From owner-chemistry@ccl.net Mon Jul 2 05:53:01 2007 From: "izwan zainurul zainurulizwan80..yahoo.com" To: CCL Subject: CCL: books Message-Id: <-34612-070630012916-28509-pXn/U8kCPHb06EGaeoAIZg]-[server.ccl.net> X-Original-From: izwan zainurul Content-Transfer-Encoding: 8bit Content-Type: multipart/alternative; boundary="0-1100722134-1183177725=:19653" Date: Fri, 29 Jun 2007 21:28:45 -0700 (PDT) MIME-Version: 1.0 Sent to CCL by: izwan zainurul [zainurulizwan80^yahoo.com] --0-1100722134-1183177725=:19653 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit Hai all, can someone suggest to me any books that discuss about 1. Binding Energy 2. Energy of formation of complex best wishes, -izwan --------------------------------- Pinpoint customers who are looking for what you sell. --0-1100722134-1183177725=:19653 Content-Type: text/html; charset=iso-8859-1 Content-Transfer-Encoding: 8bit
Hai all,
 
can someone suggest to me any books that discuss about
1. Binding Energy
2. Energy of formation of complex
 
best wishes,
-izwan

Pinpoint customers who are looking for what you sell. --0-1100722134-1183177725=:19653-- From owner-chemistry@ccl.net Mon Jul 2 07:05:01 2007 From: "Tapta Kanchan Roy ch05ph03]_[uohyd.ernet.in" To: CCL Subject: CCL:G: Optimization problems by CASSCF Message-Id: <-34613-070702070201-15787-BoQz8J5iIohQeFWNDFjUyg[]server.ccl.net> X-Original-From: "Tapta Kanchan Roy" Date: Mon, 2 Jul 2007 07:01:57 -0400 Sent to CCL by: "Tapta Kanchan Roy" [ch05ph03|a|uohyd.ernet.in] Dear all, I am trying to optimize a molecule contains nitrogens hydrogens and one chlorine atom in CASSCF(8,8)/aug-cc-pvdz level of theoy ( 210 basis functions). But in the first cycle only the run terminated showing convergence failure. I am providing last few lines of the output below. I have also tried with CASSCF(8,6)/aug-cc-pvdz and CASSCF(6,6)/aug-cc-pvdz and using the additional keywords like guess=alter and guess=permute, but I got the same results. Please suggest what to change and correct Thanks Regards T.K.Roy ********************** ITN= 61 MaxIt= 64 E= -788.9207475905 DE=-5.69D-06 Acc= 1.00D-08 Lan= 0 ITN= 62 MaxIt= 64 E= -788.9207534054 DE=-5.81D-06 Acc= 1.00D-08 Lan= 0 ITN= 63 MaxIt= 64 E= -788.9207593754 DE=-5.97D-06 Acc= 1.00D-08 Lan= 0 ITN= 64 MaxIt= 64 E= -788.9207655258 DE=-6.15D-06 Acc= 1.00D-08 Lan= 0 ... Do an extra-iteration for final printing. Final one electron symbolic density matrix: 1 2 3 4 5 1 .197555D+01 2 .225320D-04 .198344D+01 3 -.610699D-05 -.797370D-06 .197328D+01 4 -.104574D-04 .330710D-04 .832318D-04 .256568D-01 5 .452880D-04 .141917D-03 -.113240D-04 -.565741D-05 .157775D-01 6 -.502650D-04 -.578564D-04 -.786480D-06 -.578304D-03 .289431D-05 6 6 .262991D-01 Convergence failure -- run terminated. Error termination via Lnk1e in /opt/g03/l510.exe at Sun Jul 1 21:30:17 2007. **************************** From owner-chemistry@ccl.net Mon Jul 2 09:10:00 2007 From: "Prof. E.-U. Wuerthwein wurthwe:uni-muenster.de" To: CCL Subject: CCL:G: MP2 Errors Message-Id: <-34614-070702085547-17038-xDFRbuPZccqzzBIMykacLw%server.ccl.net> X-Original-From: "Prof. E.-U. Wuerthwein" Content-Type: TEXT/PLAIN; charset=US-ASCII; format=flowed Date: Mon, 2 Jul 2007 13:57:35 +0200 (MES) MIME-Version: 1.0 Sent to CCL by: "Prof. E.