From owner-chemistry@ccl.net Mon May 24 05:35:00 2010 From: "CompChem Group compchemgroup1{=}gmail.com" To: CCL Subject: CCL: Heat of atomization Message-Id: <-41934-100524053413-1163-3vaqPnbq5WNCZfQkWGszWA##server.ccl.net> X-Original-From: CompChem Group Content-Type: multipart/alternative; boundary=001636833cead21202048753bdef Date: Mon, 24 May 2010 10:34:03 +0100 MIME-Version: 1.0 Sent to CCL by: CompChem Group [compchemgroup1**gmail.com] --001636833cead21202048753bdef Content-Type: text/plain; charset=ISO-8859-1 Dear Dvir, All questions can be simply answered in details by reading the atomization method in the following book: COMPUTATIONAL CHEMISTRY "Introduction to the Theory and Applications of Molecular and Quantum Mechanics" Errol Lewars pages 276-278. Good luck, Don, CCG1 2010/5/23 Dvir Doron dvir.doron!A!gmail.com > > Sent to CCL by: "Dvir Doron" [dvir.doron#gmail.com] > Hi, > how can I calculate heat of atomization so that I can estimate the heat of > formation for molecules? A detailed description would be appreciated. > What is a practical and accurate approach to computing heats of formation > for molecules (directly from ab-initio, dft, or parametric approach)? > Thanks, > Dvir> > > --001636833cead21202048753bdef Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable
Dear Dvir,
All questions can be simply answered in deta= ils by reading the atomization method in the following book:
COMPUTATION= AL CHEMISTRY "Introduction to the Theory and Applications of Molecular= and Quantum Mechanics" Errol Lewars pages 276-278.
Good luck,
Don,
CCG1

2010/5/23 Dvir= Doron dvir.doron!A!gmail.com <owner-chemistry(a)ccl.ne= t>

Sent to CCL by: "Dvir =A0Doron" [dvir.doron#gmail.com]
Hi,
how can I calculate heat of atomization so that I can estimate the heat of = formation for molecules? A detailed description would be appreciated.
What is a practical and accurate approach to computing heats of formation f= or molecules (directly from ab-initio, dft, or parametric approach)?
Thanks,
Dvir



