From chemistry-request@server.ccl.net Wed Nov 20 10:07:04 2002 Received: from ribotargets.com ([194.129.39.11]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id gAKF73u25649 for ; Wed, 20 Nov 2002 10:07:04 -0500 Received: from szilva (helo=localhost) by echo.ribotargets.com with local-esmtp (Exim 3.13 #1) id 18EWMi-0007nr-00; Wed, 20 Nov 2002 15:02:08 +0000 Date: Wed, 20 Nov 2002 15:02:08 +0000 (GMT) From: Szilveszter Juhos To: antonio luiz oliveira de noronha cc: chemistry@ccl.net Subject: Re: CCL:GAMESS compilation In-Reply-To: Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII On Tue, 19 Nov 2002, antonio luiz oliveira de noronha wrote: > ======================== blas ============================== > Tue Nov 19 14:14:17 BRST 2002 > g77 -c -O2 -malign-double -fautomatic -Wno-globals -fno-globals blas.f > g77: blas.f: No such file or directory > g77: No input files Though I've never seen GAMESS but I am afraid it is not missing f2c (g77) but simply the input file is missing. Still if you think it is f2c, I strongly recommend to download and compile gcc-2.95.3 since RedHat/Mandrake/SuSE gcc is non-standard. http://gcc.gnu.org/gcc-2.95/ Szilva From chemistry-request@server.ccl.net Wed Nov 20 12:36:45 2002 Received: from cornell.edu ([132.236.56.6]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id gAKHaju29018 for ; Wed, 20 Nov 2002 12:36:45 -0500 Received: from cornell.edu (lock.lassp.cornell.edu [128.84.241.198]) by cornell.edu (8.9.3/8.9.3) with ESMTP id MAA19862 for ; Wed, 20 Nov 2002 12:36:40 -0500 (EST) Sender: cc236@cornell.edu Message-ID: <3DDBC828.4E5E1257@cornell.edu> Date: Wed, 20 Nov 2002 12:36:40 -0500 From: Connie Chang X-Mailer: Mozilla 4.79 [en] (X11; U; Linux 2.4.18-10smp i686) X-Accept-Language: en MIME-Version: 1.0 To: chemistry@ccl.net Subject: Gaussian98W and charged molecules (again) Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Hi -- I'm sorry to bother everyone again... But I have another question about Gaussian... I was finally able to get Gaussian to geometrically optimize my charged (-1) molecule with the following Route specification: # PM3 SCF=vshift=500 SCF=(MaxCyc=1200) Opt However, when I ran the job again and added the Freq keyword, although the geometry optimized, the SCF energy calculation in the Freq part of the job oscillates again until the job terminates with a UNABLE TO ACHIEVE SELF-CONSISTENCE error. Why does this happen? If I have the following route specification #PM3 SCF=vshift=500 SCG=(Maxcyc=1200) Opt Freq Test Does Gaussian know to use my prior specifications for finding the SCF (i.e. the Vshift and the increased MaxCyc) or does it use it but still fail? Does anyone have any suggestions? And thanks again for all your previous suggestions! Connie From chemistry-request@server.ccl.net Wed Nov 20 14:33:16 2002 Received: from cornell.edu ([132.236.56.6]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id gAKJXGu32145 for ; Wed, 20 Nov 2002 14:33:16 -0500 Received: from cornell.edu (lock.lassp.cornell.edu [128.84.241.198]) by cornell.edu (8.9.3/8.9.3) with ESMTP id OAA11749; Wed, 20 Nov 2002 14:33:11 -0500 (EST) Sender: cc236@cornell.edu Message-ID: <3DDBE376.CBDEFB03@cornell.edu> Date: Wed, 20 Nov 2002 14:33:10 -0500 From: Connie Chang X-Mailer: Mozilla 4.79 [en] (X11; U; Linux 2.4.18-10smp i686) X-Accept-Language: en MIME-Version: 1.0 To: jmmckel@attglobal.net, chemistry@ccl.net Subject: Re: CCL:Gaussian98W and charged molecules (again) References: <3DDBC828.4E5E1257@cornell.edu> <3DDB9C86.60127AF1@attglobal.net> Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Hi again -- I did indeed try it. It gave me the oscillating SCF energies at the frequency job step (which was internal job step #2). And now that I think about it, I think it did use the SCF options I specified for the Opt step because the calculation only terminated in error after iteration 1200 (and not the usual 250). Do you have any ideas why these SCF options would prompt a successful convergemce for the optimization, but not the frequency? Thanks, -Connie jmmckel@attglobal.net wrote: > Connie Chang wrote: > > > Hi -- > > > > I'm sorry to bother everyone again... But I have another question about > > Gaussian... > > > > I was finally able to get Gaussian to geometrically optimize my charged > > (-1) molecule with the following Route specification: > > > > # PM3 SCF=vshift=500 SCF=(MaxCyc=1200) Opt > > > > However, when I ran the job again and added the Freq keyword, although > > the geometry optimized, the SCF energy calculation in the Freq part of > > the job oscillates again until the job terminates with a > > UNABLE TO ACHIEVE SELF-CONSISTENCE error. Why does this happen? If I > > have the