From owner-chemistry@ccl.net Mon Jul 20 01:34:01 2009 From: "Tamar Ansbacher tamar.ansbacher/./mail.huji.ac.il" To: CCL Subject: CCL:G: center of mass Message-Id: <-39813-090720012640-23303-+Ba3Dkx1C8WC5jJIHlha7w|-|server.ccl.net> X-Original-From: Tamar Ansbacher Content-Type: multipart/alternative; boundary=0016e6db61c07fe57e046f1c5fa1 Date: Mon, 20 Jul 2009 08:25:58 +0300 MIME-Version: 1.0 Sent to CCL by: Tamar Ansbacher [tamar.ansbacher(_)mail.huji.ac.il] --0016e6db61c07fe57e046f1c5fa1 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit but you can ask for center of mass (at least in gaussian09 ) and you can use any viewer that reads the xyz coordinates to see the 0.0 0.0 0.0 point by adding a dummy atom there, or asking to view the axes system. On Sun, Jul 19, 2009 at 2:48 PM, s. Bill s_bill36[a]yahoo.co.uk < owner-chemistry * ccl.net> wrote: > Sorry, but this is a charge center (not mass center). > and how can I visualize it. > > > --- On *Sun, 19/7/09, Tamar Ansbacher tamar.ansbacher]*[mail.huji.ac.il > * wrote: > > > From: Tamar Ansbacher tamar.ansbacher]*[mail.huji.ac.il ccl.net> > Subject: CCL:G: center of mass > To: "Bill, S. H. " > Date: Sunday, 19 July, 2009, 9:54 AM > > Hi Bill > any QM package (e.g., gaussian gamess orca etc. ) > can give you the standard orientation of the molecule > with 0.0 0.0 0.0 at the center of mass > Tamar > > On Sat, Jul 18, 2009 at 10:49 PM, S. Bill S_Bill36=yahoo.co.uk < > owner-chemistry%ccl.net >wrote: > >> >> Sent to CCL by: "S. Bill" [S_Bill36|a|yahoo.co.uk] >> Dear CCL users >> I was wonder if you know a simple program can be used to determine and >> visualise the center of mass of a molecule. >> Thanks in advance >> bill>> >> E-mail to subscribers: CHEMISTRY%ccl.netor use:>> >> E-mail to administrators: CHEMISTRY-REQUEST%ccl.netor use>> >> >> > > --0016e6db61c07fe57e046f1c5fa1 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable
but you can ask for center of mass (at least in gauss= ian09 )
and you can use any viewer that reads the xyz coordinates to see the 0= .0 0.0 0.0 point by adding a dummy atom there, or asking to view the axes s= ystem.
=A0

On Sun, Jul 19, 2009 at 2:48 PM, s. Bill s_bill3= 6[a]yahoo.co.uk <owner-chemistry * ccl.net> wrote:
Sorry, but this is a charge center (not mass center).and how can I visualize it.


--- On Sun, 19/7/09, Tamar Ansba= cher tamar.ansbacher]*[mail.huji.ac.il <owner-chemistry:_:ccl.net> wrote:

From: Tamar Ansbacher tamar.ansbacher]*[mail.huji.ac.il <owne= r-chemistry:_:ccl.net>=
Subject: CCL:G: center of mass
To: "Bill, S. H. " <s_bill36= :_:yahoo.co.uk>Date: Sunday, 19 July, 2009, 9:54 AM

Hi Bill
any QM package (e.g., gaussian gamess orca etc.= )
can give you the standard orientation of the molecule
with 0.0 0.0= 0.0 at the center of mass
Tamar

On Sat, Jul 18, 2009 at 10:49 PM, S. Bill S_Bill= 36=3Dyah= oo.co.uk <owner-chemistry%ccl.n= et> wrote:

Sent to CCL by: = "S. =A0Bill" [S_Bill36|a|yahoo.co.uk]
Dear CCL users
I was wonder if you know a simple program can be used to = determine and visualise the center of mass of a molecule.
Thanks in adva= nce
bill