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--001636833cead21202048753bdef-- From owner-chemistry@ccl.net Mon May 24 08:48:00 2010 From: "comp chem Group compchemgroup1=-=gmail.com" To: CCL Subject: CCL: Regarding sulfate ions Message-Id: <-41935-100524050210-5762-F8MrUIawu1/bKScXRlizng(a)server.ccl.net> X-Original-From: "comp chem Group " Date: Mon, 24 May 2010 05:02:08 -0400 Sent to CCL by: "comp chem Group " [compchemgroup1:-:gmail.com] Dear M. Ibrahim, I still remember the questions related to sulfate ions. The person sent this message asked very important questions, but so far, no body couldnt answer his/her questions. I am amazing from your answer, how you want to consider strange ion in the docking process, even though it is not found in the nature and consequentially, it has not any biological or chemical role i.e. it has not any effect on the active center. However, how and why you goverened his or her trial as a blind trick? The principle of simulation is to try to mimic the nature not to consider a strange ion come from crystallization. My believing is if the colleague found the sulfate ions dont not belong to the interested protein, he/she should remove them. He/she expected all things you said in your answers and removing the sulfate ions will affect the geometry and thus he/she inquires about the validity of alternatives he/she suggested. My recommendation to the colleague is if he/she found the sulfate ions belong to the pocket of protein, they should be considered otherwise they must be removed. And replacing them by water molecules need to test because as I think it is a new trick and may be a good trick. Hopefully from the colleague, to tell CCL what is happen for geometry including the active center with and without the explicit water molecules. Don, CCG1 From owner-chemistry@ccl.net Mon May 24 09:23:00 2010 From: "Rinderspacher, Berend (Cont, ARL/WMRD) berend.rinderspacher:_:us.army.mil" To: CCL Subject: CCL:G: Gaussian Error in Internal coordinates (UNCLASSIFIED) Message-Id: <-41936-100524082551-9834-WDDRBac+2owD1JKRRtyKCw^-^server.ccl.net> X-Original-From: "Rinderspacher, Berend (Cont, ARL/WMRD)" Content-class: urn:content-classes:message Content-Type: multipart/signed; protocol="application/x-pkcs7-signature"; micalg=SHA1; boundary="----=_NextPart_000_0020_01CAFB1A.B7665960" Date: Mon, 24 May 2010 08:25:36 -0400 MIME-Version: 1.0 Sent to CCL by: "Rinderspacher, Berend (Cont, ARL/WMRD)" [berend.rinderspacher~!~us.army.mil] This is a multi-part message in MIME format. ------=_NextPart_000_0020_01CAFB1A.B7665960 Content-Type: text/plain; charset="us-ascii" Content-Transfer-Encoding: 7bit Classification: UNCLASSIFIED Caveats: NONE Dear Vignesh, The problem lies in the internal coordinates. I've noticed this error during PES scans where the (automatically assigned) internal coordinates become collinear. If you do not need to constrain your optimization along specific coordinates, optimizing along the Cartesians should be your method of choice. Sincerely, Christopher -----Original Message----- Dear Ol Ga, Thank you very much for your suggestion. However, strangely, it didn't work out in my case. However, when I gave "Cartesian" keyword, as follows, # ROM062X/3-21G Opt=(Loose,Cartesian) Test The job is running fine (as of now!). Sincerely, Vignesh On Sat, May 22, 2010 at 11:22 PM, Ol Ga eurisco1{}pochta.ru wrote: Sent to CCL by: "Ol Ga" [eurisco1[]pochta.ru ] Dear Vigneshwar Ramakrishnan, I observed this error. It depends on both options - method + basis. If you choose the level of theory, you should change some positions of atoms - increase slightly some bond lengths. I made this tune of my "tight" structure (changed position of 6 atoms from 100 atoms) and new "expanded" structure converged smoothly without this error. Anyway, you can optimize your structure on other level and than start the optimization at the desired level of theory from previously optimized point. It is an option. Sincerely, Ol Ga -------------------------------------------------- > From: "Vigneshwar Ramakrishnan vmsrvignesh++gmail.com " > Sent: Saturday, May 22, 2010 12:34 PM To: "Ga, Ol " > Subject: CCL:G: Gaussian Error in Internal coordinates > > > Sent to CCL by: "Vigneshwar Ramakrishnan" [vmsrvignesh##gmail.com ] > Dear All, > > I am using (actually, learning!) Gaussian to investigate the properties of DNA. I generated a 2bp-DNA structure and submitted the *.com file with ROM062X/3-21G method. However, I get the following error when the job runs. Could anyone please help me understand the meaning of this error message and give pointers as to how to fix it? > > Cartesian Forces: Max 0.107961092 RMS 0.021734872 > > GradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGrad > Berny optimization. > NTrRot= -1 NTRed= 730 NAtoms= 126 NSkip= 358 IsLin=F > Error in internal coordinate system. > Error termination via Lnk1e in /app1/em64t/g09/l103.exe at Sat May 22 16:05:45 2010. > Job cpu time: 0 days 0 hours 0 minutes 2.9 seconds. > > > Thank you very much, > Sincerely, > Vignesh > > Graduate Student, > Dept. of Chem and Biomolecular Engg, > National University of Singapore. > Singapore.E-mail to subscribers: CHEMISTRY]-[ccl.net or use: E-mail to administrators: CHEMISTRY-REQUEST]-[ccl.net or use -- R.Vigneshwar Graduate Student, Dept. of Chemical & Biomolecular Engg, National University of Singapore, Singapore "Strive for Excellence, Never be satisfied with the second Best!!" I arise in the morning torn between a desire to improve the world and a desire to enjoy the world. This makes it hard to plan the day. (E.B. 