From owner-chemistry@ccl.net Thu Jun 11 02:06:00 2009 From: "Jerome Kieffer jerome.Kieffer|-|terre-adelie.org" To: CCL Subject: CCL: Application in idle time in a distributed Windows PC network (with 32 bit XPs)? Message-Id: <-39493-090610165006-26568-XdtEp4ebe3Le48Syl5X6sw:-:server.ccl.net> X-Original-From: Jerome Kieffer Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset=ISO-8859-15 Date: Wed, 10 Jun 2009 22:49:07 +0200 Mime-Version: 1.0 Sent to CCL by: Jerome Kieffer [jerome.Kieffer__terre-adelie.org] On Tue, 9 Jun 2009 17:28:13 +0200 "andras.borosy[a]givaudan.com" wrote: > Do you know an application which is capable to generate COSMO files and=20 > can be run in idle time in a distributed Windows PC network (with 32 bit= =20 > XPs)? I am doing this on linux computers but as -the Turbomole binary for windows exists -Bash, Perl and Python scripting languages are available within cygwin -many queueing manager exist for windows (PBS/torque at least) This should be possible. I am doing this with MOPAC and we notices an accelerated =ABdeath=BB of standard desktop computer (lifetime shrinking to 3 years, overheated hard-disks dieing) Nevertheless, maintaining crappy winXP computer is the hell, go for a dual-quadCPU at 1000=A4 you will get more out of it. With my best regards, --=20 J=E9r=F4me KIEFFER =20 http://www.terre-adelie.org From owner-chemistry@ccl.net Thu Jun 11 04:58:02 2009 From: "li_qiang_000739(a)wuxiapptec.com li_qiang_000739(a)wuxiapptec.com" To: CCL Subject: CCL: =?gb2312?B?tPC4tDogRG8geW91IGhhdmUgdGhlIGV4cGVyaWVuY2UgYWJvdXQgU3RlcmVv?= =?gb2312?B?IExDRCBtb25pdG9yIGZvciBtb2xlY3VsYXIgbW9kZWxpbmc/?= Message-Id: <-39494-090611045607-28549-FghTnz87uRThZEpb/aHNEA(-)server.ccl.net> X-Original-From: "li_qiang_000739##wuxiapptec.com" Content-Language: zh-CN Content-Transfer-Encoding: base64 Content-Type: text/plain; charset="gb2312" Date: Thu, 11 Jun 2009 16:55:32 +0800 MIME-Version: 1.0 Sent to CCL by: "li_qiang_000739*_*wuxiapptec.com" [li_qiang_000739*_*wuxiapptec.com] DQpNYW55IHRoYW5rcyBmb3IgVmluY2VudC5MZXJvdXgsIFdhcnJlbiBEZUxhbm8gYW5kIFBhc2Nh bCBNdWxsZXIncyByZXBseS4NCg0KSXQncyBkaWZmaWN1bHQgdG8gZmluZCBhIGxhcmdlciBDUlQg bW9uaXRvci4gSSB3aWxsIHdhaXQgdGhlIG5ldyBkcml2ZXIuDQoNCkJlc3QgcmVnYXJkcywNCg0K 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Subject: CCL: Computer touls Message-Id: <-39495-090610131745-27777-1o9enmOXiGEeBxE4sfyklw++server.ccl.net> X-Original-From: Elda Rossi Content-Transfer-Encoding: 7bit Content-Type: text/html; charset=ISO-8859-1 Date: Wed, 10 Jun 2009 18:37:02 +0200 (MEST) MIME-Version: 1.0 Sent to CCL by: Elda Rossi [e.rossi##cineca.it] Daniel Kovich daniel.kovich],[gmail.com ha scritto:
Dear all,
Is there, in this forum, some one who is expert in fortran? I need some help to finalize the model of the Saccharomyces cerevisae's making.
  Thank you.
Dr. Dan
Univ Trieste Italy
Dear Dan,
yes, we are expert in Fortran and we work for a Consortium you University is part of.
So it is our job (and pleasure) to support you for this type of problems.
