From chemistry-request@ccl.net Thu Jul 1 03:26:40 2004 Received: from mail.interware.hu (mail.interware.hu [195.70.32.130]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i618Qdq1016013 for ; Thu, 1 Jul 2004 03:26:39 -0500 Received: from caracas-1582.adsl.interware.hu ([213.178.106.46] helo=cthulhu) by mail.interware.hu with smtp (Exim 4.34 #1 (Debian)) id 1Bfwz7-0001bJ-Pq for ; Thu, 01 Jul 2004 10:31:58 +0200 Message-ID: <000d01c45f4e$8f7d2e10$0200a8c0@cthulhu> From: "Tamas E. Gunda" To: References: <000b01c45ede$6d804510$b400a8c0@fedor> Subject: Re: CCL: software to convert XYZ format to PDB ? Date: Thu, 1 Jul 2004 10:34:08 +0100 MIME-Version: 1.0 Content-Type: text/plain; charset="koi8-r" Content-Transfer-Encoding: 7bit X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 6.00.2800.1409 X-MimeOLE: Produced By Microsoft MimeOLE V6.00.2800.1409 X-Spam-Status: No, hits=0.8 required=7.5 tests=MY_DSL autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net Hmm... I would be also interested to know such program. Even the "big" commercial ones usually produce "correct" pdb files only, if one uses their own peptide builder. To recognize automatically the amino acids, enzyme prostetic groups, nucleosides, which are defined in the pdb format, is not simple. Tamas E. Gunda tgunda [AT] puma.unideb.hu ----- Original Message ----- From: "Michael" To: Sent: Wednesday, June 30, 2004 21:11 PM Subject: CCL:CCL software to convert XYZ format to PDB ? > Dear CCLers, > > > > I need to convert protein structure presented as XYZ (Cartesian coordinate > file) > > to the PDB file format. > > The problem is that many software packages can do the job but not > completely. > > In other words, when such software reads an XYZ file (see the fragment > below): > > > > N -1.21000 43.30600 -19.48400 > > C -1.45100 43.83100 -20.83200 > > C -1.89300 45.28700 -20.70900 > > O -1.42200 46.16400 -21.43800 > > > > it generates the following PDB analog with unknown residual names and > numbers: > > > > ATOM 462 N UNK A 1 -1.210 43.306 -19.484 1.00 0.00 > > ATOM 463 C UNK A 1 -1.451 43.831 -20.832 1.00 0.00 > > ATOM 464 C UNK A 1 -1.893 45.287 -20.709 1.00 0.00 > > ATOM 465 O UNK A 1 -1.422 46.164 -21.438 1.00 0.00 > > > > while the correct pdb file must specify the residual names and numbers: > > > > ATOM 462 N VAL 32 -1.210 43.306 -19.484 1.00 14.04 > N > > ATOM 463 CA VAL 32 -1.451 43.831 -20.832 1.00 6.48 > C > > ATOM 464 C VAL 32 -1.893 45.287 -20.709 1.00 8.17 > C > > ATOM 465 O VAL 32 -1.422 46.164 -21.438 1.00 10.91 > O > > > > I would highly appreciate if somebody can point me to the reliable free > software for Windows. > > > > Kind regards, > > Michael > > > > > -= This is automatically added to each message by the mailing script =- > To send e-mail to subscribers of CCL put the string CCL: on your Subject: line > and send your message to: CHEMISTRY|at|ccl.net > > Send your subscription/unsubscription requests to: CHEMISTRY-REQUEST|at|ccl.net > HOME Page: http://www.ccl.net | Jobs Page: http://www.ccl.net/jobs > > If your mail is bouncing from CCL.NET domain send it to the maintainer: > Jan Labanowski, jlabanow|at|nd.edu (read about it on CCL Home Page) > -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+ > > > > > > From chemistry-request@ccl.net Thu Jul 1 04:51:46 2004 Received: from shiva.jussieu.fr (shiva.jussieu.fr [134.157.0.129]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i619pjq1023008 for ; Thu, 1 Jul 2004 04:51:45 -0500 Received: from ds10.itodys.jussieu.fr (ds10.itodys.jussieu.fr [134.157.24.13]) by shiva.jussieu.fr (8.12.11/jtpda-5.4) with ESMTP id i619v4RU095245 for ; Thu, 1 Jul 2004 