions to it. It has not (yet) overtaken Gaussian in popularity, but maybe if( or when) it does we’ll be wondering what the advantages of GTO’s are. I’m not holding my breath. All the best Dr Laurence Cuffe From owner-chemistry@ccl.net Wed Sep 7 11:02:01 2005 From: "CCL" To: CCL Subject: CCL: need the free energy values of water species Message-Id: <-29089-050907055116-2188-W+2w8DanHA1q/kw2MH4VTw|*|server.ccl.net> X-Original-From: jaturong pratuangdejkul Content-Transfer-Encoding: 8bit Content-Type: multipart/alternative; boundary="0-1514753334-1126083073=:58211" Date: Wed, 7 Sep 2005 09:51:13 +0100 (BST) MIME-Version: 1.0 Sent to CCL by: jaturong pratuangdejkul [jr_pk2001|*|yahoo.com] --0-1514753334-1126083073=:58211 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit Dear all, I would like to know the experimental values of free energy of 1. Water 2. Hydronium (H3O+) ion 3. Hydroxide (OH-) ion 4. Proton (H+) in gas-phase and condensed phase (solvate-phase) If someone know, or the source that I can retrieve these values, could you please inform me. Thank you very much for your kind consideration. Best regards, Pong Jaturong jr_pk2001|*|yahoo.com Send instant messages to your online friends http://uk.messenger.yahoo.com --0-1514753334-1126083073=:58211 Content-Type: text/html; charset=iso-8859-1 Content-Transfer-Encoding: 8bit
Dear all,

I would like to know the experimental values of free energy of
 
1. Water
2. Hydronium (H3O+) ion
3. Hydroxide (OH-) ion
4. Proton (H+)

in gas-phase and condensed phase (solvate-phase)

If someone know, or the source that I can retrieve these values,
could you please inform me.
Thank you very much for your kind consideration.