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VQQLEwNQS0kxGDAWBgNVBAMTD0RPRCBFTUFJTCBDQS0xOQIDIrD/MHUGCyqGSIb3DQEJEAILMWag ZDBdMQswCQYDVQQGEwJVUzEYMBYGA1UEChMPVS5TLiBHb3Zlcm5tZW50MQwwCgYDVQQLEwNEb0Qx DDAKBgNVBAsTA1BLSTEYMBYGA1UEAxMPRE9EIEVNQUlMIENBLTE5AgMisP8wDQYJKoZIhvcNAQEB BQAEgYAGvOWCKrJkRLLZeW/wWYatb/g1a/7N6clg1P6NECA9xtf9hOFNkJRR9mDJ1P9GnVMJGtZh 7HKoqlppKmM8sg8lfgU7K2U1SkJkGOBMqstNYqR7JSYlVjizw4AVGCdNB89gTLaRfcsb1YGntxK/ Bz7gBFS/f96wlic2/DXSOHTtigAAAAAAAA== ------=_NextPart_000_0020_01CAFB1A.B7665960-- From owner-chemistry@ccl.net Mon May 24 09:57:00 2010 From: "Chris Perry christopher.perry2|a|wits.ac.za" To: CCL Subject: CCL:G: G03/09 Tuple Error Message-Id: <-41937-100524085320-525-gNptjfO0p7SLTJECOEeF/Q]*[server.ccl.net> X-Original-From: "Chris Perry" Date: Mon, 24 May 2010 08:53:18 -0400 Sent to CCL by: "Chris Perry" [christopher.perry2++wits.ac.za] Dear All I've been having trouble performing frequency calculations on various cobalt corrin systems using both G03 and G09 with TCP-Linda. The calculations crash with a Tuple error. The error only seems to occurs when the number of basis functions exceeds around 1200, and only for frequency calculations; single point or geometry optimizations work fine. Below is a section of the output file containing the error: Leave Link 801 at Wed May 19 17:34:20 2010, MaxMem= 2684354560 cpu: 0.6 (Enter /home/gaussian/g03/linda-exe/l1101.exel) Using compressed storage, NAtomX= 106. Will process 107 centers per pass. Tuple error for IPart= 1 tuple: Results -- FocDA expected length 358481565 found length 178389347 Error termination in TplErr. Error termination via Lnk1e in /home/gaussian/g03/linda-exe/l1101.exel at Wed May 19 17:35:19 2010. Job cpu time: 0 days 0 hours 1 minutes 24.7 seconds. File lengths (MBytes): RWF= 3163 Int= 0 D2E= 0 Chk= 130 Scr= 1 Is anybody able to shed any light on this? Thanks in advance Chris From owner-chemistry@ccl.net Mon May 24 10:33:01 2010 From: "Loriano Storchi redo###thch.unipg.it" To: CCL Subject: CCL:G: Xeon versus Opteron or Athlon processors Message-Id: <-41938-100521130053-4566-HRt02wi6rU1oYmJTjOJirw:server.ccl.net> X-Original-From: Loriano Storchi Content-Type: TEXT/PLAIN; charset=US-ASCII; format=flowed Date: Fri, 21 May 2010 17:40:36 +0200 (CEST) MIME-Version: 1.0 Sent to CCL by: Loriano Storchi [redo!^!thch.unipg.it] On Sun, 9 May 2010, Jerome Kieffer jerome.Kieffer!=!terre-adelie.org wrote: > Sent to CCL by: Jerome Kieffer [jerome.Kieffer .. terre-adelie.org] > On Sat, 8 May 2010 06:47:20 -0400 > "Adel A. El-Azhary azhary%a%ksu.edu.sa" wrote: > >> Did anyone try to run G09 or G03 on Intel Xeon and AMD Opteron or Athlon processors and which one has better price/speed ratio. Dear Adel, the result depends also on which compiler do you use, for example if you use intel compiler you can obtain some misleading results: http://www.osnews.com/story/22683/Intel_Forced_to_Remove_Cripple_AMD_Function_from_Compiler_ all the best loriano From owner-chemistry@ccl.net Mon May 24 11:08:01 2010 From: "Mark Ji h-ji(_)northwestern.edu" To: CCL Subject: CCL: Linux server Message-Id: <-41939-100523112742-21264-roagpShDETIAiQj90KqGCQ|,|server.ccl.net> X-Original-From: "Mark Ji" Date: Sun, 23 May 2010 11:27:41 -0400 Sent to CCL by: "Mark Ji" [h-ji/a\northwestern.edu] Dear CCLer: I would like to buy one linux server which can run different computer modeling programs such as Accelrys discovery studio, Tripos Sybyl and Schrondinger for structure-based inhibitor design. I am wondering hom many CPUs and what types of linux servers I should consider. Thank you in advance! Mark Ji From owner-chemistry@ccl.net Mon May 24 11:53:00 2010 From: "Barry Hardy barry.hardy,vtxmail.ch" To: CCL Subject: CCL: eCheminfo summer workshops in Drug Design & Predictive Toxicology Message-Id: <-41940-100524113759-21631-rTEd6iMaa+auc+9fsk6PFw.@.server.ccl.net> X-Original-From: Barry Hardy Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-15; format=flowed Date: Mon, 24 May 2010 17:37:47 +0200 MIME-Version: 1.0 Sent to CCL by: Barry Hardy [barry.hardy : vtxmail.ch] Final programs for this year's eCheminfo summer workshops in Oxford on drug design and predictive toxicology are now available: Drug Design: http://barryhardy.blogs.com/files/echeminfodrugdesignbrochure-ox710-web1.pdf and/or http://barryhardy.blogs.com/cheminfostream/2010/05/echeminfo-2010-drug-design-workshop-in-oxford-detailed-program.html Predictive Toxicology http://barryhardy.blogs.com/files/echeminfopredictivetoxbrochure-ox810-web1.pdf and/or http://barryhardy.blogs.com/theferryman/2010/05/developing-new-predictive-toxicology-strategies.html and the time together should be an excellent chance for a combination of strategy innovation, collaboration and hands-on group work. Hope you can join us! best regards Barry Barry Hardy PhD Director, Community of Practice & Research Activities and OpenTox Project Coordinator (www.opentox.org) Douglas Connect Switzerland Tel: +41 61 851 0170 Email: barry.hardy -(at)- douglasconnect.com From owner-chemistry@ccl.net Mon May 24 12:28:00 2010 From: "Greg Warren greg * eyesopen.com" To: CCL Subject: CCL: Regarding sulfate ions Message-Id: <-41941-100524113201-8116-RG4R9l9ct8ALjU4UEF3lQg:+:server.ccl.net> X-Original-From: Greg Warren Content-Language: en-US Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset="us-ascii" Date: Mon, 24 May 2010 08:31:51 -0700 MIME-Version: 1.0 Sent to CCL by: Greg Warren [greg(_)eyesopen.com] Dear Don, I must disagree with your statement below and say that sulfate ions are phy= siologically important. A publication in Am J Physiol Cell Physiol 264: C1= 231-C1237, 1993 estimated that sulfate concentration in