Please do not hesitate to contact us by sending a mail to our help desk
superc.++.cineca.it

Regards,
Elda Rossi



-- 
Elda Rossi
   CINECA
   via Magnanelli 6/3,
   40033 Casalecchio di Reno (Bologna) - Italy
   tel: +39 051 6171515
   Fax: +39 051 6132198
   eMail: e.rossi.++.cineca.it
From owner-chemistry@ccl.net Thu Jun 11 09:12:01 2009 From: "Jacopo Sgrignani sgrigna**gmail.com" To: CCL Subject: CCL: QM/MM molecular dynamics Message-Id: <-39496-090611091000-19683-4QkiKnl5fBkbcGKRXCmRWA : server.ccl.net> X-Original-From: Jacopo Sgrignani Content-Type: multipart/alternative; boundary=0015174bee8890e6a8046c11aa0a Date: Thu, 11 Jun 2009 14:23:58 +0200 MIME-Version: 1.0 Sent to CCL by: Jacopo Sgrignani [sgrigna*gmail.com] --0015174bee8890e6a8046c11aa0a Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Dear all could anybody suggest me some references about molecular dynamics of metalloproteins with semiempirical quantum potentials? Thanks a lot Jacopo --0015174bee8890e6a8046c11aa0a Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Dear all
could anybody suggest me some references about molecular dynamics of metalloproteins with semiempirical quantum potentials?
Thanks a lot

Jacopo
--0015174bee8890e6a8046c11aa0a-- From owner-chemistry@ccl.net Thu Jun 11 10:29:00 2009 From: "Barry Hardy barry.hardy ~~ vtxmail.ch" To: CCL Subject: CCL: eCheminfo 2009 Community of Practice Meeting Program Message-Id: <-39497-090611102542-21493-qb1yJAWj7Rhgb94hGf3L3w(!)server.ccl.net> X-Original-From: Barry Hardy Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Thu, 11 Jun 2009 16:25:02 +0200 MIME-Version: 1.0 Sent to CCL by: Barry Hardy [barry.hardy\a/vtxmail.ch] The eCheminfo 2009 community of practice meeting on drug discovery informatics will take place at Bryn Mawr College, Philadelphia 13-16 October 2009. This annual community of practice meeting is taking place for the fifth time and brings together a unique combination of pharmaceutical and healthcare industry experts, principal investigators and researchers > from the academic and government sectors, and leaders from innovative enterprises. The smaller and more intimate meeting format pursued has fostered the type of collaboration not always found at large conferences. The preliminary program with abstracts received so far is now available at http://echeminfo.com/COMTY_conferencesprog09 and will be updated as remaining abstracts are received. The topics addressed this year will include Structure-based Drug Design Applications and Methods, Macromolecular Interactions and Networks, Data Analysis and Visualisation, PDB Ligands, and Predictive Toxicology. A pre-conference best practices workshop on Binding Energy prediction will take place October 12, 2009. This meeting will take place concurrently with the InnovationWell 2009 meeting addressing the topics of Collaboration in Discovery and Development, Translational Bioinformatics, Systems Biology and Biomarkers, Blood Brain Barrier modeling and Predictive Toxicology. Below is a short summary of the eCheminfo program. best regards Barry Hardy eCheminfo Community of Practice Douglas Connect Tel: +41 61 851 0170 email: barry.hardy -(at)- douglasconnect.com Latest Advances in Drug Discovery Informatics eCheminfo 2009 InterAction Meeting October 13-16, 2009 Bryn Mawr College, Bryn Mawr, Philadelphia, USA Conference Link with Abstracts: http://echeminfo.com/comty_conferences Program as pdf download: http://barryhardy.blogs.com/files/echeminfoprogrambrynmawr09.pdf Program Summary Monday 12 October Pre-conference Workshop on Drug Binding Affinities Co-Chaired by Scott Brown (Abbott Laboratories) and Judith Lalonde (Bryn Mawr College) Tuesday 13 October Structure-Based Drug Design Applications, Chaired by Alan Cheng (Amgen) Macromolecular Interactions and Networks, Chaired by Emil Alexov (Clemson University) Wednesday 14 October Structure-Based Drug Design Methods, Chaired by Natasja Brooijmans (Wyeth) Data Analysis and Visualisation Applications in Chemical Biology, Chaired by Brian Marsden (Structural Genomics Consortium Oxford) Thursday 15 October PDB Ligands, Chaired by John Westbrook (Rutgers