Best regards,

Send instant messages to your online friends http://uk.messenger.yahoo.com --0-1514753334-1126083073=:58211-- From owner-chemistry@ccl.net Wed Sep 7 11:28:10 2005 From: "CCL" To: CCL Subject: CCL: Manual calculation of the CBS-QB3 enthalpy Message-Id: <-29091-050907111605-24194-W+2w8DanHA1q/kw2MH4VTw^server.ccl.net> X-Original-From: Jim Pfaendtner Content-Transfer-Encoding: 7bit Content-Type: text/plain Date: Wed, 07 Sep 2005 10:16:15 -0500 Mime-Version: 1.0 Sent to CCL by: Jim Pfaendtner [pfaendtner^northwestern.edu] Hi, I was wondering if it is difficult to manually calculate the CBS-QB3 enthalpy from all of the independent stepwise calculations? Has anyone had success matching a manual calculation with the G03 output? Thanks, Jim From owner-chemistry@ccl.net Wed Sep 7 12:36:40 2005 From: "CCL" To: CCL Subject: CCL: W:Any open-source molecular descriptor software for short peptides? Message-Id: <-29092-050907052345-1234-W+2w8DanHA1q/kw2MH4VTw##server.ccl.net> X-Original-From: "Noel O'Boyle" Content-Transfer-Encoding: 7bit Content-Type: text/plain Date: Wed, 07 Sep 2005 10:23:45 +0100 Mime-Version: 1.0 Sent to CCL by: "Noel O'Boyle" [noel.oboyle2##mail.dcu.ie] The Chemistry Development Kit (cdk.sf.net), or JOELIB (joelib.sf.net), come to mind. Nole On Tue, 2005-09-06 at 15:45 -0400, CCL wrote: > Sent to CCL by: "Lei Huang" [hxbus]* > Dear CCLers: > > Could anyone recommend a nice open-source molecular descriptor calculation software for short peptides with 8-15 amino acid long? I tried to search the archives but only got the internal error message. Thanks. > > Lei Huang > University of Illinois at Chicago (M/C563) > Chicago, IL 60612 > Email: hxbus at yahoo.com> > > From owner-chemistry@ccl.net Wed Sep 7 15:39:19 2005 From: "CCL" To: CCL Subject: CCL: Phil Magee-Obituary of a QSAR Pioneer Message-Id: <-29093-050907134653-25476-7f10ZblEHwpmmBHIzImROA!=!server.ccl.net> X-Original-From: "Block, John" Content-class: urn:content-classes:message Content-Type: multipart/alternative; boundary="----_=_NextPart_001_01C5B3CD.2DA545F1" Date: Wed, 7 Sep 2005 09:57:06 -0700 MIME-Version: 1.0 Sent to CCL by: "Block, John" [john.block!=!oregonstate.edu] This is a multi-part message in MIME format. ------_=_NextPart_001_01C5B3CD.2DA545F1 Content-Type: text/plain; charset="US-ASCII" Content-Transfer-Encoding: quoted-printable Dr. Philip Stewart Magee Jr. Dec. 9, 1926 - June 27, 2005 =20 Philip S. Magee, President of BIOSAR Consulting. and former research chemist for Chevron Ortho Division, died June 27, 2005 after a brief and courageous fight with cancer. Phil was born in Kecoughtan, VA, but spent most of his life in California, growing up in Coronado near San Diego. His lifelong love of chemistry began at age ten, when he stocked a basement lab with equipment and chemicals obtained from a local chemist. During World War II he was an officer candidate at University of Southern California and attended Navy Air Corps Training in Corpus Christi, Texas. After the war, he returned to USC, and, after starting out as a chemical engineer, he received a B.S. in chemistry in 1952. He then went to UCLA and obtained a PhD in Physical Chemistry in 1955 working under Saul Winstein. The two would remain close friends until Winsteins's death in 1969. =20 As a research chemist he worked for Standard Oil, Chevron Ortho Division, in Richmond for 28 years. The important products he developed included acephate, one of the most potent and important commercial organophosphorous insecticides ever produced. It was introduced in 1971 as Orthene(r). He also developed methamidophos, which was marketed as Monitor(r), in 1973. He held numerous other patents for phosphorus and sulfur insecticides and herbicides, and was an acknowledged authority in their synthesis and use. =20 At Chevron, Phil became involved in 1968 in what was then the new field of quantitative structure-activity relationships, or QSAR. In 1975 he attended the first QSAR Gordon Conference, and was one of the founders and first chairman, in 1990, of the International QSAR and Modeling Society. He continued to attend QSAR Gordon Conferences, and chaired committees and QSAR meetings until 2003, when a stroke forced him to curtail his traveling. Some highlights of his career in structure-activity studies include developing the Parameter Focusing approach in 1983, the factoring of lipophilicity and other physicochemical properties in 1990, and a hypermolecule approach to QSAR in 1997. He was a regular presenter at national ACS meetings, a member of the AGRO and COMP divisions, and a 50-year member of the Society. He authored over 70 papers, numerous texts and symposia proceedings, and held over two dozen industrial patents. =20 Throughout his career, Phil was involved in teaching and extramural research. He gave numerous extension courses in organic chemistry and QSAR for UC Berkeley Extension. He was a guest lecturer and adjunct professor at the Oregon State University College of Pharmacy, and he held an adjunct professorship in dermatology at UCSF Medical School, working with Howard Maybach. After retiring from industry, in 1983 he formed BIOSAR Consulting, a research and educational consulting firm. For the next 20 years, he studied a variety of topics, including the mechanism and prediction of allergic contact dermatitis, the tumorigenicity of anthraquinones, diffusion of pesticides from polymers, the energetics of chromatographic systems, chemoprevention by dithiolthiones, and transdermal drug delivery. Most recently, he was studying the interface between statistics, quantum chemistry, and molecular modeling, and the structure and energetics of nonexistent compounds. During this period he was also a consultant for Cellegy Pharmaceutical, Mitsubishi agricultural products, and several other US and foreign firms. =20 Phil was an active person all his life, enjoying weightlifting, fishing, camping and motorcycling. He held black belts in two systems of Jujitsu. He is survived by his wife, his two sons and a daughter, and was a loving grandfather of 13 grandchildren and three great-grandchildren. =20 (Obituary written by Dr. Doug Henry, one of Phil's close friends.) =20 John H. Block Phone: 541-737-5779 College of Pharmacy Fax: 541-737-3999 Oregon State University Corvallis, OR 97331 John.Block!=!oregonstate.edu blockj!=!onid.orst.edu =20 =20 ------_=_NextPart_001_01C5B3CD.2DA545F1 Content-Type: text/html; charset="US-ASCII" Content-Transfer-Encoding: quoted-printable

Dr. Philip Stewart Magee = Jr.

Dec. 9, 1926 - June 27, = 2005

 

Philip S. Magee, President of BIOSAR Consulting. and = former research chemist for Chevron Ortho Division, died June 27, 2005 after a = brief and courageous fight with cancer.  Phil was born in Kecoughtan, VA, but spent most of his life in = California, growing up in Coronado near San = Diego.  His lifelong love of chemistry began at age ten, when he stocked a = basement lab with equipment and chemicals obtained from a local chemist. During World = War II he was an officer candidate at University of Southern California and = attended Navy Air Corps Training in Corpus Christi, Texas. After the war, he returned to USC, and, after starting out as a chemical = engineer, he received a B.S. in chemistry in 1952.  He then went to UCLA and = obtained a PhD in Physical Chemistry in 1955 working under Saul Winstein.  The two = would remain close friends until Winsteins's death in = 1969.