the cytoplasm of hu= man bronchial epithelial cell was greater than 0.3 mM. In cases of low chl= oride concentrations the level can be as high as 2 mM. Sulfate is a physi= ologically important ion and while sulfate present in a crystal structure m= ay and probably is an artifact of the experiment it may not be. There is n= o way to prove that the sulfate modeled or observed isn't structurally or f= unctionally relevant. One could attempt to solve the structure under diffe= rent conditions where sulfate concentrations are physiological and show tha= t no sulfate is present in the low sulfate concentration structure. Unfort= unately, even that experiment is not proof but a strong indication. The wh= olesale removal of experimental data (sulfate, chloride, ammonium ions, etc= .) is a dangerous practice. In the case of protein crystal structures I wo= uld be very hesitant to remove (and remodel - most likely in the absence of= experimental data) information without overwhelming evidence that the data= is an artifact. Regards, Greg -----Original Message----- > From: owner-chemistry+greg=3D=3Deyesopen.com.:.ccl.net [mailto:owner-chemistr= y+greg=3D=3Deyesopen.com.:.ccl.net] On Behalf Of comp chem Group compchemgrou= p1=3D-=3Dgmail.com Sent: Monday, May 24, 2010 3:02 AM To: Greg Warren Subject: CCL: Regarding sulfate ions Sent to CCL by: "comp chem Group " [compchemgroup1:-:gmail.com] Dear M. Ibrahim, I still remember the questions related to sulfate ions. The person sent thi= s message asked very important questions, but so far, no body couldnt answe= r his/her questions. I am amazing from your answer, how you want to conside= r strange ion in the docking process, even though it is not found in the na= ture and consequentially, it has not any biological or chemical role i.e. i= t has not any effect on the active center. However, how and why you goveren= ed his or her trial as a blind trick? The principle of simulation is to try= to mimic the nature not to consider a strange ion come from crystallizatio= n. My believing is if the colleague found the sulfate ions dont not belong= to the interested protein, he/she should remove them. He/she expected all = things you said in your answers and removing the sulfate ions will affect t= he geometry and thus he/she inquires about the validity of alternatives he/= she suggested. My recommendation to the colleague is if he/she found the s= ulfate ions be! long to the pocket of protein, they should be considered otherwise they mu= st be removed. And replacing them by water molecules need to test because a= s I think it is a new trick and may be a good trick. Hopefully from the col= league, to tell CCL what is happen for geometry including the active center= with and without the explicit water molecules. =20 Don, CCG1 -=3D This is automatically added to each message by the mailing script =3D-http://www.ccl.net/cgi-bin/ccl/send_ccl_messageSubscribe/Unsubscribe:=20Job: http://www.ccl.net/jobs=20http://www.ccl.net/spammers.txt From owner-chemistry@ccl.net Mon May 24 13:02:00 2010 From: "Soren Eustis soren.eustis,,env.ethz.ch" To: CCL Subject: CCL: Linux server Message-Id: <-41942-100524122730-16061-wqbBvo1KvyyKDN6vxFYqyQ|,|server.ccl.net> X-Original-From: Soren Eustis Content-transfer-encoding: quoted-printable Content-type: text/plain; charset="ISO-8859-1" Date: Mon, 24 May 2010 18:27:17 +0200 Mime-version: 1.0 Sent to CCL by: Soren Eustis [soren.eustis|,|env.ethz.ch] I would suggest looking at the workstations available at JNCS.com. I have had very good luck with their systems. Regards, Soren=20 --=20 Dr. Soren N. Eustis ETH =AD Zurich Institute for Biogeochemistry and Pollutant Dynamics Universitatstrasse 16 8092 Zurich +41 44 632 93 48 (office) +41 44 632 14 38 (fax) soren_-_env.ethz.ch From owner-chemistry@ccl.net Mon May 24 13:37:00 2010 From: "javier sacristan jsacristan a ictp.csic.es" To: CCL Subject: CCL: any website to download zelite, silicates (AMH-3) coordinates file Message-Id: <-41943-100524132405-25376-V61husxkRmr2WU+S+BTKFg^server.ccl.net> X-Original-From: "javier sacristan" Date: Mon, 24 May 2010 13:24:02 -0400 Sent to CCL by: "javier sacristan" [jsacristan]*[ictp.csic.es] Hi CCLrs I have been looking for AMH-3 silicate coordinates file for a while but I have not found anything. So, I hope that any of you know a good and free website to download coordinate files of silicates such as AMH-3. thanks for reading jS From owner-chemistry@ccl.net Mon May 24 14:11:00 2010 From: "Radoslaw Kaminski rkaminski.rk]^[gmail.com" To: CCL Subject: CCL: any website to download zelite, silicates (AMH-3) coordinates file Message-Id: <-41944-100524140811-3694-KLwTQe4+ELzLK9je4SJdDg() server.ccl.net> X-Original-From: Radoslaw Kaminski Content-Type: multipart/alternative; boundary=0016363ba3e6c4775504875aeb94 Date: Mon, 24 May 2010 14:07:59 -0400 MIME-Version: 1.0 Sent to CCL by: Radoslaw Kaminski [rkaminski.rk**gmail.com] --0016363ba3e6c4775504875aeb94 Content-Type: text/plain; charset=ISO-8859-1 Hi, Try Inorganic Crystal Structure Database. This is the free version here: http://icsd.ill.eu/icsd/index.html All the best, Radek 2010/5/24 javier sacristan jsacristan a ictp.csic.es < owner-chemistry~!~ccl.net> > > Sent to CCL by: "javier sacristan" [jsacristan]*[ictp.csic.es] > Hi CCLrs > > I have been looking for AMH-3 silicate coordinates file for a while but I > have not found anything. So, I hope that any of you know a good and free > website to download coordinate files of silicates such as AMH-3. > > > thanks for reading > > > jS> > > --0016363ba3e6c4775504875aeb94 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Hi,