-=3D This is automatically added to each message= by the mailing script =3D-

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<= /td>


--0016e6db61c07fe57e046f1c5fa1-- From owner-chemistry@ccl.net Mon Jul 20 02:52:01 2009 From: "Berger Raphael berger^^chem.helsinki.fi" To: CCL Subject: CCL:G: center of mass Message-Id: <-39814-090720014953-31277-jShlJeYtnjKXGtLCg6zBpQ[*]server.ccl.net> X-Original-From: Berger Raphael Content-Type: MULTIPART/MIXED; BOUNDARY="-696203250-1942603731-1248066751=:6031" Date: Mon, 20 Jul 2009 08:12:31 +0300 (EEST) MIME-Version: 1.0 Sent to CCL by: Berger Raphael [berger|*|chem.helsinki.fi] This message is in MIME format. The first part should be readable text, while the remaining parts are likely unreadable without MIME-aware tools. ---696203250-1942603731-1248066751=:6031 Content-Type: TEXT/PLAIN; charset=iso-8859-1; format=flowed Content-Transfer-Encoding: 8BIT Maybe something like: awk '{mass+=$1;x+=$1*$2;y=$1*$3;z=$1*$4} END {x=x/mass;y=y/mass;z=z/mass; print "Q "x" "y" "z"\n"}' h2o with a file h2o containing, the atomic mass in the first, the x,y and z coordinates in the second to fourth column. (for example h2o: 15.99 0 0 0 1.01 1 0 0 1.01 0 1 0 ) then attach the output line to your .xyz file increment the integer on top of that file by 1 and run molden. best regards Raphael > To: "Bill, S. H. " > Date: Sunday, 19 July, 2009, 9:54 AM > > Hi Bill > any QM package (e.g., gaussian gamess orca etc. ) > can give you the standard orientation of the molecule > with 0.0 0.0 0.0 at the center of mass > Tamar > > On Sat, Jul 18, 2009 at 10:49 PM, S. Bill S_Bill36=yahoo.co.uk > wrote: > > Sent to CCL by: "S.  Bill" [S_Bill36|a|yahoo.co.uk] > Dear CCL users > I was wonder if you know a simple program can be > used to determine and visualise the center of mass > of a molecule. > Thanks in advance > bill > > > > -= This is automatically added to each message by > the mailing script =- > > E-mail to subscribers: CHEMISTRY%ccl.net or use: >      http://www.ccl.net/cgi-bin/ccl/send_ccl_message > > E-mail to administrators: CHEMISTRY-REQUEST%ccl.net > or use >      http://www.ccl.net/cgi-bin/ccl/send_ccl_message>      http://www.ccl.net/chemistry/sub_unsub.shtml > > Before posting, check wait time at: > http://www.ccl.net> Conferences: > http://server.ccl.net/chemistry/announcements/conferences/ > > Search Messages: > http://www.ccl.net/chemistry/searchccl/index.shtml > >      http://www.ccl.net/spammers.txt > > RTFI: > http://www.ccl.net/chemistry/aboutccl/instructions/ > > > > > > ---696203250-1942603731-1248066751=:6031-- From owner-chemistry@ccl.net Mon Jul 20 03:28:00 2009 From: "Klenner.+*+.bioinformatik.uni-frankfurt.de" To: CCL Subject: CCL: Database of molecules isolated from natural products requiered (with explicit mention to the source/s from which each one is isolated) Message-Id: <-39815-090719175553-13511-hCtCYJtpARj6C3rljWVD0g+*+server.ccl.net> X-Original-From: Klenner*bioinformatik.uni-frankfurt.de Content-Disposition: inline Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; DelSp="Yes"; format="flowed" Date: Sun, 19 Jul 2009 23:00:30 +0200 MIME-Version: 1.0 Sent to CCL by: Klenner]*[bioinformatik.uni-frankfurt.de Hi, you could try Analyticon's database, that you can find here: http://www.ac-discovery.com But I am not sure whether the give the information of the source or not. regards, Alex Zitat von "Gerard Pujadas gerard.pujadas::gmail.com" : > Dear CCL subscribers, > > I am looking for free or commercial databases of 2D or 3D molecular > structures isolated from natural products (different from the Beilstein > database), that mention the source from which each molecule is isolated (and > ideally links to the bibliographic reference that describes the method used > to isolate each one). > > I know that ZINC has a natural products subset but the source of the > molecules is difficult to find because it is catalog-oriented (and the > source is usually not reported in the catalog) ... > > With many thanks in advances for your help > > Yours sincerely > > Best > > Gerard > From owner-chemistry@ccl.net Mon Jul 20 08:35:00 2009 From: "Serdar Badoglu sbadoglu * gazi.edu.tr" To: CCL Subject: CCL:G: Mixed basis set in Gaussian 03 Message-Id: <-39816-090720083325-26573-p1QPwjrIrL314PrmQgs/GA _ server.ccl.net> X-Original-From: "Serdar Badoglu" Date: Mon, 20 Jul 2009 08:33:21 -0400 Sent to CCL by: "Serdar Badoglu" [sbadoglu+*+gazi.edu.tr] Hi all. I want to use mixed basis sets approach in Gaussian 03 for a molecule which contains C, H, N plus some other post-3rd row elements. Like LANL2DZ for Co and 6-31G* for C H N. But I have no idea on how to do it. Can you guide me? Regards. From owner-chemistry@ccl.net Mon Jul 20 10:21:00 2009 From: "Gerard Pujadas gerard.pujadas[]gmail.com" To: CCL Subject: CCL: Is there any database that classifies ligands in PDB complexes according to their biological effect on their target? Message-Id: <-39817-090720101925-13800-l3qT1mT3l0zAqT4B8+J9Pw..server.ccl.net> X-Original-From: Gerard Pujadas Content-Type: multipart/alternative; boundary=0016364c7dbd77a624046f23d295 Date: Mon, 20 Jul 2009 16:19:12 +0200 MIME-Version: 1.0 Sent to CCL by: Gerard Pujadas [gerard.pujadas###gmail.com] --0016364c7dbd77a624046f23d295 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Dear CCL subscribers, sorry for cross-posting I wonder if there is any database that classifies ligands in PDB complexes according to their biological effect on their corresponding target (*i.e.*they become classified as inhibitors, activators, agonists, antagonists, etc. of their corresponding target) For instance, I would like to retrieve in an easy way which are the PDB files that correspond to complexes between one enzyme and one competitive inhibitor for this inhibitor. Then, I would like to know which are the three-letter code in the PDB file that identifies each inhibitor. Any help should be highly appreciated Best regards Gerard --0016364c7dbd77a624046f23d295 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Dear CCL subscribers,