 

As a research chemist he worked for Standard Oil, = Chevron Ortho Division, in Richmond for 28 years. The important products he developed included acephate, one = of the most potent and important commercial organophosphorous insecticides ever produced. It was introduced in 1971 as Orthene®.  He also = developed methamidophos, which was marketed as Monitor®, in 1973.  He = held numerous other patents for phosphorus and sulfur insecticides and herbicides, and was = an acknowledged authority in their synthesis and = use.

 

At Chevron, Phil became involved in 1968 in what was = then the new field of quantitative structure-activity relationships, or QSAR. = In 1975 he attended the first QSAR Gordon Conference, and was one of the = founders and first chairman, in 1990, of the International QSAR and Modeling = Society.  He continued to attend QSAR Gordon Conferences, and chaired committees = and QSAR meetings until 2003, when a stroke forced him to curtail his = traveling.  Some highlights of his career in structure-activity studies include = developing the Parameter Focusing approach in 1983, the factoring of lipophilicity and = other physicochemical properties in 1990, and a hypermolecule approach to QSAR = in 1997.  He was a regular presenter at national ACS meetings, a = member of the AGRO and COMP divisions, and a 50-year member of the Society.  He = authored over 70 papers, numerous texts and symposia proceedings, and held over two = dozen industrial patents.

 

Throughout his career, Phil was involved in teaching = and extramural research.  He gave numerous extension courses in organic = chemistry and QSAR for UC Berkeley Extension.  He was a guest lecturer and = adjunct professor at the Oregon State University College of Pharmacy, and he = held an adjunct professorship in dermatology at UCSF Medical School, working = with Howard Maybach.  After retiring from industry, in 1983 he formed = BIOSAR Consulting, a research and educational consulting firm.  For the next 20 years, = he studied a variety of topics, including the mechanism and prediction of allergic = contact dermatitis, the tumorigenicity of anthraquinones, diffusion of = pesticides from polymers, the energetics of chromatographic systems, chemoprevention by dithiolthiones, and transdermal drug delivery.  Most recently, he = was studying the interface between statistics, quantum chemistry, and molecular = modeling, and the structure and energetics of nonexistent compounds.  During = this period he was also a consultant for Cellegy Pharmaceutical, Mitsubishi = agricultural products, and several other US and foreign firms.

 

Phil was an active person all his life, enjoying weightlifting, fishing, camping and motorcycling. He held black belts in = two systems of Jujitsu. He is survived by his wife, his two sons and a = daughter, and was a loving grandfather of 13 grandchildren and three = great-grandchildren.

 

(Obituary written by Dr. Doug Henry, one of = Phil’s close friends.)

 

John H. Block           &n= bsp;        Phone:  541-737-5779

College of Pharmacy    &nbs= p;    Fax:      = 541-737-3999

Oregon State University

Corvallis<= /strong>, OR 97331=

John.Block!=!oregonstate.edu=

blockj!=!onid.orst.edu

 

 

------_=_NextPart_001_01C5B3CD.2DA545F1-- From owner-chemistry@ccl.net Wed Sep 7 20:30:28 2005 From: "CCL" To: CCL Subject: CCL: W:Announcing the release of VigyaanCD v1.0 Message-Id: <-29094-050907202853-29182-eSc6C2yCCSce8pLLLmWjCA]~[server.ccl.net> X-Original-From: "Pratul K. Agarwal" Sent to CCL by: "Pratul K. Agarwal" [pagarwal]~[linus.ornl.gov] Vigyaan (http://www.vigyaancd.org/) is an electronic workbench for bioinformatics, computational biology and computational chemistry. New in version 1.0: Based on KNOPPIX v3.7, most software packages updated, new applications added. At present the following ready to use software comes on VigyaanCD: Arka/GP, Artemis, Bioperl, BLAST (NCBI-tools), ClustalW/ClustalX, Cn3D, EMBOSS tools, Garlic, Glimmer, GROMACS, Ghemical, GNU R, Gnuplot, GIMP, ImageMagick, Jmol, MPQC, MUMer, NJPlot, Open Babel, Octave, PSI3, PyMOL, Ramachandran plot viewer, Rasmol, Raster3D, Seaview, TINKER, XDrawChem, Xmgr and Xfig. GNU C/C++/Fortran compilers and additional Linux tools (such as ps2pdf) are also available. VigyaanCD also provides tools required to compile and install other applications (from source). Therefore, making testing of 'Linux' applications possible on computers with other OS.