Try Inorganic Crystal Structure Database. This is the free versi= on here:

http://icsd.= ill.eu/icsd/index.html

All the best,

Radek


2010/5/24 javier sacristan jsacristan a ict= p.csic.es <owner-chemistry~!~ccl.net>

Sent to CCL by: "javier =A0sacristan" [jsacristan]*[ictp.csic.es]
Hi CCLrs

I have been looking for AMH-3 silicate coordinates file for a while but I h= ave not found anything. So, I hope that any of you know a good and free web= site to download coordinate files of silicates such as AMH-3.


thanks for reading


jS



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--0016363ba3e6c4775504875aeb94-- From owner-chemistry@ccl.net Mon May 24 15:34:00 2010 From: "maxim totrov max(-)molsoft.com" To: CCL Subject: CCL: Regarding sulfate ions Message-Id: <-41945-100524151607-32758-BXf4oXJGMLJqud5nvITAFA~~server.ccl.net> X-Original-From: maxim totrov Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=US-ASCII; format=flowed; delsp=yes Date: Mon, 24 May 2010 12:15:53 -0700 Mime-Version: 1.0 (Apple Message framework v936) Sent to CCL by: maxim totrov [max\a/molsoft.com] I was wondering if anyone has encountered an actual example where sulfate is functionally important. While theoretically i would agree with Greg, having actually looked at quite a number of structures i have to say every single sulfate i have seen so far looked like a crystallization artifact. Either you see them suspended in space between multiple protein molecules within crystallographic cell, or in the active sites where they typically overlap with the real ligand/ substrate as observed in alternative X-ray structures. In the latter case, sulfates seem to mimic acidic moieties such as phosphates or carboxylates of the 'true' ligand. Obviously, keeping the latter kind of sulfate in a docking study may not be a good idea. Just my 2 cents, Max Totrov > > Sent to CCL by: Greg Warren [greg(_)eyesopen.com] > Dear Don, > > I must disagree with your statement below and say that sulfate ions > are physiologically important. A publication in Am J Physiol Cell > Physiol 264: C1231-C1237, 1993 estimated that sulfate concentration > in the cytoplasm of human bronchial epithelial cell was greater than > 0.3 mM. In cases of low chloride concentrations the level can be as > high as 2 mM. Sulfate is a physiologically important ion and while > sulfate present in a crystal structure may and probably is an > artifact of the experiment it may not be. There is no way to prove > that the sulfate modeled or observed isn't structurally or > functionally relevant. One could attempt to solve the structure > under different conditions where sulfate concentrations are > physiological and show that no sulfate is present in the low sulfate > concentration structure. Unfortunately, even that experiment is not > proof but a strong indication. The wholesale removal of > experimental data (sulfate, chloride, ammonium ions, etc.) is a > dangerous practice. In the case of protein crystal structures I > would be very hesitant to remove (and remodel - most likely in the > absence of experimental data) information without overwhelming > evidence that the data is an artifact. > > Regards, > > Greg > > -----Original Message----- >> From: owner-chemistry+greg==eyesopen.com()ccl.net [mailto:owner-chemistry+greg==eyesopen.com()ccl.net >> ] On Behalf Of comp chem Group compchemgroup1=-=gmail.com > Sent: Monday, May 24, 2010 3:02 AM > To: Greg Warren > Subject: CCL: Regarding sulfate ions > > > Sent to CCL by: "comp chem Group " [compchemgroup1:-:gmail.com] > Dear M. Ibrahim, > I still remember the questions related to sulfate ions. The person > sent this message asked very important questions, but so far, no > body couldnt answer his/her questions. I am amazing from your > answer, how you want to consider strange ion in the docking process, > even though it is not found in the nature and consequentially, it > has not any biological or chemical role i.e. it has not any effect > on the active center. However, how and why you goverened his or her > trial as a blind trick? The principle of simulation is to try to > mimic the nature not to consider a strange ion come from > crystallization. My believing is if the colleague found the sulfate > ions dont not belong to the interested protein, he/she should remove > them. He/she expected all things you said in your answers and > removing the sulfate ions will affect the geometry and thus he/she > inquires about the validity of alternatives he/she suggested. My > recommendation to the colleague is if he/she found the sulfate ions > be! > long to the pocket of protein, they should be considered otherwise > they must be removed. And replacing them by water molecules need to > test because as I think it is a new trick and may be a good trick. > Hopefully from the colleague, to tell CCL what is happen for > geometry including the active center with and without the explicit > water molecules. > > Don, > CCG1 > > > > -= This is automatically added to each message by the mailing script > =-http://www.ccl.net/cgi-bin/ccl/send_ccl_messageSubscribe/ > Unsubscribe:http://www.ccl.net/spammers.txt > > > -To recover the email address of the author of the message, please > change> Conferences: http://server.ccl.net/chemistry/announcements/ > conferences/> > From owner-chemistry@ccl.net Mon May 24 16:09:00 2010 From: "Mahmoud A. A. Ibrahim m.ibrahim*compchem.net" To: CCL Subject: CCL: Regarding sulfate ions Message-Id: <-41946-100524134228-11177-t2dkCZuhhBM8+vzdYhEGuw===server.ccl.net> X-Original-From: "Mahmoud A. A. Ibrahim" Content-Type: multipart/alternative; boundary=001517447abe692a2704875a8f67 Date: Mon, 24 May 2010 18:42:09 +0100 MIME-Version: 1.0 Sent to CCL by: "Mahmoud A. A. Ibrahim" [m.ibrahim : compchem.net] --001517447abe692a2704875a8f67 Content-Type: text/plain; charset=ISO-8859-1 Dear Don Thanks for your reply and sorry if you considered my reply was aggressive; although I don't see why you considered it aggressive. You are absolutely right, we learn from each other, and I am still young researcher and seek to get advice from the others. If you don't mind, let's try to answer the following questions: * Sulfate ion mostly comes from buffer solution? that is right. * it doesn't occur in nature? That is right too in our case which comes from buffer (but it occurs in nature) * But, why it binds at that place close to the active site? it binds because there is/are a charged atoms(ionized)/group at that site. * in nature, these charged atoms/groups are neutralized? I think so, but they neutralized with oppositely charged ions rather than sulfate ion which takes their place and helped to crystallize the protein. * may be the active site is not ionized but just the desired place bears a charge. it may be. But, the inhibitor is bounded to the active site (which is close to the sulfate ion) in presence of the sulfate ion, so the electrostatic environment of the active site was suitable for binding. Are you sure the same ligand will bind at the same efficiency in the absence of the sulfate ion (i.e. in different electrostatic environment)? I don't think so. In my opinion, she should run MM simulation without sulfate ion and watch what will happen, but there is one issue, during MM simulation, you neutralize your system, so make sure there are no ions added in the place of sulfate ion (and sure one or two ions will be added). May be I am wrong, but that is what I believe. I haven't worked before on a similar system, so I could support you with reference supported or declined my words. I took forward to hearing from you. Thanks in advance Sincerely; M. Ibrahim On Mon, May 24, 2010 at 10:02 AM, comp chem Group compchemgroup1=-=gmail.com wrote: > > Sent to CCL by: "comp chem Group " [compchemgroup1:-:gmail.com] > Dear M. Ibrahim, > I still remember the questions related to sulfate ions. The person sent > this message asked very important questions, but so far, no body couldnt > answer his/her questions. I am amazing from your answer, how you want to > consider strange ion in the docking process, even though it is not found in > the nature and consequentially, it has not any biological or chemical role > i.e. it has not any effect on the active center. However, how and why you > goverened his or her trial as a blind trick? The principle of simulation is > to try to mimic the nature not to consider a strange ion come from > crystallization. My believing is if the colleague found the sulfate ions > dont not belong to the interested protein, he/she should remove them. He/she > expected all things you said in your answers and removing the sulfate ions > will affect the geometry and thus he/she inquires about the validity of > alternatives he/she suggested. My recommendation to the colleague is if > he/she found the sulfate ions be! > long to the pocket of protein, they should be considered otherwise they > must be removed. And replacing them by water molecules need to test because > as I think it is a new trick and may be a good trick. Hopefully from the > colleague, to tell CCL what is happen for geometry including the active > center with and without the explicit water molecules. > > Don, > CCG1> > > -- Mahmoud A. A. Ibrahim Current Address 7.05, School of Chemistry, The University of Manchester, Oxford Road, Manchester, M13 9PL, United Kingdom. Home Address Chemistry Department, Faculty of Science, Minia University, Minia 61519, Egypt. Contact Information Email: m.ibrahim/./compchem.net Website: www.compchem.net Fax No.: +20862342601 --001517447abe692a2704875a8f67 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Dear Don
Thanks for your reply and sorry if you considered my reply was= aggressive; although I don't see why you considered it aggressive.
You are=A0absolutely=A0right, we learn from each other, and I am sti= ll young researcher and seek to get advice from the others.
If you don't mind, let's try to answer the following questions= :
* Sulfate ion mostly comes from buffer solution? that is right.= =A0
* it doesn't occur in nature? That is right too in our ca= se which comes from buffer (but it occurs in nature)
* But, why it binds at that place close to the active site? it binds b= ecause there is/are a charged atoms(ionized)/group at that site.
= * in nature, these charged atoms/groups are neutralized? I think so, but th= ey neutralized with=A0oppositely=A0charged ions rather than sulfate ion whi= ch takes=A0their=A0place and helped to=A0crystallize=A0the protein.
* may be the active site is not=A0ionized=A0but just the desired place= bears a charge. it may be. But, the inhibitor is bounded to the active sit= e (which is close to the sulfate ion) in presence of the sulfate ion, so th= e electrostatic environment of the active site was suitable for binding. Ar= e you sure the same ligand will bind at the same=A0efficiency=A0in the abse= nce of the sulfate ion (i.e. in different electrostatic environment)? I don= 't think so.
In my opinion, she should run MM simulation without sulfate ion and wa= tch what will happen, but there is one issue, during MM simulation, you neu= tralize your system, so make sure there are no ions added in the place of s= ulfate ion (and sure one or two ions will be added).
May be I am wrong, but that is what I believe.=A0I haven't worked = before on a similar system, so I could support you with reference supported= or declined my words.
I took forward to hearing from you.
Thanks in advance
Sincerely;
M. Ibrahim