following route specification > > > > #PM3 SCF=vshift=500 SCG=(Maxcyc=1200) Opt Freq Test > > > > Does Gaussian know to use my prior specifications for finding the SCF > > (i.e. the Vshift and the increased MaxCyc) or does it use it but still > > fail? > > Did you try it? > > > > > > > Does anyone have any suggestions? > > > > And thanks again for all your previous suggestions! > > > > Connie > > > > -= This is automatically added to each message by mailing script =- > > CHEMISTRY@ccl.net -- To Everybody | CHEMISTRY-REQUEST@ccl.net -- To Admins > > Ftp: ftp.ccl.net | WWW: http://www.ccl.net/chemistry/ | Jan: jkl@ccl.net From chemistry-request@server.ccl.net Wed Nov 20 19:25:16 2002 Received: from ultra.chem.ucsb.edu ([128.111.114.119]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id gAL0PFu05242 for ; Wed, 20 Nov 2002 19:25:16 -0500 Received: from localhost (bushnell@localhost) by ultra.chem.ucsb.edu (8.12.3/8.12.3) with ESMTP id gAL0PCAH003333; Wed, 20 Nov 2002 16:25:12 -0800 (PST) Date: Wed, 20 Nov 2002 16:25:12 -0800 (PST) From: John Bushnell To: Connie Chang cc: chemistry@ccl.net Subject: Re: CCL:Gaussian98W and charged molecules (again) In-Reply-To: <3DDBC828.4E5E1257@cornell.edu> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII X-Virus-Scanned: by amavisd-milter (http://amavis.org/) Hi, I think your problem now is that Gaussian only does numerical frequency calculations with PM3 (according to the manual we have). So Gaussian needs to do a whole slew of SCF's to get frequencies. I have had difficult cases where getting convergence was hard, but became impossible at some point as Gaussian perturbs the structure and redoes the SCF for a frequency calculation. This is particularly bad for cases where the minimum has symmetry, but the perturbed species do not. Fortunately, Gaussian now can do analytical frequencies for DFT. I would be surprised if adding SCF=qc did not help unless for some reason this was not supported for PM3. But you never know. - John On Wed, 20 Nov 2002, Connie Chang wrote: > Hi -- > > I'm sorry to bother everyone again... But I have another question about > Gaussian... > > I was finally able to get Gaussian to geometrically optimize my charged > (-1) molecule with the following Route specification: > > # PM3 SCF=vshift=500 SCF=(Maxcyc=1200) Opt > > However, when I ran the job again and added the Freq keyword, although > the geometry optimized, the SCF energy calculation in the Freq part of > the job oscillates again until the job terminates with a > UNABLE TO ACHIEVE SELF-CONSISTENCE error. Why does this happen? If I > have the following route specification > > #PM3 SCF=vshift=500 SCG=(Maxcyc=1200) Opt Freq Test > > Does Gaussian know to use my prior specifications for finding the SCF > (i.e. the Vshift and the increased MaxCyc) or does it use it but still > fail? > > Does anyone have any suggestions? > > And thanks again for all your previous suggestions! > > Connie > > > -= This is automatically added to each message by mailing script =- > CHEMISTRY@ccl.net -- To Everybody | CHEMISTRY-REQUEST@ccl.net -- To Admins > Ftp: ftp.ccl.net | WWW: http://www.ccl.net/chemistry/ | Jan: jkl@ccl.net > > > > > From chemistry-request@server.ccl.net Wed Nov 20 16:19:59 2002 Received: from manatee.bmrb.wisc.edu ([144.92.167.238]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id gAKLJxu02489 for ; Wed, 20 Nov 2002 16:19:59 -0500 Received: from bmrb.wisc.edu (stingray.bmrb.wisc.edu [144.92.167.197]) by manatee.bmrb.wisc.edu (Postfix) with ESMTP id DA5763D4A2 for ; Wed, 20 Nov 2002 15:18:47 -0600 (CST) Sender: elu@bmrb.wisc.edu Message-ID: <3DDC070A.B4F542D9@bmrb.wisc.edu> Date: Wed, 20 Nov 2002 16:04:58 -0600 From: Eldon Ulrich X-Mailer: Mozilla 4.72 [en] (X11; U; Linux 2.2.14-5.0 i686) X-Accept-Language: en MIME-Version: 1.0 To: chemistry@ccl.net Subject: Re: CCL: PDB H atom name convention Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Dear All, H atom nomenclature for amino acids and nucleic acids have been explicitly defined by IUPAC. The nomenclature is provided with diagrams in the publication "Recommendations for the Presentation of NMR Structures of Proteins and Nucleic Acids," Pure & Appl. Chem. 70, 117-142, 1998. The article also can be viewed as a PDF file from the BMRB web site at this URL: http://www.bmrb.wisc.edu/bmrb/features/ Select IUPAC Recommendations. PDB files can now be downloaded with either the original PDB nomenclature or with the IUPAC nomenclature for the H atoms. Best regards, Eldon ********************************************** * Eldon L. Ulrich, Ph.D. * * Senior Scientist * * Dept. of Biochemistry * * 433 Babcock Drive * * Univ. of Wisconsin-Madison 53706-1544 * * * * E-mail: elu@bmrb.wisc.edu * * Tel: (608) 265-5741 * ********************************************** From chemistry-request@server.ccl.net Wed Nov 20 05:00:50 2002 Received: from mailrelay.tugraz.at ([129.27.3.7]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id gAKA0nu17110 for ; Wed, 20 Nov 2002 05:00:50 -0500 Received: from novzid.tu-graz.ac.at (novzid.tu-graz.ac.at [129.27.3.150]) by mailrelay.tugraz.at (8.12.6/8.12.6) with ESMTP id gAKA0laD029329; Wed, 20 Nov 2002 11:00:47 +0100 (MET) Received: from ZID/SpoolDir by novzid.tu-graz.ac.at (Mercury 1.48); 20 Nov 02 11:00:47 +0100 Received: from SpoolDir by ZID (Mercury 1.48); 20 Nov 02 11:00:43 +0100 Received: from TweedleDum.local. (129.27.168.77) by novzid.tu-graz.ac.at (Mercury 1.48) with ESMTP; 20 Nov 02 11:00:33 +0100 Date: Wed, 20 Nov 2002 11:00:59 +0100 Subject: Re: CCL:Release of CML2.0 (Chemical Markup Language) ... Content-Type: text/plain; charset=US-ASCII; format=flowed Mime-Version: 1.0 (Apple Message framework v540) Cc: Alk Dransfeld To: Computational Chemistry List From: Alk Dransfeld In-Reply-To: <5.1.1.6.0.20021118202510.029a1808@hermes.cam.ac.uk> Message-Id: Content-Transfer-Encoding: 7bit X-Mailer: Apple Mail (2.540) X-Virus-Scanned: by amavisd-milter (http://amavis.org/) Dear Computational Chemists (CCs), The dedication of a complete namespace ( Computational Chemistry Markup Language, CCML ) to CCs in CML2 shows how important this field of research is. The main aspect of storing results in archives and/or dictionaries, whether CML based or not, is for CCs to be able to REtrieve instead of REcalculate. Therefore, an effective mechanism to find things in CML is essential. On Tue, 19 Nov 2002 09:59:10, Peter Murray-Rust wrote: > ... > Several other modules are under active development > - Computational Chemistry Markup Language (CCML) ... > - CMLReaction. CML already supports reactions ... > - CMLQuery. This is being built on the emerging XML Query language > ... Why wait for an "emerging XML Query language" when the Xpath mechanism is already developed under surveillance of W3C and is already supported in various toolkits (for instance the PERL module XML::XPath from http://xml.sergeant.org/xpath.xml) ? Is Xpath ( http://www.w3.org/TR/xpath ) inappropriate to deal with CML? Is this because the addressability in CML is poor? I think CCs community should follow this weeks CLRC meeting in United Kingdom to see where+how they go and look for data. Best regards -Alk. From chemistry-request@server.ccl.net Wed Nov 20 09:29:16 2002 Received: from smtp.uh.cu ([216.72.24.105]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id gAKETAu24576 for ; Wed, 20 Nov 2002 09:29:12 -0500 Received: from fq.uh.cu (canaria.qct.fq.oc.uh.cu [192.168.3.4]) by smtp.uh.cu (Postfix) with ESMTP id AE3ED34734 for ; Wed, 20 Nov 2002 10:28:35 -0500 (CST) Received: from localhost (yoa@localhost) by fq.uh.cu (8.9.0/8.8.7) with SMTP id KAA14000 for ; Wed, 20 Nov 2002 10:49:00 -0500 Date: Wed, 20 Nov 2002 10:49:00 -0500 (CST) From: yoana perez badel To: chemistry@ccl.net Subject: about G94 calculation. Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi everyone I need your help. I'm calculating a small radicals with Gaussian 94 and a mistake appears at the end of the output I don't know the meaning of it. The mistake is: >>>>>>>>>> Convergence criterion not met. Annihilation of the first spin contaminant: S**2 before annihilation 0.7563, after 0.7500 Convergence failure -- run terminated. Does anyone have any suggestions? Thanks. From chemistry-request@server.ccl.net Wed Nov 20 12:14:09 2002 Received: from nomina.net.lu.se ([130.235.132.90]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id gAKHE8u28483 for ; Wed, 20 Nov 2002 12:14:09 -0500 Received: from csxp (CS-XP1800.mig.lu.se [130.235.104.90]) by nomina.net.lu.se (8.9.3/8.9.0) with SMTP id SAA03826 for ; Wed, 20 Nov 2002 18:14:32 +0100 (MET) Message-ID: <000c01c290b8$a553f400$5a68eb82@csxp> From: =?iso-8859-1?Q?Seth_Malmersj=F6?= To: Subject: Calcium binding proteins in AutoDock Date: Wed, 20 Nov 2002 18:17:03 +0100 MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="----=_NextPart_000_0009_01C290C1.06F96250" X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 6.00.2720.3000 X-MIMEOLE: Produced By Microsoft MimeOLE V6.00.2600.0000 This is a multi-part message in MIME format. ------=_NextPart_000_0009_01C290C1.06F96250 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Hi! =20 Does anyone know how to treat a calcium binding protein in AutoDock?=20 Any suggestions on the non-bonding parameters for calcium? Thank you! Seth ------=_NextPart_000_0009_01C290C1.06F96250 Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable

Hi!

 

Does anyone know how to treat a = calcium=20 binding protein in AutoDock?

Any suggestions on the = non-bonding=20 parameters for calcium?

 

Thank = you!

 

Seth

------=_NextPart_000_0009_01C290C1.06F96250-- From chemistry-request@server.ccl.net Wed Nov 20 16:01:58 2002 Received: from po4.wam.umd.edu ([128.8.10.166]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id gAKL1wu02203 for ; Wed, 20 Nov 2002 16:01:58 -0500 Received: from arwen.wam.umd.edu (arwen.umd.edu [129.2.68.73]) by po4.wam.umd.edu (8.9.3/8.9.3) with ESMTP id QAA01620 for ; Wed, 20 Nov 2002 16:01:49 -0500 (EST) Message-Id: <5.1.1.6.0.20021120134715.00aa8900@imap.wam.umd.edu> X-Sender: oliwalk@imap.wam.umd.edu X-Mailer: QUALCOMM Windows Eudora Version 5.1.1 Date: Wed, 20 Nov 2002 16:04:40 -0800 To: chemistry@ccl.net From: olivier walker Subject: Ramachadran plot for the 20 amino acids Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii"; format=flowed Hi all, This question is not entirely related to computational chemistry but I need it to move forward in my program. Does anyone know where I can find Ramachadran plot for each of the 20 amino-acid (or the allowed phi and psi angles to rotate around N---Calpha----C) I found it for some of them in Fasman's book "prediction of protein structure and the principles of protein conformation" but I would like to know if this kind of information exists for all amino acid. (book, review or web site) Thanks in advance Olivier ************************************************** Olivier WALKER Department of Chemistry and Biochemistry University of Maryland College Park, MD 20742 ************************************************** E-mail : oliwalk@wam.umd.edu ************************************************** From chemistry-request@server.ccl.net Wed Nov 20 09:31:47 2002 Received: from GWIA.HSC.WVU.EDU ([157.182.105.18]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id gAKEVlu24652 for ; Wed, 20 Nov 2002 09:31:47 -0500 Received: from HSC-DOM5-MTA by GWIA.HSC.WVU.EDU with Novell_GroupWise; Wed, 20 Nov 2002 09:31:47 -0500 Message-Id: X-Mailer: Novell GroupWise Internet Agent 6.0.2 Date: Wed, 20 Nov 2002 09:31:44 -0500 From: "Peter Gannett" To: , Subject: Re: CCL:computer methods in chemistry Mime-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Disposition: inline Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id gAKEVlu24653 Omar: I'm not sure what the question is. Are you looking for a syllabus or freeware? Pete Gannett >>> omar Deeb 11/19/02 10:49PM >>> Dear ccl users, We are interested in giving our undergraduate students a new course titled "computer methods in chemistry" or "chemistry and computer". In this course , we want the students to use the computer in all the fields of chemistry. It is not exactly a computational chemistry or molecular modeling course rather than using computers in chemistry and the molecular moldeling will be one of the experiments . The course will be one lecture a week plus one lab. (3 credit hours) Any suggestions. Thanks in advance Dr. Omar Deeb Alquds University --------------------------------- Do you Yahoo!? Yahoo! Web Hosting - Let the expert host your site