sorry for cross-posting

I wonder if the= re is any database that classifies ligands in PDB complexes according to th= eir biological effect on their corresponding target (i.e. they becom= e classified as inhibitors, activators, agonists, antagonists, etc. of thei= r corresponding target)

For instance, I would like to retrieve in an easy way which are the PDB= files that correspond to complexes between one enzyme and one competitive = inhibitor for this inhibitor. Then, I would like to know which are the thre= e-letter code in the PDB file that identifies each inhibitor.

Any help should be highly appreciated

Best regards

Gerard=
--0016364c7dbd77a624046f23d295-- From owner-chemistry@ccl.net Mon Jul 20 10:56:00 2009 From: "Phil McHale PMcHale#%#cambridgesoft.com" To: CCL Subject: CCL: Database of molecules isolated from natural products requiered (with explicit mention to the source/s from which each one is isolated) Message-Id: <-39818-090720011549-22148-Rvzsb2Isti43yk1KUovmsA]-[server.ccl.net> X-Original-From: "Phil McHale" Content-class: urn:content-classes:message Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset="us-ascii" Date: Mon, 20 Jul 2009 01:15:05 -0400 MIME-Version: 1.0 Sent to CCL by: "Phil McHale" [PMcHale[a]cambridgesoft.com] CambridgeSoft offers the Traditional Chinese Medicines database which contains 2D structures of over 10,000 compounds isolated from some 4500 natural sources. See http://www.cambridgesoft.com/databases/details/?db=3D3 for more details. Regards Phil McHale > From: owner-chemistry+pmchale=3D=3Dcambridgesoft.com*_*ccl.net [mailto:owner-chemistry+pmchale=3D=3Dcambridgesoft.com*_*ccl.net] On = Behalf Of Gerard Pujadas gerard.pujadas::gmail.com Sent: Sunday, July 19, 2009 10:23 AM To: Phil McHale Subject: CCL: Database of molecules isolated from natural products requiered (with explicit mention to the source/s from which each one is isolated) Dear CCL subscribers, I am looking for free or commercial databases of 2D or 3D molecular structures isolated from natural products (different > from the Beilstein database), that mention the source from which each molecule is isolated (and ideally links to the bibliographic reference that describes the method used to isolate each one). I know that ZINC has a natural products subset but the source of the molecules is difficult to find because it is catalog-oriented (and the source is usually not reported in the catalog) ... With many thanks in advances for your help Yours sincerely Best Gerard From owner-chemistry@ccl.net Mon Jul 20 11:31:02 2009 From: "Ben Roberts roberts,+,qtp.ufl.edu" To: CCL Subject: CCL:G: Mixed basis set in Gaussian 03 Message-Id: <-39819-090720110232-5584-XE9JAWaPxR/RScLgsZTP2g|-|server.ccl.net> X-Original-From: Ben Roberts Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=US-ASCII; format=flowed; delsp=yes Date: Mon, 20 Jul 2009 10:08:32 -0400 Mime-Version: 1.0 (Apple Message framework v935.3) Sent to CCL by: Ben Roberts [roberts]~[qtp.ufl.edu] Hi Serdar, You need the GEN "basis set", along with a basis set specification. See here: http://www.gaussian.com/g_tech/g_ur/k_gen.htm Also, if you want to use a basis set that relies on effective core potentials, you need to use GENECP instead of GEN. The GENECP "basis set" is equivalent to using the GEN "basis set" as well as the PSEUDO=READ or PSEUDO=CARDS keyword (the latter two are equivalent to each other). If you specify effective core potentials using any of these methods, you will also need to give details of the effective core potentials. See here: http://www.gaussian.com/g_tech/g_ur/k_pseudo.htm For example, this is how you might use it in a real file: #P HF/GENECP OPT ... Co 0 <= basis set (GEN) specification LANL2DZ **** C H N 0 6-31G* **** Co 0 <= pseudopotential (GENECP or PSEUDO=READ or PSEUDO=CARDS) specification LANL2DZ <> Hope that helps. Regards, Ben On 20/7/2009, at 8:33 a.m., Serdar Badoglu sbadoglu * gazi.edu.tr wrote: > > Sent to CCL by: "Serdar Badoglu" [sbadoglu+*+gazi.edu.tr] > Hi all. I want to use mixed basis sets approach in Gaussian 03 for a > molecule which contains C, H, N plus some other post-3rd row > elements. Like LANL2DZ for Co and 6-31G* for C H N. But I have no > idea on how to do it. Can you guide me? Regards. > > > > -= This is automatically added to each message by the mailing script > =- > To recover the email address of the author of the message, please > change> Conferences: http://server.ccl.net/chemistry/announcements/ > conferences/> -- Benjamin P. Roberts Postdoctoral