-U. Wuerthwein" [wurthwe*uni-muenster.de] Have you tried "MP2(FullDirect)"? With %mem=200000000 or even less I expect that your job will run. Good luck! Ernst On Sun, 1 Jul 2007, Soren Eustis soren . jhu.edu wrote: > Date: Sun, 1 Jul 2007 02:27:33 -0400 > From: Soren Eustis soren . jhu.edu > Reply-To: CCL Subscribers > To: "Wuerthwein, Ernst-ulrich " > Subject: CCL:G: MP2 Errors > > Anyone have any ideas on this error I keep receiving from G03 when doing > larger MP2 jobs? This current error is for a 14 atom system (8 heavy). I > am wondering if I am running up against a limitation of memory (I am using > 2GB) or diskspace (allowing 10GB). I am running on a dual 3GHz xeon system. > > > > > . > > > > Inv2: IOpt= 1 Iter= 1 AM= 1.23D-14 Conv= 1.00D-12. > > Inverted reduced A of dimension 408 with in-core refinement. > > End of Minotr Frequency-dependent properties file 721 does not exist. > > MDV= 183500800. > > Form MO integral derivatives with frozen-active canonical formalism. > > Discarding MO integrals. > > Reordered first order wavefunction length = 203957535 > > In DefCFB: NBatch= 1, ICI= 35, ICA=170, LFMax= 29 > > Large arrays: LIAPS= 1946796480, LIARS= 390843600 words. > > Internal consistency error detected in FileIO for unit 1 I= 6 J= 0 > IFail= 1. > > > > > > dumping /fiocom/, unit = 1 NFiles = 102 SizExt = 524288 WInBlk = > 512 > > defal = T LstWrd = -1657244160 FType=2 FMxFil=10000 > > > > Number 0 0 0 0 0 0 > 22 23 > > Base 74894504 1955328 6093824 60264448 69413888-1657776128 > 6226944 14673920 > > End 74894848 1958400 6142976 60306432 70628864-1657244160 > 14673564 48862620 > > End1 74894848 1958400 6142976 60306432 70628864 > > > > > > . > > > > Thanks! > > > > Soren N. Eustis > > Graduate Research Assistant > > Department of Chemistry > > Johns Hopkins University > > Remsen Hall > > 3400 N Charles Street > > Baltimore, MD 21218 > > (410) 516-4675 (office) > > (410) 925-5167 (cell) > > (410) 516-8420 (fax) > > soren- -jhu.edu > > ________________________________________________________________________ | | | Prof.Dr.Ernst-Ulrich Wuerthwein E-Mail: wurthwe(a)uni-muenster.de | | Institut fuer Organische Chemie Phone: +251/83-33261 | | Corrensstrasse 40 Fax: +251/83-39772 | | D-48149 Muenster Germany | | http://www.uni-muenster.de/Chemie/OC/research/wue/euw.htm | |______________________________________________________________________| From owner-chemistry@ccl.net Mon Jul 2 09:45:01 2007 From: "Bhabani S Mallik mbhabani~!~yahoo.com" To: CCL Subject: CCL: Managing downloaded reference pdf files Message-Id: <-34615-070702092646-25563-G3/oCO6gvKBz9uz1yNCquQ##server.ccl.net> X-Original-From: "Bhabani S Mallik" Date: Mon, 2 Jul 2007 09:26:43 -0400 Sent to CCL by: "Bhabani S Mallik" [mbhabani_+_yahoo.com] Dear All, I want to manage all my reference pdf files ( huge number) with a proper way. I mean is there any software which can convert all my files to browsable html pages with title, author, year of publication and a link to that pdf file ? From owner-chemistry@ccl.net Mon Jul 2 10:35:00 2007 From: "Qian Wang xie.wang---gmail.com" To: CCL Subject: CCL:G: Optimization problems by CASSCF Message-Id: <-34616-070702103338-4514-frxas/4RFX6MuFTYTaVqVA.:.server.ccl.net> X-Original-From: "Qian Wang" Content-Disposition: inline Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Mon, 2 Jul 2007 10:33:32 -0400 MIME-Version: 1.0 Sent to CCL by: "Qian Wang" [xie.wang-x-gmail.com] Hi Tapta, I am not expert on cas, but it looks that your wavefunction did not converge. if you are sure of approriate active space orbitals, try gaussian manual: Efficiency considerations: scf energies and gradients: problem convergence cases. Other thing you can try is to use scf=(maxcyc=n), set n > 64. you can also reduce SCF convergence criterion: scf=singlepoint, but i don't know