From chemistry-request@ccl.net Wed May 18 01:09:06 2005 Received: from server.ccl.net (ccl [127.0.0.1]) by server.ccl.net (8.13.1/8.13.1) with ESMTP id j4I595X5010837 for ; Wed, 18 May 2005 01:09:05 -0400 Received: (from apache@localhost) by server.ccl.net (8.13.1/8.13.1/Submit) id j4I595Gw010836 for chemistry /a\ ccl.net; Wed, 18 May 2005 01:09:05 -0400 Date: Wed, 18 May 2005 01:09:05 -0400 Message-Id: <200505180509.j4I595Gw010836 /a\ server.ccl.net> X-Authentication-Warning: server.ccl.net: apache set sender to chemistry-request /a\ ccl.net using -f From: "Xi, , Chen" To: chemistry /a\ ccl.net X-Web-Message-Number: 050518010643-10755 Subject: W:How to parameters Mg+2 and Zn+2 in AUTODOCK? X-Spam-Status: No, score=-2.8 required=5.0 tests=ALL_TRUSTED autolearn=failed version=3.0.3 X-Spam-Checker-Version: SpamAssassin 3.0.3 (2005-04-27) on server.ccl.net Dear CCLers, In my study AUTODOCK3.05 tools was employed to dock a ligand containg CNOPH elments into a receptor containing Zn+2 and Mg+2 metal ions. Zn+2 was bonded with amino residues of the recepter and Mg+2 was binded with amin residue, hydroxide ion and water mocules. I use the "mkgpf3" script to generate the gpf file. Before this step, the variable "PROTEIN_ATOMTYPES" in file gpf3gen.awk was set with value "CNOSHZM". Then I use mkdpf3 to generate dpf file without any other modification. Then I run AUTOGRID3 and AUTODOCK3. In the log file of AUTOGRID3 output, I found Zn was set to atom type 8 without name and an error message -- "Devided by zero was prevented. Was atom 3309 and 3320 the same?". However, I did not find any atom situated too close in the receptor. In the AUTODOCK3 output, I found most of the resulted conformations have large docking energies. Visualizing the docking results with adt, I found in most docked conformation that one oxygen atom of the ligand almost take the place of Mg+2 atom. I am puzzled with the problem. It seems that the problem is caused by parameters for Zn+2 and Mg+2 are not suitable in my study case. Could you give me a solution to fix these problems? Thanks you very much! Sincerely Xi Chen -------------------------------- Dr. Xi Chen 409 College of Pharmacy,907 Rose street Lexingtong, KY 40536, USA Tel: 859-323-4669 Email: xchen7 /a\ uky.edu --------------------------------- From chemistry-request@ccl.net Wed May 18 02:29:34 2005 Received: from jamia-physics.net ([202.141.140.172]) by server.ccl.net (8.13.1/8.13.1) with ESMTP id j4I6TRJR013887 for ; Wed, 18 May 2005 02:29:28 -0400 Received: from jamia-physics.net (flamingo [10.45.0.10]) by jamia-physics.net (8.12.10/8.11.2) with ESMTP id j4I5RvWK015197 for ; Wed, 18 May 2005 10:57:57 +0530 From: "Haider Abbas" To: chemistry () ccl.net Subject: request Date: Wed, 18 May 2005 11:58:08 +0630 Message-Id: <20050518052646.M10069 () jamia-physics.net> X-Mailer: Open WebMail 2.50 20050106 X-OriginatingIP: 10.45.0.40 (haider) MIME-Version: 1.0 Content-Type: text/plain; charset=iso-8859-1 X-Spam-Status: No, score=0.8 required=5.0 tests=DEAR_SOMETHING autolearn=no version=3.0.3 X-Spam-Checker-Version: SpamAssassin 3.0.3 (2005-04-27) on server.ccl.net Dear sir, could you please suggest me some free available code for the calculation of transition states, geometry optimization,energy...etc of some large organic laser dye molecules, just as