Research Associate Quantum Theory Project University of Florida 2301 New Physics Building #92 PO Box 118435 Gainesville FL 32611-8435 USA Phone: +1 352 392 6712 Cell: +1 352 222 3677 Member of the Royal Australian Chemical Institute and of the American Chemical Society From owner-chemistry@ccl.net Mon Jul 20 12:45:00 2009 From: "Fedor Goumans fedor.goumans]~[googlemail.com" To: CCL Subject: CCL:G: Mixed basis set in Gaussian 03 Message-Id: <-39820-090720105440-30120-h65nYlogQQrtNsJG9qauQg++server.ccl.net> X-Original-From: Fedor Goumans Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset=ISO-8859-1 Date: Mon, 20 Jul 2009 15:40:40 +0200 MIME-Version: 1.0 Sent to CCL by: Fedor Goumans [fedor.goumans a googlemail.com] Hi Serdar, This can be done with the 'gen' keyword: http://www.gaussian.com/g_tech/g_ur/k_gen.htm http://www.gaussian.com/g_tech/g_ur/k_pseudo.htm So you write, e.g. b3lyp/gen pseud=3Dread and then after your geometry you give the basis set specifications per atom, followed by the ECPs if I remember correctly, like so: C H N 0 6-31G* ***** Co 0 LANL2DZ **** Co 0 LANL2DZ You have to be careful that now you have specified 'spherical' basis sets for your main group atoms (i.e. 5 d-functions for polarisation), while for the 'standard 6-31G*' Gaussian will generate cartesian basis functions (i.e. 6 d-functions), so you have to be careful, for instance, if you are calculating addition or dissociation energies of ligands, make sure that all calculations are done in either 5D or 6D (it's a good idea to check the nr. of basis functions used). hope this helps, Fedor 2009/7/20 Serdar Badoglu sbadoglu * gazi.edu.tr : > > Sent to CCL by: "Serdar =A0Badoglu" [sbadoglu+*+gazi.edu.tr] > Hi all. I want to use mixed basis sets approach in Gaussian 03 for a mole= cule which contains C, H, N plus some other post-3rd row elements. Like LAN= L2DZ for Co and 6-31G* for C H N. But I have no idea on how to do it. Can y= ou guide me? Regards. > > > > -=3D This is automatically added to each message by the mailing script = =3D-> =A0 =A0 =A0http://www.ccl.net/cgi-bin/ccl/send_ccl_message> =A0 =A0 =A0http://www.ccl.net/cgi-bin/ccl/send_ccl_message> =A0 =A0 =A0http://www.ccl.net/chemistry/sub_unsub.shtml> =A0 =A0 =A0http://www.ccl.net/spammers.txt> > > From owner-chemistry@ccl.net Mon Jul 20 13:19:00 2009 From: "Neha Awasthi neha.awasthi%%gmail.com" To: CCL Subject: CCL:G: Package for CCSD(T) Message-Id: <-39821-090720124438-3152-8RhzcKNqo5QOw5NTZoFqTg{=}server.ccl.net> X-Original-From: "Neha Awasthi" Date: Mon, 20 Jul 2009 12:44:34 -0400 Sent to CCL by: "Neha Awasthi" [neha.awasthi-#-gmail.com] Hello CCL community, I wanted to ask for advise for a reliable program for performing CCSD and CCSD(T) calculations using (aug)-cc-pVxZ (where x = D, T, Q...) basis sets. I have tried Gaussian, G03, and it turns out to be very inefficient (save large scratch files, and slow) for small molecules upto ~5 atoms. Please let me know which package/program is considered reliable as well as has good performance. It would be ideal to have one with a free license or free to download :) I will compile all responses and post them. Thank you, Neha From owner-chemistry@ccl.net Mon Jul 20 13:54:00 2009 From: "Jan Labanowski janl()speakeasy.net" To: CCL Subject: CCL: CCG Excellence Award for the Fall 2009 ACS Meeting Message-Id: <-39822-090720130647-14070-5ZVM6tUpweGubr5Svxneqw * server.ccl.net> X-Original-From: "Jan Labanowski" Date: Mon, 20 Jul 2009 13:06:44 -0400 Sent to CCL by: "Jan Labanowski" [janl=speakeasy.net] It is my pleasure to announce to CCL: 2009 Press Release Chemical Computing Group Announces Winners of the CCG Excellence Award for the Fall 2009 ACS National Meeting MONTREAL, Canada, July 20, 2009 Chemical Computing Group (CCG) and the American Chemical Society's (ACS) Division of Computers in Chemistry (COMP) congratulate the winners of the CCG Excellence Awards for the Fall 2009 ACS National Meeting in Washington. CCG will recognize the following winners' works at the award presentation ceremony during the COMP Division Poster Session on Tuesday August 18, 2009. Each winner will receive $1,150 US for travel costs to Washington, as well as a one-year license for the newest version of the Molecular Operating Environment (MOE). The winners are: -- Kiumars Shahrokh, University of Utah A first set of QM-coupled AMBER ff99 compatible heme parameters for the P450 catalytic cycle -- Fangyu Ding, SUNY Stony Brook Drug Pressure Induced Mutations in HIV-1 Protease alter Flap Conformations -- Sourav Das, Rensselaer Polytechnic Institute Pair-wise Property-Encoded Shape Distributions: Binding affinity prediction of protein-ligand complexes -- James Fells, University of Memphis Binary QSAR study for identifying selective LPA3 antagonists -- Lai Xu, UCLA Dynamics of 1,3-Dipolar Cycloadditions of Diazonium Betaines to Acetylene and Ethylene: Bending Vibrations Facilitate Reaction, About CCG Excellence Award The CCG Excellence Award is granted semi-annually as an opportunity to invest in the future of scientific research and to encourage a new generation of computational chemists. Awardees are selected on the quality and significance of the research to be presented, as well as the strength of the supporting letter and supplemental materials. For more information on the CCG Excellence Awards and eligibility criteria, visit http://www.chemcomp.com/ssupport-academic.htm. Chemical Computing Group Inc. (http://www.chemcomp.com) is a leading supplier of software solutions for Life Sciences. CCGs drug discovery software platform is the Molecular Operating Environment (MOE) that integrates visualization, molecular modeling simulations and methodology development in one package. CCGs informatics platform is PSILO which is used for macromolecular structure registration, version control and web-based searching. CCG's products and services are used by biologists, medicinal chemists and computational chemists in pharmaceutical/biotechnology companies, government organizations and universities throughout the world. CCG is headquartered in Montreal, Canada. For additional information please contact: Anna Cappello Marketing Director (514) 393-1055 info[-]chemcomp.com From owner-chemistry@ccl.net Mon Jul 20 14:35:01 2009 From: "aa aa**chemaxon.hu" To: CCL Subject: CCL: Program announcement and call for participants: ChemAxon's 2009 US UGM: September 15-16, San Diego, CA Message-Id: <-39823-090716135642-24847-FJWZI1aTdbEjVGPzaO0pJQ---server.ccl.net> X-Original-From: aa Content-Type: multipart/alternative; boundary="------------000600010903050600060002" Date: Thu, 16 Jul 2009 19:11:28 +0200 MIME-Version: 1.0 Sent to CCL by: aa [aa#%#chemaxon.hu] This is a multi-part message in MIME format. --------------000600010903050600060002 Content-Type: text/plain; charset=ISO-8859-1; format=flowed Content-Transfer-Encoding: 7bit Please excuse cross postings. The program is now available for ChemAxon's 2009 US User Group Meeting which will be held on Tuesday and Wednesday, September 15-16th at the Catamaran Resort Hotel & Spa, Mission Boulevard, San Diego, CA. The meeting will preceded by a training day on September 14th. Program: http://www.chemaxon.com/UGM/09/US/program.html The meeting will feature presentations from ChemAxon users, lightning presentations/exhibition from ChemAxon Partners and the latest updates on product developments, as well as discussion shaping future product development. Preceding the meeting will be an end user and developer training day on September 14th, for beginner to advanced level users to become familiar with ChemAxon's toolkits and end user applications. To see the topics and schedule visit: http://www.chemaxon.com/training/UGM0609.html To find out more about the meeting and training day, register or submit a poster abstract (open until September 1st) and view the program, please visit: http://www.chemaxon.com/UGM/09/. To review the archives of previous meetings, including original presentations and meeting reports > from Yvonne Martin and Wendy Warr visit: http://www.chemaxon.com/UGM/ugm_land.html We look forward to seeing you there. Alex *Expected and confirmed guest speakers:* * Isabella Haight - Abbott Laboratories * Kirsten Blumeyer - Celgene * Orion Jankowski - Edison Pharmaceuticals * Hongzhou Zhang - Eli Lilly and Co. * Yingyao Zhou - Genomics Institute of the Novartis Research Foundation * TBA - GlaxoSmithKline * John McNeil - John McNeil & Co * Tianhong Zhang - Pfizer * Craig Martin - SkunkWerks Software * Nicholas Goncharoff - SureChem * Tobias Kind - UC Davis Genome Center -- Metabolomics * Craig Knox - University of Alberta * Oleg Ursu - University of New Mexico ChemAxon Partners participants (tbc) - see partner listing here: http://www.chemaxon.com/partners/integrators.html -- *Alex Allardyce* Marketing Dir. *ChemAxon* *Ltd*. Maramaros koz 3/A, Budapest, 1037, Hungary Tel: +361 453 0435 skype: alex_allardyce --------------000600010903050600060002 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Please excuse cross postings.