if it is good for your geometry optimization. or you can reduce your active space so the scf convergence would be easier. Good luck, Qian On 7/2/07, Tapta Kanchan Roy ch05ph03]_[uohyd.ernet.in wrote: > > Sent to CCL by: "Tapta Kanchan Roy" [ch05ph03|a|uohyd.ernet.in] > Dear all, > I am trying to optimize a molecule contains nitrogens hydrogens and one chlorine atom in CASSCF(8,8)/aug-cc-pvdz level of theoy ( 210 basis functions). But in the first cycle only the run terminated showing convergence failure. I am providing last few lines of the output below. I have also tried with CASSCF(8,6)/aug-cc-pvdz and CASSCF(6,6)/aug-cc-pvdz and using the additional keywords like guess=alter and guess=permute, but I got the same results. > Please suggest what to change and correct > Thanks > Regards > T.K.Roy > ********************** > ITN= 61 MaxIt= 64 E= -788.9207475905 DE=-5.69D-06 Acc= 1.00D-08 Lan= 0 > ITN= 62 MaxIt= 64 E= -788.9207534054 DE=-5.81D-06 Acc= 1.00D-08 Lan= 0 > ITN= 63 MaxIt= 64 E= -788.9207593754 DE=-5.97D-06 Acc= 1.00D-08 Lan= 0 > ITN= 64 MaxIt= 64 E= -788.9207655258 DE=-6.15D-06 Acc= 1.00D-08 Lan= 0 > ... Do an extra-iteration for final printing. > Final one electron symbolic density matrix: > 1 2 3 4 5 > 1 .197555D+01 > 2 .225320D-04 .198344D+01 > 3 -.610699D-05 -.797370D-06 .197328D+01 > 4 -.104574D-04 .330710D-04 .832318D-04 .256568D-01 > 5 .452880D-04 .141917D-03 -.113240D-04 -.565741D-05 .157775D-01 > 6 -.502650D-04 -.578564D-04 -.786480D-06 -.578304D-03 .289431D-05 > 6 > 6 .262991D-01 > Convergence failure -- run terminated. > Error termination via Lnk1e in /opt/g03/l510.exe at Sun Jul 1 21:30:17 2007. > ****************************> > > > From owner-chemistry@ccl.net Mon Jul 2 13:19:00 2007 From: "Jeff Nauss jnauss+/-accelrys.com" To: CCL Subject: CCL: Accelrys Customer Training Events for July and August Message-Id: <-34617-070702130121-16323-O2r6XFMGWd0ek2eZKjz2Zg-*-server.ccl.net> X-Original-From: Jeff Nauss Content-Type: text/plain; charset="US-ASCII" Date: Mon, 2 Jul 2007 10:01:08 -0700 MIME-Version: 1.0 Sent to CCL by: Jeff Nauss [jnauss%a%accelrys.com] Accelrys Inc. are holding the following training workshops during July and August. These events are designed to help you get more value from your Accelrys software, helping you to better accomplish your research goals. Cost for the on-line presentations is $175 per three hour session for all customers. ON-LINE TRAINING Introduction to Discovery Studio 3 July (4pm BST) Insight II to Discovery Studio Migration 6 July (4pm BST) Sequence Analysis for Homology Modeling 10 July (4pm BST) Protein Homology Modeling in Discovery Studio 11 July (4pm BST) Simulations in Discovery Studio (Part 1) 12 July (4pm BST) Simulations in Discovery Studio (Part 2) 13 July (4pm BST) Solvation Models in CHARMm 18 July (7am PDT) Docking & Scoring in Discovery Studio 23 July (4pm BST) De Novo Design with Discovery Studio 24 July (4pm BST) Catalyst to Discovery Studio Migration 25 July (4pm BST) Pharmacophore Modeling with Discovery Studio (Part 1) 26 July (4pm BST) Pharmacophore Modeling with Discovery Studio (Part 2) 27 July (4pm BST) Introduction to Discovery Studio 2 Aug (7am PDT) Catalyst Migration 8 Aug (4pm BST) Insight II to Discovery Studio Migration 15 Aug (7am PDT) Introduction to Materials Studio 21 Aug (4pm BST) Scripting in Materials Studio 22 Aug (4pm BST) Further details can be found on our website at http://www.accelrys.com/services/training/general/calendar.html. Questions regarding scheduling and content should be directed