11:57:04 +0200 (CEST) X-Ids: 167 Received: by ds10.itodys.jussieu.fr (8.12.1/1.1.2.11/09Jul02-1200PM) id i619v3Xn018074; Thu, 1 Jul 2004 11:57:03 +0200 (MEST) Date: Thu, 1 Jul 2004 11:57:03 +0200 (MEST) From: Michel Petitjean Message-Id: <200407010957.i619v3Xn018074~at~ds10.itodys.jussieu.fr> To: chemistry~at~ccl.net Subject: CCL: Re: software to convert XYZ format to PDB ? X-Miltered: at shiva.jussieu.fr with ID 40E3DFF0.001 by Joe's j-chkmail (http://j-chkmail.ensmp.fr)! X-Antivirus: scanned by sophie at shiva.jussieu.fr X-Spam-Status: No, hits=0.0 required=7.5 tests=none autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net To: Subject: CCL:software to convert XYZ format to PDB ? Imagine that you are the programmer: how could you know from the atomic symbols and the X,Y,Z coordinates what could be the residue ? The N,CA,C,O coordinates of all residues of all known proteins in the PDB offer quite similar 3D patterns. If the residue information is not read by the programme, it will not be output by the programme. Michel Petitjean, Email: petitjean~at~itodys.jussieu.fr ITODYS (CNRS, UMR 7086) ptitjean~at~ccr.jussieu.fr 1 rue Guy de la Brosse Phone: +33 (0)1 44 27 48 57 75005 Paris, France. FAX : +33 (0)1 44 27 68 14 http://petitjeanmichel.free.fr/itoweb.petitjean.html ................................................................... Tamas E. Gunda wrote: > > I need to convert protein structure presented as XYZ (Cartesian coordinate > file) > to the PDB file format. > The problem is that many software packages can do the job but not > completely. > In other words, when such software reads an XYZ file (see the fragment > below): > > N -1.21000 43.30600 -19.48400 > C -1.45100 43.83100 -20.83200 > C -1.89300 45.28700 -20.70900 > O -1.42200 46.16400 -21.43800 > > it generates the following PDB analog with unknown residual names and > numbers: > > ATOM 462 N UNK A 1 -1.210 43.306 -19.484 1.00 0.00 > ATOM 463 C UNK A 1 -1.451 43.831 -20.832 1.00 0.00 > ATOM 464 C UNK A 1 -1.893 45.287 -20.709 1.00 0.00 > ATOM 465 O UNK A 1 -1.422 46.164 -21.438 1.00 0.00 > > while the correct pdb file must specify the residual names and numbers: > > ATOM 462 N VAL 32 -1.210 43.306 -19.484 1.00 14.04 > N > ATOM 463 CA VAL 32 -1.451 43.831 -20.832 1.00 6.48 > C > ATOM 464 C VAL 32 -1.893 45.287 -20.709 1.00 8.17 > C > ATOM 465 O VAL 32 -1.422 46.164 -21.438 1.00 10.91 > O > From chemistry-request@ccl.net Thu Jul 1 05:32:51 2004 Received: from cirse.extra.cea.fr (cirse.extra.cea.fr [132.166.172.102]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i61AWoq1026567 for ; Thu, 1 Jul 2004 05:32:51 -0500 Received: from argiope.saclay.cea.fr (argiope.saclay.cea.fr [132.166.192.108]) by cirse.extra.cea.fr (8.12.10/CEAnet-Internet.3.0) with ESMTP id i61Ac9TA002659 for ; Thu, 1 Jul 2004 12:38:10 +0200 (MEST) Received: from muguet.saclay.cea.fr (unverified) by argiope.saclay.cea.fr (Content Technologies SMTPRS 4.3.12) with ESMTP id for ; Thu, 1 Jul 2004 12:38:09 +0200 Received: from llb.saclay.cea.fr (llb.saclay.cea.fr [132.166.17.100]) by muguet.saclay.cea.fr (8.12.10/CEAnet-internes.3.0) with ESMTP id i61Ac8u1028210 for ; Thu, 1 Jul 2004 12:38:08 +0200 (MEST) Received: from [132.166.18.220] (llb1220.saclay.cea.fr [132.166.18.220]) by llb.saclay.cea.fr (8.12.10/jtpda-5.3.2) with ESMTP id i61Ac6J1024528 for ; Thu, 1 Jul 2004 12:38:07 +0200 (MEST) Mime-Version: 1.0 (Apple Message framework v618) In-Reply-To: <200407010957.i619v3Xn018074^at^ds10.itodys.jussieu.fr> References: <200407010957.i619v3Xn018074^at^ds10.itodys.jussieu.fr> Content-Type: text/plain; charset=ISO-8859-1; format=flowed Message-Id: From: hinsen^at^cnrs-orleans.fr