The program is now available for ChemAxon's 2009 US User Group Meeting which will be held on Tuesday and Wednesday, September 15-16th at the Catamaran Resort Hotel & Spa, Mission Boulevard, San Diego, CA. The meeting will preceded by a training day on September 14th.

Program: http://www.chemaxon.com/UGM/09/US/program.html

The meeting will feature presentations from ChemAxon users, lightning presentations/exhibition from ChemAxon Partners and the latest updates on product developments, as well as discussion shaping future product development.

Preceding the meeting will be an end user and developer training day on September 14th, for beginner to advanced level users to become familiar with ChemAxon's toolkits and end user applications. To see the topics and schedule visit: http://www.chemaxon.com/training/UGM0609.html

To find out more about the meeting and training day, register or submit a poster abstract (open until September 1st) and view the program, please visit: http://www.chemaxon.com/UGM/09/. To review the archives of previous meetings, including original presentations and meeting reports from Yvonne Martin and Wendy Warr visit: http://www.chemaxon.com/UGM/ugm_land.html

We look forward to seeing you there.

Alex

Expected and confirmed guest speakers:
* Isabella Haight  -  Abbott Laboratories
* Kirsten Blumeyer  -  Celgene
* Orion Jankowski  -  Edison Pharmaceuticals
* Hongzhou Zhang  -  Eli Lilly and Co.
* Yingyao Zhou  -  Genomics Institute of the Novartis Research Foundation
* TBA  -  GlaxoSmithKline
* John McNeil  -  John McNeil & Co
* Tianhong Zhang  -  Pfizer
* Craig Martin  -  SkunkWerks Software
* Nicholas Goncharoff  -  SureChem
* Tobias Kind  -  UC Davis Genome Center – Metabolomics
* Craig Knox  -  University of Alberta
* Oleg Ursu  -  University of New Mexico

ChemAxon Partners participants (tbc) - see partner listing here: http://www.chemaxon.com/partners/integrators.html

--
Alex Allardyce
Marketing Dir.
ChemAxon Ltd.
Maramaros koz 3/A, Budapest, 1037, Hungary
Tel: +361 453 0435
skype: alex_allardyce

--------------000600010903050600060002-- From owner-chemistry@ccl.net Mon Jul 20 15:45:01 2009 From: "Kalju Kahn kalju]![chem.ucsb.edu" To: CCL Subject: CCL:G: Package for CCSD(T) Message-Id: <-39824-090720150725-21440-ojukA5bhWNi+ADWeuLvmUw^^^server.ccl.net> X-Original-From: "Kalju Kahn" Content-Transfer-Encoding: 8bit Content-Type: text/plain;charset=iso-8859-1 Date: Mon, 20 Jul 2009 12:06:52 -0700 MIME-Version: 1.0 Sent to CCL by: "Kalju Kahn" [kalju()chem.ucsb.edu] Neha, I have found DIRCCR12 a good free choice on a desktop system. Water in aug-cc-pV6Z basis (443 bf, run with very tight SCF, integral, and CC convergence criteria) took 754 min on dual-core E8400 ~ 3.00GHz with 8 GB RAM Please note that you need to tighten some convergence criteria with aug basis (how much depends on your needed accuracy, of course). And when you have more than about 500 basis functions, you will need more than 8 GB of RAM. You can get the software (after e-mailing Dr. Jozef Noga) from http://www-laog.obs.ujf-grenoble.fr/~valiron/ccr12/. Psi3 (http://www.psicode.org/index.html) is another nice choice if you need a very fast and free code. However, I spent a significantly more effort getting it working (at least with the old 3.2 version), and experienced a share of crashes during some more demanding calculations. Formic acid CCSD/cc-pV5Z calculation (518 AO, 383 symmetry orbitals in Cs symmetry) completed in 1100 minutes with default settings on (now almost too old) Core 2 6300 ~ 1.86GHz. I think most CC codes will use disk for reading and writing very large files, so make sure that you have an appropriate hardware (minimally a pair of fast disks in RAID0 for scratch space) to support these calculations. Best wishes, Kalju > > Sent to CCL by: "Neha Awasthi" [neha.awasthi-#-gmail.com] > Hello CCL community, > > I wanted to ask for advise for a reliable program for performing CCSD and > CCSD(T) calculations using (aug)-cc-pVxZ (where x = D, T, Q...) basis > sets. > I have tried Gaussian, G03, and it turns out to be very inefficient (save > large scratch files, and slow) for small molecules upto ~5 atoms. > > Please let me know which package/program is considered reliable as well as > has good performance. > > It would be ideal to have one with a free license or free to download :) > I will compile all responses and post them. > > Thank you, > Neha> > > ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Dr. Kalju Kahn Department of Chemistry and Biochemistry UC Santa Barbara, CA 93106 From owner-chemistry@ccl.net Mon Jul 20 16:20:01 2009 From: "Sebastian Kozuch kozuchs(!)yahoo.com" To: CCL Subject: CCL:G: Package for CCSD(T) Message-Id: <-39825-090720151427-27215-6wh0IGZ9or7AyzimESmmTg .. server.ccl.net> X-Original-From: Sebastian Kozuch Content-Type: multipart/alternative; boundary="0-2078458255-1248113301=:27622" Date: Mon, 20 Jul 2009 11:08:21 -0700 (PDT) MIME-Version: 1.0 Sent to CCL by: Sebastian Kozuch [kozuchs^^yahoo.com] --0-2078458255-1248113301=:27622 Content-Type: text/plain; charset=us-ascii MOLPRO is very efficient but it's not free. It has a trial although. For free programs you may try ORCA or GAMESS. xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx ..........Sebastian Kozuch........... xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx ...The Lise Meitner-Minerva Center... .for Computational Quantum Chemistry. ...Hebrew University of Jerusalem.... .....kozuchs],[yfaat.ch.huji.ac.il..... http://yfaat.ch.huji.ac.il/kozuch.htm xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx ________________________________ > From: Neha Awasthi neha.awasthi%%gmail.com To: "Kozuch, Sebastian " Sent: Monday, July 20, 2009 7:44:34 PM Subject: CCL:G: Package for CCSD(T) Sent to CCL by: "Neha Awasthi" [neha.awasthi-#-gmail.com] Hello CCL community, I wanted to ask for advise for a reliable program for performing CCSD and CCSD(T) calculations using (aug)-cc-pVxZ (where x = D, T, Q...) basis sets. I have tried Gaussian, G03, and it turns out to be very inefficient (save large scratch files, and slow) for small molecules upto ~5 atoms. Please let me know which package/program is considered reliable as well as has good performance. It would be ideal to have one with a free license or free to download :) I will compile all responses and post them. Thank you, Nehahttp://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt--0-2078458255-1248113301=:27622 Content-Type: text/html; charset=us-ascii
MOLPRO is very efficient but it's not free. It has a trial although.
For free programs you may try ORCA or GAMESS.
 