to workshops * accelrys.com. -- Jeffrey L. Nauss, Ph.D. Lead Training Scientist Accelrys 10188 Telesis Court, Suite 100 San Diego, CA 92121-4779 Phone: +1-858-799-5555 Fax: +1-858-799-5100 http://www.accelrys.com/services/training/ From owner-chemistry@ccl.net Mon Jul 2 14:40:00 2007 From: "Jerome Kieffer jerome.Kieffer+/-terre-adelie.org" To: CCL Subject: CCL: Managing downloaded reference pdf files Message-Id: <-34618-070702140928-14977-wRZUBQJskNNhBPM9RKHbjg*server.ccl.net> X-Original-From: Jerome Kieffer Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=ISO-8859-15 Date: Mon, 2 Jul 2007 19:09:17 +0200 Mime-Version: 1.0 Sent to CCL by: Jerome Kieffer [jerome.Kieffer]=[terre-adelie.org] On Mon, 2 Jul 2007 09:26:43 -0400 "Bhabani S Mallik mbhabani~!~yahoo.com" wrote: > > Sent to CCL by: "Bhabani S Mallik" [mbhabani_+_yahoo.com] > Dear All, > > I want to manage all my reference pdf files ( huge number) with a proper way. > I mean is there any software which can convert all my files to browsable > html pages with title, author, year of publication and a link to that pdf file ? have a look at jabref (it is free) -- Jérôme KIEFFER : http://www.terre-adelie.org À vélo, prendre une rue à contre-sens est moins dangeureux que prendre un boulevard dans le sens légal. À qui la faute ? From owner-chemistry@ccl.net Mon Jul 2 15:14:01 2007 From: "Yousef Sharifi ysharifi*gmail.com" To: CCL Subject: CCL: Rate of reaction Message-Id: <-34619-070702143112-19119-m/tnUWX/mB+LPLbghNs37g[]server.ccl.net> X-Original-From: "Yousef Sharifi" Date: Mon, 2 Jul 2007 14:31:09 -0400 Sent to CCL by: "Yousef Sharifi" [ysharifi^-^gmail.com] I am trying to use TST to estimate the activation energy for Ch3+H2->Ch4+H. If you consider the reaction rate as r= A*T^n*exp(-E/RT), how do you calculate the activation energy for various temperature ranges? for example 700k-1500k? How do you calculate the temperature power--n? Thanks From owner-chemistry@ccl.net Mon Jul 2 21:19:01 2007 From: "ZhengJingjing zheng_jingjing%%hotmail.com" To: CCL Subject: CCL: Rate of reaction Message-Id: <-34620-070702174826-25545-kxaPs1U02SJ6uxhs2wfdVg!=!server.ccl.net> X-Original-From: ZhengJingjing Content-Type: multipart/alternative; boundary="_2830e18f-b9ef-4a3b-936d-f5193f9700de_" Date: Mon, 2 Jul 2007 21:16:00 +0000 MIME-Version: 1.0 Sent to CCL by: ZhengJingjing [zheng_jingjing-x-hotmail.com] --_2830e18f-b9ef-4a3b-936d-f5193f9700de_ Content-Type: text/plain; charset="gb2312" Content-Transfer-Encoding: 8bit You can try to use POLYRATE program. POLYRATE has a lot of test runs for this reaction. This paper is perhaps helful: Journal of Chemical Physics 117, 10675-10687 (2002).Jingjing> From: owner-chemistry(_)ccl.net> To: zheng_jingjing(_)hotmail.com> Subject: CCL: Rate of reaction> Date: Mon, 2 Jul 2007 14:31:09 -0400> > > Sent to CCL by: "Yousef Sharifi" [ysharifi^-^gmail.com]> I am trying to use TST to estimate the activation energy for Ch3+H2->Ch4+H. If you consider the reaction rate as r= A*T^n*exp(-E/RT), how do you calculate the activation energy for various temperature ranges? for example 700k-1500k? How do you calculate the temperature power--n? > > Thanks> > > _________________________________________________________________ ̽Ë÷ Windows Vista µÄÊÀ½ç http://search.live.com/results.aspx?q=windows+vista&mkt=zh-cn&FORM=LIVSOP --_2830e18f-b9ef-4a3b-936d-f5193f9700de_ Content-Type: text/html; charset="gb2312" Content-Transfer-Encoding: 8bit You can try to use POLYRATE program. POLYRATE has a lot of test runs for this reaction.