<= div class=3D"gmail_quote">On Mon, May 24, 2010 at 10:02 AM, comp chem Group= compchemgroup1=3D-=3Dgmail.com <owner-chemistry/./ccl= .net> wrote:

Sent to CCL by: "comp chem Group " [compchemgroup1:-:gmail.com]
Dear M. Ibrahim,
I still remember the questions related to sulfate ions. The person sent thi= s message asked very important questions, but so far, no body couldnt answe= r his/her questions. I am amazing from your answer, how you want to conside= r strange ion in the docking process, even though it is not found in the na= ture and consequentially, it has not any biological or chemical role i.e. i= t has not any effect on the active center. However, how and why you goveren= ed his or her trial as a blind trick? The principle of simulation is to try= to mimic the nature not to consider a strange ion come from crystallizatio= n. =A0My believing is if the colleague found the sulfate ions dont not belo= ng to the interested protein, he/she should remove them. He/she expected al= l things you said in your answers and removing the sulfate ions will affect= the geometry and thus he/she inquires about the validity of alternatives h= e/she suggested. =A0My recommendation to the colleague is if he/she found t= he sulfate ions be!
=A0long to the pocket of protein, they should be considered otherwise they = must be removed. And replacing them by water molecules need to test because= as I think it is a new trick and may be a good trick. Hopefully from the c= olleague, to tell CCL what is happen for geometry including the active cent= er with and without the explicit water molecules.

Don,
CCG1



-=3D This is automatically added to each message by the mailing script =3D-=
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--
=A0 =A0 =A0 =A0 =A0 = =A0 =A0 =A0 =A0Mahmoud A. A. Ibrahim =A0 =A0 =A0 =A0
=A0 =A0 =A0 =A0 = =A0 =A0 =A0 =A0 =A0 =A0 =A0 Current Address
=A0 =A0 =A0 =A0 =A0 =A0 =A0= =A0 7.05, School of Chemistry,
=A0 =A0 =A0 =A0 =A0 =A0 =A0The Universi= ty of Manchester,
=A0 =A0 =A0 =A0 Oxford Road, Manchester, M13 9PL,
=A0 =A0 =A0 =A0 =A0= =A0 =A0 =A0 =A0 =A0 =A0 United Kingdom.

=A0 =A0 =A0 =A0 =A0 =A0 = =A0 =A0 =A0 =A0 =A0 =A0Home Address
=A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0= Chemistry Department,
=A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 Faculty o= f Science,
=A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0Minia Univers= ity,
=A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 Minia 61519,
=A0 = =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0Egypt.