Subject: Re: CCL:software to convert XYZ format to PDB ? Date: Thu, 1 Jul 2004 12:38:34 +0200 To: chemistry^at^ccl.net X-Mailer: Apple Mail (2.618) X-Spam-Status: No, hits=1.0 required=7.5 tests=NO_REAL_NAME autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id i61AWqq1026574 On Jul 1, 2004, at 11:57, Michel Petitjean wrote: > Imagine that you are the programmer: how could you know from > the atomic symbols and the X,Y,Z coordinates what could be > the residue ? The N,CA,C,O coordinates of all residues of > all known proteins in the PDB offer quite similar 3D patterns. If I had to do this (fortunately I don't), I'd first identify the peptide planes as patterns of pairwise distances (they are quite rigid). I'd then identify the sidechains atom by atom starting from the C-alphas, again by distance criteria. Not a trivial task, but not an impossible one either. --------------------------------------------------------------------- Konrad Hinsen Laboratoire Lion Brillouin, CEA Saclay, 91191 Gif-sur-Yvette Cedex, France Tel.: +33-1 69 08 79 25 Fax: +33-1 69 08 82 61 E-Mail: hinsen^at^llb.saclay.cea.fr --------------------------------------------------------------------- From chemistry-request@ccl.net Thu Jul 1 13:30:35 2004 Received: from mxout4.cac.washington.edu (mxout4.cac.washington.edu [140.142.33.19]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i61IUYHN000353 for ; Thu, 1 Jul 2004 13:30:34 -0500 Received: from smtp.washington.edu (smtp.washington.edu [140.142.32.139]) by mxout4.cac.washington.edu (8.12.11+UW04.02/8.12.11+UW04.03) with ESMTP id i61IZsNT006562 for ; Thu, 1 Jul 2004 11:35:54 -0700 Received: from [192.168.1.69] (varani-fw.chem.washington.edu [128.95.128.128]) (authenticated bits=0) by smtp.washington.edu (8.12.11+UW04.02/8.12.11+UW04.03) with ESMTP id i61IZsaU005861 (version=TLSv1/SSLv3 cipher=RC4-MD5 bits=128 verify=NOT) for ; Thu, 1 Jul 2004 11:35:54 -0700 Message-ID: <40E45989.9090503_at_u.washington.edu> Date: Thu, 01 Jul 2004 20:35:53 +0200 From: Carsten Detering Organization: University of Washington User-Agent: Mozilla/5.0 (Windows; U; Windows NT 5.1; en-US; rv:1.7) Gecko/20040616 X-Accept-Language: en-us, en MIME-Version: 1.0 To: chemistry_at_ccl.net Subject: gaussian03 optimization to transition state Content-Type: text/plain; charset=us-ascii; format=flowed Content-Transfer-Encoding: 7bit X-Spam-Status: No, hits=0.0 required=7.5 tests=none autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net Hi all, I would like to optimize a complex involving a bifurcated hydrogen bond between three nitrogen atoms (trimethylamine and triazen) to a saddle point (which I know exists from previous Mopac calculations). Taking this header line in the input file B3LYP/6-31g* POpt=(Saddle=1) nosymmetry test the optimization finishes with an error optimization stopped --wrong number of Negative eigenvalues: Desired= 1 Actual= 2 --Flag reset to prevent archiving Then I get, at the bottom, the typical proverb that you see only when a calculation has successfully finished, and then Could anybody make some suggestions how to fix this? Thanks a lot in advance, Carsten From chemistry-request@ccl.net Thu Jul 1 13:16:07 2004 Received: from turmiel.ch.uj.edu.pl (turmiel.ch.uj.edu.pl [149.156.71.252]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i61IG5HN032148 for ; Thu, 1 Jul 2004 13:16:06 -0500 Received: from landisl (ha2rtr.agh.edu.pl [149.156.124.18]) (authenticated bits=0) by turmiel.ch.uj.edu.pl (8.12.8/8.12.8) with ESMTP id i61ILP5U020868 (version=TLSv1/SSLv3 cipher=RC4-MD5 bits=128 verify=NO) for ; Thu, 1 Jul 2004 20:21:25 +0200 Date: Thu, 1 Jul 2004 20:21:24 +0200 (=?ISO-8859-2?Q?