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
..........Sebastian Kozuch...........
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
...The Lise Meitner-Minerva Center...
.for Computational Quantum Chemistry.
...Hebrew University of Jerusalem....
.....kozuchs],[yfaat.ch.huji.ac.il.....
http://yfaat.ch.huji.ac.il/kozuch.htm
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx


From: Neha Awasthi neha.awasthi%%gmail.com <owner-chemistry],[ccl.net>
To: "Kozuch, Sebastian " <kozuchs],[yahoo.com>
Sent: Monday, July 20, 2009 7:44:34 PM
Subject: CCL:G: Package for CCSD(T)


Sent to CCL by: "Neha  Awasthi" [neha.awasthi-#-gmail.com]
Hello CCL community,

I wanted to ask for advise for a reliable program for performing CCSD and CCSD(T) calculations using (aug)-cc-pVxZ (where x = D, T, Q...) basis sets.
I have tried Gaussian, G03, and it turns out to be very inefficient (save large scratch files, and slow) for small molecules upto ~5 atoms.

Please let me know which package/program is considered reliable as well as has good performance.

It would be ideal to have one with a free license or free to download :)
I will compile all responses and post them.

Thank you,
Neha



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--0-2078458255-1248113301=:27622-- From owner-chemistry@ccl.net Mon Jul 20 16:55:00 2009 From: "Kalju Kahn kalju|*|chem.ucsb.edu" To: CCL Subject: CCL: Is there any database that classifies ligands in PDB complexes according to their biological effect on their target? Message-Id: <-39826-090720154317-7349-ydE9fsujSd52x5eWAw+jrw*server.ccl.net> X-Original-From: "Kalju Kahn" Content-Transfer-Encoding: 8bit Content-Type: text/plain;charset=iso-8859-1 Date: Mon, 20 Jul 2009 12:43:05 -0700 MIME-Version: 1.0 Sent to CCL by: "Kalju Kahn" [kalju\a/chem.ucsb.edu] Gerard, I do not know the answer but please keep in mind that in multi-substrate enzymes (which most enzymes are), the terms competitive/uncompetitive/non-competitive are not as simple as intro textbooks lead us to think. For example, in the case of a bi-substrate enzyme with ordered sequential mechanism, inhibitor that will structurally resemble the second substrate acts as a competitive inhibitor with respect to the second substrate but will be uncompetitive with respect to the first. Take p38 MAP kinase, where the protein binds first, followed by ATP. ATP analogs will obviously compete with ATP, but are uncompetitive with the protein substrate. And molecules that will bind to the protein binding site will be competitive with the protein substrate but not with ATP. I think (do not have my Segel book with me) that such molecules will be non-competitive with respect to ATP. In some other kinases, ATP and substrate protein binding is random, and the modes of inhibition would be different. The situations with receptors is not much better. Depending on the level of constitutive activity of a receptor, and the level of the native ligand (which both are species and individual/disease dependent), a compound could be classified as an inverse agonist or antagonist. Thus, one has to be careful when working with a database with such tags. My $0.02 Kalju > Dear CCL subscribers, > > sorry for cross-posting > > I wonder if there is any database that classifies ligands in PDB complexes > according to their biological effect on their corresponding target > (*i.e.*they become classified as inhibitors, activators, agonists, > antagonists, > etc. of their corresponding target) > > For instance, I would like to retrieve in an easy way which are the PDB > files that correspond to complexes between one enzyme and one competitive > inhibitor for this inhibitor. Then, I would like to know which are the > three-letter code in the PDB file that identifies each inhibitor. > > Any help should be highly appreciated > > Best regards > > Gerard > ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Dr. Kalju Kahn Department of Chemistry and Biochemistry UC Santa Barbara, CA 93106 From owner-chemistry@ccl.net Mon Jul 20 17:29:00 2009 From: "John