= =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 Contact Information
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--001517447abe692a2704875a8f67-- From owner-chemistry@ccl.net Mon May 24 16:44:00 2010 From: "John McKelvey jmmckel##gmail.com" To: CCL Subject: CCL: Linux server Message-Id: <-41947-100524143223-27724-OuRVGla+UnjWOzBfzWcJqQ++server.ccl.net> X-Original-From: John McKelvey Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset=ISO-8859-1 Date: Mon, 24 May 2010 14:32:12 -0400 MIME-Version: 1.0 Sent to CCL by: John McKelvey [jmmckel=gmail.com] I heartily agree with Soren. I have bought 7 cpu/memory/motherboard or complete assembled units from them over the past 10 years. They have good service and 3 year warranties on all their hardware, and still help out in diagnosing problems long after the original warranty has expired. John McKelvey On Mon, May 24, 2010 at 12:27 PM, Soren Eustis soren.eustis,,env.ethz.ch wrote: > > Sent to CCL by: Soren Eustis [soren.eustis|,|env.ethz.ch] > I would suggest looking at the workstations available at JNCS.com. =A0I h= ave > had very good luck with their systems. > > Regards, > > Soren > > > -- > Dr. Soren N. Eustis > ETH =AD Zurich > Institute for Biogeochemistry and Pollutant Dynamics > Universitatstrasse 16 > 8092 Zurich > > +41 44 632 93 48 (office) > +41 44 632 14 38 (fax) > > soren###env.ethz.ch > > > > - This is automatically added to each message by the mailing script -> =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> > > --=20 John McKelvey 10819 Middleford Pl Ft Wayne, IN 46818 260-489-2160 jmmckel.:.gmail.com From owner-chemistry@ccl.net Mon May 24 17:19:01 2010 From: "CompChem Group compchemgroup1]-[gmail.com" To: CCL Subject: CCL: Regarding sulfate ions Message-Id: <-41948-100524141544-11462-EBDBcjz64yYBfQ+sGABRNA#,#server.ccl.net> X-Original-From: CompChem Group Content-Type: multipart/alternative; boundary=0016e6db2d7bb7a42104875b063d Date: Mon, 24 May 2010 19:15:31 +0100 MIME-Version: 1.0 Sent to CCL by: CompChem Group [compchemgroup1++gmail.com] --0016e6db2d7bb7a42104875b063d Content-Type: text/plain; charset=ISO-8859-1 Dear Greg, Thanks for your prefect answer. I know the physiological importance of sulfate ion in human cell. Our answers are consistent. In some cases the sulfate ion comes from the buffer during the crystallization process. In this case it will be considered as an interference ion and therefore it should be removed. Hence, one should think in a reasonable way to compensate the removal of such ions which in turn may have an effect on the geometry of protein. In this context, I agree with you that one needs to overwhelming evidence to prove that sulfate ions are artifact. Thanks Don CCG1 2010/5/24 Greg Warren greg * eyesopen.com > > Sent to CCL by: Greg Warren [greg(_)eyesopen.com] > Dear Don, > > I must disagree with your statement below and say that sulfate ions are > physiologically important. A publication in Am J Physiol Cell Physiol 264: > C1231-C1237, 1993 estimated that sulfate concentration in the cytoplasm of > human bronchial epithelial cell was greater than 0.3 mM. In cases of low > chloride concentrations the level can be as high as 2 mM. Sulfate is a > physiologically important ion and while sulfate present in a crystal > structure may and probably is an artifact of the experiment it may not be. > There is no way to prove that the sulfate modeled or observed isn't > structurally or functionally relevant. One could attempt to solve the > structure under different conditions where sulfate concentrations are > physiological and show that no sulfate is present in the low sulfate > concentration structure. Unfortunately, even that experiment is not proof > but a strong indication. The wholesale removal of experimental data > (sulfate, chloride, ammonium ions, etc.) is a dangerous practice. In the > case of protein crystal structures I would be very hesitant to remove (and > remodel - most likely in the absence of experimental data) information > without overwhelming evidence that the data is an artifact. > > Regards, > > Greg > > -----Original Message----- > > From: owner-chemistry+greg==eyesopen.com()ccl.net [mailto: > owner-chemistry+greg ==eyesopen.com()ccl.net] On > Behalf Of comp chem Group compchemgroup1=-=gmail.com > Sent: Monday, May 24, 2010 3:02 AM > To: Greg Warren > Subject: CCL: Regarding sulfate ions > > > Sent to CCL by: "comp chem Group " [compchemgroup1:-:gmail.com] > Dear M. Ibrahim, > I still remember the questions related to sulfate ions. The person sent > this message asked very important questions, but so far, no body couldnt > answer his/her questions. I am amazing from your answer, how you want to > consider strange ion in the docking process, even though it is not found in > the nature and consequentially, it has not any biological or chemical role > i.e. it has not any effect on the active center. However, how and why you > goverened his or her trial as a blind trick? The principle of simulation is > to try to mimic the nature not to consider a strange ion come from > crystallization. My believing is if the colleague found the sulfate ions > dont not belong to the interested protein, he/she should remove them. He/she > expected all things you said in your answers and removing the sulfate ions > will affect the geometry and thus he/she inquires about the validity of > alternatives he/she suggested. My recommendation to the colleague is if > he/she found the sulfate ions be! > long to the pocket of protein, they should be considered otherwise they > must be removed. And replacing them by water molecules need to test because > as I think it is a new trick and may be a good trick. Hopefully from the > colleague, to tell CCL what is happen for geometry including the active > center with and without the explicit water molecules. > > Don, > CCG1Job: > http://www.ccl.net/jobs> > > - This is automatically added to each message by the mailing script -> > > --0016e6db2d7bb7a42104875b063d Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable
Dear Greg,

Thanks for your prefect= answer. I know the physiological importance of sulfate ion in human cell. Our answers= are consistent. In some cases the sulfate ion comes from the buffer during the = crystallization process. In this case it will be considered as an interference ion and ther= efore it should be removed. Hence, one should think in a <= meta name=3D"Originator" content=3D"Microsoft Word 10">reasonable way to compensate the removal of such ions which in turn may have an effect on the geometry of protein. I= n this context, I agree with you that one needs to overwhelming evidence to p= rove that sulfate ions are artifact.