University) Predictive Toxicology, Co-Chaired by Richard Judson (US EPA) and Vladimir Poroikov (Institute of Biomedical Chemistry of the Russian Academy of Medical Sciences) Friday 16 October Predictive Toxicology, Co-Chaired by Richard Judson (US EPA) and Vladimir Poroikov (Institute of Biomedical Chemistry of the Russian Academy of Medical Sciences) Registration Enquiries: Nicki Douglas, Douglas Connect, Baermeggenweg 14, 4314 Zeiningen, Switzerland. Tel: +41 61 851 0461. echeminfo -(at)- douglasconnect.com From owner-chemistry@ccl.net Thu Jun 11 12:44:01 2009 From: "Ol Ga eurisco1]^[pochta.ru" To: CCL Subject: CCL: casscf convergence Message-Id: <-39498-090611120420-9345-XZRDMublr/wV0SdRz5ONvw..server.ccl.net> X-Original-From: "Ol Ga" Date: Thu, 11 Jun 2009 12:04:16 -0400 Sent to CCL by: "Ol Ga" [eurisco1-*-pochta.ru] Dear Rajagopala Reddy Seelam, First, you are calculating the _ground_ state. I looked on the orbitals of B7 cluster and I think that the CASSCF solution seems to be plagued by intruder states. The choice of flexible enough is difficult task and requires practice. Sincerely, Ol Ga > Sent to CCL by: "Rajagopala Reddy Seelam" [rajagopalaseelam]|[gmail.com] > Dear CCL members, > I am doing CASSCF(9,9) calculations on a boron cluster having 7 > boron atoms.I am calculating first excited state of that cluster.But > my job is not converging even after 115 steps.That is not worrying > me but the energy is diverging.B7 first excited state energy roughly > around -172.53 hartrees.But it is now going towards -4603.54 > hartrees.Is there any problem with my active space or it is only > matter of convergence criteria. Below I am attaching input and output files. > The input is as follows > %mem= 1GB > #p casscf(9,9,nroot=1) Symm=Loose aug-cc-pvdz scf(maxcyc=999) > Distortion along normal mode N 4 by + 0.250 Q > 0 2 > 5 0.000000 0.000000 0.323955 > 5 0.000000 1.651157 -0.058734 > 5 0.000000 -1.641000 -0.049251 > 5 -1.421148 0.820500 -0.049251 > 5 1.421148 0.820500 -0.049251 > 5 -1.429945 -0.825578 -0.058735 > 5 1.429945 -0.825578 -0.058735 > 9 10 11 > this is the output last part > ITN=115 MaxIt=999 E= -4601.8497836710 DE=-8.86D+00 Acc= 1.00D-05 Lan= 46 > In Davids. NSec= 15876 > IMaxHF,MaxMI,MSekIn,IFactt,WhenSc,nroot 50 50 2 2 2 1 > ( 1) EIGENVALUE -0.46018498E+04 From owner-chemistry@ccl.net Thu Jun 11 18:34:00 2009 From: "Tae Bum Lee tzl0002,,auburn.edu" To: CCL Subject: CCL:G: ionic radii of group I atom in UAKS model Message-Id: <-39499-090611183045-22874-Mzko45kY7zYPeskfe0v3vw#%#server.ccl.net> X-Original-From: "Tae Bum Lee" Date: Thu, 11 Jun 2009 18:30:41 -0400 Sent to CCL by: "Tae Bum Lee" [tzl0002||auburn.edu] Hi, Does anybody know how to get the value of ionic radii when the UAKS model of CPCM is applied? I am wondering where this ionic radius information is available. Any reference or place of information in G03 source code is helpful. I got the information of ionic radii of Pauling and UFF for (C)PCM method in G03 from literature. My interesting ions are Li+, Na+, and K+. > From G03 reference manual, the UAKS model comes from the optimized United atom topological model with PBE0/6-31G(d). May I calculate it in my hands with another DFT method? Regards, TaeBum From owner-chemistry@ccl.net Thu Jun 11 23:52:01 2009 From: "Tae Bum Lee taebumlee*gmail.com" To: CCL Subject: CCL:G: ionic radii of group I atom in UAKS model Message-Id: <-39500-090611182556-22393-/XpCIFhiSbd64I78zd8lHw##server.ccl.net> X-Original-From: "Tae Bum Lee" Date: Thu, 11 Jun 2009 18:25:53 -0400 Sent to CCL by: "Tae Bum Lee" [taebumlee%gmail.com] Hi, Does anybody know how to get the value of ionic radii when the UAKS model of CPCM is applied? I am wondering where this ionic radius information is available. Any reference or place of information in G03 source code is helpful. I got the information of ionic radii of Pauling and UFF for (C)PCM method in G03 from literature. My interesting ions are Li+, Na+, and K+. > From G03 reference manual, the UAKS model comes from the optimized United atom topological model with PBE0/6-31G(d). May I calculate it in my hands with another DFT method? Regards, TaeBum