This paper is perhaps helful: Journal of Chemical Physics 117, 10675-10687 (2002).

Jingjing

> From: owner-chemistry(_)ccl.net
> To: zheng_jingjing(_)hotmail.com
> Subject: CCL: Rate of reaction
> Date: Mon, 2 Jul 2007 14:31:09 -0400
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> Sent to CCL by: "Yousef Sharifi" [ysharifi^-^gmail.com]
> I am trying to use TST to estimate the activation energy for Ch3+H2->Ch4+H. If you consider the reaction rate as r= A*T^n*exp(-E/RT), how do you calculate the activation energy for various temperature ranges? for example 700k-1500k? How do you calculate the temperature power--n?
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̽Ë÷ Windows Vista µÄÊÀ½ç Á˽⸠ü¶àÐÅÏ¢£¡ --_2830e18f-b9ef-4a3b-936d-f5193f9700de_-- From owner-chemistry@ccl.net Mon Jul 2 21:54:01 2007 From: "Andreas Bender andreas.bender=cantab.net" To: CCL Subject: CCL: New Postgraduate Cheminformatics Course at IBAB Bangalore Message-Id: <-34621-070702192106-7939-6dnlDDGNaP9xBOCQlmcxng__server.ccl.net> X-Original-From: "Andreas Bender" Date: Mon, 2 Jul 2007 19:21:03 -0400 Sent to CCL by: "Andreas Bender" [andreas.bender-.-cantab.net] Dear CCL'lers, I am glad to announce that the IBAB Bangalore, one of the premier bioinformatics institutions of India, is about to start a postgraduate course in Cheminformatics, with the first batch commencing in November 2007. Funded by an endowment by the AstraZeneca Research Foundation India, the course will have the same 18-months structure as the established bioinformatics course, with 12 months teaching and 6 months spent as an intern in the pharmaceutical or chemical and related industries. IBAB is particularly proud that until now for all participants in the bioinformatics course an internship in industry could be provided, with >90% of the alumni taking up employment in the desired industry afterwards. This success is expected to continue with the new cheminformatics class. Applications will close 1 September 2007 with entrance tests on 9 September 2007 and the first course day on 15 November 2007. For further information please see the IBAB Cheminformatics Diploma website at http://www.ibab.ac.in/prog_cheminformatics.html or the general IBAB site at http://www.ibab.ac.in. Currently we are in the process of identifying suitable internship placements for the students of the course. Cheminformatics and CADD groups among Indian pharmaceutical and related industries are very welcome to contact me if they see potential for a mutually beneficial project with a student of the course. Students bring both chemistry and informatics background before starting the course and will have spent a whole year studying cheminformatics techniques (including practicals) before starting the internship around November 2008. In case of any questions regarding the contents of the course please contact me directly or with any other questions feel free to contact IBAB at http://www.ibab.ac.in/abt_contact_us.htm. Best wishes, Andreas -- Andreas Bender, PhD - http://www.andreasbender.de Postdoctoral Fellow, Lead Discovery Informatics Novartis, Cambridge/MA From owner-chemistry@ccl.net Mon Jul 2 22:30:00 2007 From: "Jian computationalboy * gmail.com" To: CCL Subject: CCL: molecular docking towards phosphorylated kinase with "SEP" in the pdb file Message-Id: <-34622-070702215646-8033-wjT7iKk1U7JHwX+cYyM5AA * server.ccl.net> X-Original-From: Jian Content-Type: multipart/alternative; boundary="----=_Part_69571_11635967.1183427785885" Date: Tue, 3 Jul 2007 09:56:25 +0800 MIME-Version: 1.0 Sent to CCL by: Jian [computationalboy##gmail.com] ------=_Part_69571_11635967.1183427785885 Content-Type: text/plain; charset=ISO-8859-1; format=flowed Content-Transfer-Encoding: 7bit Content-Disposition: inline Dear All: I am performing molecular docking towards protein kinase with phosphorylation on the serine(Ser) residue. This ester of serine and phosphoric acid was referd to phosphoserine,which is a component of many proteins as the result of posttranslational modifications. I found "SEP" residues in the original PDB file downloaded from the Protein Data Bank in the "HETATM" session. Can any one tell me how to prepare the receptor file for docking? Do I need delete the phosphate group and rename the "SEP" to "SER" in the PDB file? Some codes for such PDB entries are: 2CDZ,2F57 Thanks in advance! Yours sincerely Jian ------=_Part_69571_11635967.1183427785885 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Content-Disposition: inline Dear All:
I am performing molecular docking towards protein kinase with phosphorylation on the serine(Ser) residue.

This ester of serine and phosphoric acid was referd to phosphoserine,which is a component of many proteins as the result of posttranslational modifications.

I found "SEP" residues in the original PDB file downloaded from the Protein Data Bank in the "HETATM" session.

Can any one tell me how to prepare the receptor file for docking? Do I need delete the phosphate group and rename the "SEP" to "SER" in the PDB file?

Some codes for such PDB entries are: 2CDZ,2F57

Thanks in advance!
Yours sincerely Jian ------=_Part_69571_11635967.1183427785885--