=8Crodkowoeuropejski_czas_letni?=) From: Mariusz Sterzel To: chemistry_at_ccl.net Subject: NMR for Nitrogen atom in Gaussian 03 In-Reply-To: Message-ID: References: <200407010957.i619v3Xn018074_at_ds10.itodys.jussieu.fr> X-X-Sender: sterzel_at_turmiel.ch.uj.edu.pl MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII X-Virus-Scanned: by amavisd-new X-Spam-Status: No, hits=0.0 required=7.5 tests=none autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net Dear All, I have run NMR calculations and I don't know for which nitrogen isotope, N^{14} or N^{15}, my calculations were performed. Can someone help me with this? There is nothing written in a gaussian log file. Best regards, Mariusz Sterzel -- Mariusz Sterzel Email sterzel_at_chemia.uj.edu.pl From chemistry-request@ccl.net Thu Jul 1 18:02:50 2004 Received: from mhub-m5.tc.umn.edu (mhub-m5.tc.umn.edu [160.94.23.35]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i61N2n8a005400 for ; Thu, 1 Jul 2004 18:02:49 -0500 Received: from trojan.software.umn.edu (trojan.software.umn.edu [128.101.65.4]) by mhub-m5.tc.umn.edu with ESMTP; Thu, 1 Jul 2004 18:08:07 -0500 (CDT) X-Umn-Remote-Mta: [N] trojan.software.umn.edu [128.101.65.4] #+LO Received: (from nobody@localhost) by trojan.software.umn.edu (8.12.9/8.12.8) id i61N818h020314; Thu, 1 Jul 2004 18:08:01 -0500 Message-Id: <200407012308.i61N818h020314_at_trojan.software.umn.edu> Date: Thu, 01 Jul 2004 18:08:01 CDT From: Yan Zhao Subject: Re: CCL:gaussian03 optimization to transition state To: Carsten Detering , chemistry_at_ccl.net MIME-Version: 1.0 Content-Type: TEXT/plain; CHARSET=US-ASCII X-Tick-Nemesis: American Maid X-remote-user-ip: 69.81.168.42 X-Spam-Status: No, hits=0.0 required=7.5 tests=none autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net Substitute "POpt=(Saddle=1)" for "opt=(ts,noeigentest,maxcycle=100)", then it will not stop because the wrong number of Negaative eigenvalues, if the optimization does not converge, you probably should try some better initial guesses of the geometry or add "calcfc" in the opt keyword. Yan On 1 Jul 2004, Carsten Detering wrote: > Hi all, > > I would like to optimize a complex involving a bifurcated hydrogen > bond between three nitrogen atoms (trimethylamine and triazen) to a > saddle point (which I know exists from previous Mopac calculations). > Taking this header line in the input file > > B3LYP/6-31g* POpt=(Saddle=1) nosymmetry test > > the optimization finishes with an error > > optimization stopped > --wrong number of Negative eigenvalues: Desired= 1 Actual= 2 > --Flag reset to prevent archiving > > Then I get, at the bottom, the typical proverb that you see only when a > calculation has successfully finished, and then > > Could anybody make some suggestions how to fix this? > > Thanks a lot in advance, > > Carsten > > > -= This is automatically added to each message by the mailing script =- > To send e-mail to subscribers of CCL put the string CCL: on your Subject: > line > and send your message to: CHEMISTRY_at_ccl.net > > Send your subscription/unsubscription requests to: CHEMISTRY-REQUEST_at_ccl.net > HOME Page: http://www.ccl.net | Jobs Page: http://www.ccl.net/jobs > > If your mail is bouncing from CCL.NET domain send it to the maintainer: > Jan Labanowski, jlabanow_at_nd.edu (read about it on CCL Home Page) > -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+ > > > > > > *************************************** Yan Zhao yzhao_at_chem.umn.edu Smith Hall 232 (612)-625-5311 Department of Chemistry University of Minnesota 207 Pleasant St SE Minneapolis, MN 55455 ***************************************