McKelvey jmmckel ~~ gmail.com" To: CCL Subject: CCL:G: Package for CCSD(T) Message-Id: <-39827-090720162917-2163-R8K9N5rHGN6PotM3Y4j8wA#server.ccl.net> X-Original-From: John McKelvey Content-Type: multipart/alternative; boundary=0016368e1b7419160c046f28fdd6 Date: Mon, 20 Jul 2009 16:29:02 -0400 MIME-Version: 1.0 Sent to CCL by: John McKelvey [jmmckel**gmail.com] --0016368e1b7419160c046f28fdd6 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Hello... You might want to look at ORCA for CCSD(T) also. The code is free for academics. John McKelvey On Mon, Jul 20, 2009 at 12:44 PM, Neha Awasthi neha.awasthi%%gmail.com < owner-chemistry]|[ccl.net> wrote: > > Sent to CCL by: "Neha Awasthi" [neha.awasthi-#-gmail.com] > Hello CCL community, > > I wanted to ask for advise for a reliable program for performing CCSD and > CCSD(T) calculations using (aug)-cc-pVxZ (where x = D, T, Q...) basis sets. > I have tried Gaussian, G03, and it turns out to be very inefficient (save > large scratch files, and slow) for small molecules upto ~5 atoms. > > Please let me know which package/program is considered reliable as well as > has good performance. > > It would be ideal to have one with a free license or free to download :) > I will compile all responses and post them. > > Thank you, > Neha> > > --0016368e1b7419160c046f28fdd6 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Hello...

You might want to look at ORCA for CCSD(T) also.=A0 The cod= e is free for academics.

John McKelvey

On Mon, Jul 20, 2009 at 12:44 PM, Neha Awasthi neha.awasthi%%gmail.com <owner-chemistry]|[ccl.net> wrote:

Sent to CCL by: "Neha =A0Awasthi" [neha.awasthi-#-gmail.com]
Hello CCL community,

I wanted to ask for advise for a reliable program for performing CCSD and C= CSD(T) calculations using (aug)-cc-pVxZ (where x =3D D, T, Q...) basis sets= .
I have tried Gaussian, G03, and it turns out to be very inefficient (save l= arge scratch files, and slow) for small molecules upto ~5 atoms.

Please let me know which package/program is considered reliable as well as = has good performance.

It would be ideal to have one with a free license or free to download :) I will compile all responses and post them.

Thank you,
Neha



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--0016368e1b7419160c046f28fdd6-- From owner-chemistry@ccl.net Mon Jul 20 19:46:00 2009 From: "Sarah MOHAMED mohamedsarah78__yahoo.fr" To: CCL Subject: CCL: PCM IO file error on G03 Message-Id: <-39828-090720193901-8542-mNYTzy0WLT3Vuacf3R6q4w-#-server.ccl.net> X-Original-From: "Sarah MOHAMED" Date: Mon, 20 Jul 2009 19:38:57 -0400 Sent to CCL by: "Sarah MOHAMED" [mohamedsarah78 ~ yahoo.fr] Dear subscribers, Thank you very much to all persons who help me to resolve my memory's problem. Today, I am facing with an other problem of PCM input/output file. Please which commandes are used in the end of the input file to create a cavity: (Rmin=0.5 and OFac=0.8?), or (RADII=PAULING, ALPHA=1.2, TABS =298.158, TSNUM=70 and TSARE=0.4), or (RADII=PAULING)?? The route section of the input file is given below: %chk=PCM.chk %mem=500MB %nproc=1 Will use up to 1 processors via shared memory. Default route: MaxDisk=2000MB ---------------------------------------------------------------------- # b3lyp/6-31g(d) opt=(maxcycle=500) scf=(qc,tight) scrf=(iefpcm,solven t=water,read) geom=connectivity Polarizable Continuum Model (PCM) ================================= Model : PCM. Atomic radii : UA0 (Simple United Atom Topological Model). Polarization charges : Total charges. Charge compensation : None. Solution method : Matrix inversion. Cavity : GePol (RMin=0.500 OFac=0.800). Default sphere list used, NSphG= 30. Tesserae with average area of 0.200 Ang**2. 1st derivatives : Analytical V*U(x)*V algorithm (CHGder, D1EAlg=0). Cavity 1st derivative terms included. Solvent : Water, Eps= 78.390000. And the end of the output file is : Error termination in NtrErr: NtrErr Called from FileIO. Please, can anyone kindly help me to identify the error and correct it. Thanks in advance. With best considerations.