Thanks

Don

CCG1



2010/5/24 Greg Warren greg * eyesopen.com <owner-chemistry|-|ccl.net>

Sent to CCL by: Greg Warren [greg(_)eyesopen.com]
Dear Don,

I must disagree with your statement below and say that sulfate ions are phy= siologically important. =A0A publication in Am J Physiol Cell Physiol 264: = C1231-C1237, 1993 estimated that sulfate concentration in the cytoplasm of = human bronchial epithelial cell was greater than 0.3 mM. =A0In cases of low= chloride concentrations the level can be as high as 2 mM. =A0 Sulfate is a= physiologically important ion and while sulfate present in a crystal struc= ture may and probably is an artifact of the experiment it may not be. =A0Th= ere is no way to prove that the sulfate modeled or observed isn't struc= turally or functionally relevant. =A0One could attempt to solve the structu= re under different conditions where sulfate concentrations are physiologica= l and show that no sulfate is present in the low sulfate concentration stru= cture. =A0Unfortunately, even that experiment is not proof but a strong ind= ication. =A0The wholesale removal of experimental data (sulfate, chloride, = ammonium ions, etc.) is a dangerous practice. =A0In the case of protein cry= stal structures I would be very hesitant to remove (and remodel - most like= ly in the absence of experimental data) information without overwhelming ev= idence that the data is an artifact.

Regards,

Greg

-----Original Message-----
> From: owner-chemistry+greg=3D=3Deyesopen.com()= ccl.net [mailto:owner-chemist= ry+greg=3D=3Deyesopen= .com()ccl.net] On Beha= lf Of comp chem Group compchemgroup1=3D-=3Dgmail.com
Sent: Monday, May 24, 2010 3:02 AM
To: Greg Warren
Subject: CCL: Regarding sulfate ions


Sent to CCL by: "comp chem Group " [compchemgroup1:-:gmail.com]
Dear M. Ibrahim,
I still remember the questions related to sulfate ions. The person sent thi= s message asked very important questions, but so far, no body couldnt answe= r his/her questions. I am amazing from your answer, how you want to conside= r strange ion in the docking process, even though it is not found in the na= ture and consequentially, it has not any biological or chemical role i.e. i= t has not any effect on the active center. However, how and why you goveren= ed his or her trial as a blind trick? The principle of simulation is to try= to mimic the nature not to consider a strange ion come from crystallizatio= n. =A0My believing is if the colleague found the sulfate ions dont not belo= ng to the interested protein, he/she should remove them. He/she expected al= l things you said in your answers and removing the sulfate ions will affect= the geometry and thus he/she inquires about the validity of alternatives h= e/she suggested. =A0My recommendation to the colleague is if he/she found t= he sulfate ions be!
=A0long to the pocket of protein, they should be considered otherwise they = must be removed. And replacing them by water molecules need to test because= as I think it is a new trick and may be a good trick. Hopefully from the c= olleague, to tell CCL what is happen for geometry including the active cent= er with and without the explicit water molecules.

Don,
CCG1



-=3D This is automatically added to each message by the mailing scrip= t =3D-http://www.ccl.net/cgi-bin/ccl/send_ccl_messa= geSubscribe/Unsubscribe: Job: http://www.ccl.net/jobs http://www.ccl.net/spammers.txt
--0016e6db2d7bb7a42104875b063d-- From owner-chemistry@ccl.net Mon May 24 17:53:01 2010 From: "Nathaniel Aaron Deskins nadeskins]![wpi.edu" To: CCL Subject: CCL: Creating surfaces from crystal structures Message-Id: <-41949-100524153945-22343-S5C7zrNjV0bzhM9dwgPLXQ#,#server.ccl.net> X-Original-From: "Nathaniel Aaron Deskins" Date: Mon, 24 May 2010 15:39:43 -0400 Sent to CCL by: "Nathaniel Aaron Deskins" [nadeskins##wpi.edu] Hello everyone, I'm looking for software that will create a surface (i.e. 111 or 110 or whatever) from a given bulk crystal structure (from a cif file or some other format). I'd really like the software to create a surface cell that I can use for some periodic simulations. I know that Materials Studio and CrystalMaker can do this, but are costly, so I'd like a cheap or free solution. Does such software exist? Thank you, Aaron From owner-chemistry@ccl.net Mon May 24 22:53:01 2010 From: "Piotr Nowak piotrnowak!^!student.uw.edu.pl" To: CCL Subject: CCL:G: Different single-point DFT energy between GAMESS and Gaussian Message-Id: <-41950-100524185020-23995-9ABQuv/af3w5XdvU09IQjw.:.server.ccl.net> X-Original-From: "Piotr Nowak" Date: Mon, 24 May 2010 18:50:18 -0400 Sent to CCL by: "Piotr Nowak" [piotrnowak~!~student.uw.edu.pl] Dear CCL users, I'm trying to reproduce single point energy obtained with Gaussian 03 using GAMESS US. Hartree-Fock energy is almost exactly the same e.g. Gaussian: -1849.26414782 GAMESS: -1849.2641478646 Unfortunately my attempts to get the same results using DFT failed. The energy differences between both programs are unreasonably huge. Here are some examples of results for different functionals (the same case as above- mentioned HF example): M05-2X Gaussian: -1855.79754118 GAMESS: -1855.7976587495 SVWN5 Gaussian: -1845.45112047 GAMESS: -1845.4510666810 Slater (also known as Dirac, one of the simplest LDA functionals, so I'm sure it has the same definition in both programs) Gaussian: -1833.20351470 GAMESS: -1833.2034704727 I have done those calculations using the same grid, using tight convergence criteria. I've found out that Gaussian uses slightly different cc-pVDZ basis set than the one present in Basis Set Exchange, but using this basis set with GAMESS has left the results unchanged. I have also tried different guesses, and SCF algorithms, but without success. Here are keywords used in inputs for above calculations. Gaussian: #p m05/cc-pvdz nosymm iop(6/7=3) scf=tight GAMESS: $BASIS EXTFIL=.TRUE. GBASIS=CCPVDZGN $END $CONTRL ISPHER=+1 SCFTYP=RHF RUNTYP=ENERGY DFTTYP=M05 $END $SYSTEM PARALL=.TRUE. MWORDS=200 $END $SCF DIRSCF=.TRUE. DIIS=.TRUE. $END $DFT NRAD=75 NLEB=302 $END I would appreciate any kind of help. Best regards, Piotr Nowak