rhodamine-6G,rhodamine-B. i have several pc running on linux. i will really appreciate thanks yours sincerely Haider Abbas From chemistry-request@ccl.net Wed May 18 08:41:55 2005 Received: from server.ccl.net (ccl [127.0.0.1]) by server.ccl.net (8.13.1/8.13.1) with ESMTP id j4ICfsI5031790 for ; Wed, 18 May 2005 08:41:54 -0400 Received: (from apache@localhost) by server.ccl.net (8.13.1/8.13.1/Submit) id j4ICfsBS031789 for chemistry () ccl.net; Wed, 18 May 2005 08:41:54 -0400 Date: Wed, 18 May 2005 08:41:54 -0400 Message-Id: <200505181241.j4ICfsBS031789 () server.ccl.net> X-Authentication-Warning: server.ccl.net: apache set sender to chemistry-request () ccl.net using -f From: "Antonio, J, Hernandez" To: chemistry () ccl.net X-Web-Message-Number: 050518084044-31704 Subject: W:MNDO-PSDCI X-Spam-Status: No, score=-2.8 required=5.0 tests=ALL_TRUSTED autolearn=failed version=3.0.3 X-Spam-Checker-Version: SpamAssassin 3.0.3 (2005-04-27) on server.ccl.net Dear Colleagues: I am trying to use MNDO-PSDCI by changing the standard MNDO parameters in MOPAC [see caption of figure 3 in: "Martin&Birge, J.Phys.Chem.A 102(1998)852" for MNDO-PSDCIs Carbon and Oxygen parameters and nobilities and for the repulsion correlation length. See also Kusnetzow et al. for Si MNDO-PSDCIs parameters]. Until now, I have not been able to find in the literature MNDO-PSDCI parameters for any other atom!!. Where can I find the missing parameters? Or even better, is there a MNDO-PSDCI code I could use?. Best Regards: Antonio J. Hernandez. From chemistry-request@ccl.net Wed May 18 10:45:03 2005 Received: from webmail.mta.ca (postal.mta.ca [138.73.1.51]) by server.ccl.net (8.13.1/8.13.1) with ESMTP id j4IEj0mb007113 for ; Wed, 18 May 2005 10:45:00 -0400 Received: from nobody by webmail.mta.ca with local (Exim 4.20) id 1DYPmm-0004DD-Bx for CHEMISTRY[at]ccl.net; Wed, 18 May 2005 11:44:36 -0300 Received: from 138.73.24.124 ( [138.73.24.124]) as user khunter[at]mailserv.mta.ca by webmail.mta.ca with HTTP; Wed, 18 May 2005 11:44:36 -0300 Message-ID: <1116427476.428b54d454c92[at]webmail.mta.ca> Date: Wed, 18 May 2005 11:44:36 -0300 From: khunter[at]mta.ca To: CHEMISTRY[at]ccl.net Subject: CCL: how does one calculate memory and disk space properly MIME-Version: 1.0 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 8bit X-Originating-IP: 138.73.24.124 X-Spam-Status: No, score=0.2 required=5.0 tests=FORGED_RCVD_HELO,NO_REAL_NAME autolearn=no version=3.0.3 X-Spam-Checker-Version: SpamAssassin 3.0.3 (2005-04-27) on server.ccl.net Our research group has been utilizing the formulas found within Gaussian's Online manual for calculating memory and disk space for MP2/6-31+G(d,p). We then over estimate the values in hopes of ensuring the calculation enough memory and disk space but alas the calculation repeatedly fail due to limitations of either memory or disk space. Any assistance on how to properly calculate these parameters would be greatly appreaciated. Ken Hunter Mount Allison University From chemistry-request@ccl.net Wed May 18 11:27:00 2005 Received: from rproxy.gmail.com (rproxy.gmail.com [64.233.170.202]) by server.ccl.net (8.13.1/8.13.1) with ESMTP id j4IFQxsR010351 for ; Wed, 18 May 2005 11:26:59 -0400 Received: by rproxy.gmail.com with SMTP id r35so87905rna for ; Wed, 18 May 2005 08:26:58 -0700 (PDT) DomainKey-Signature: a=rsa-sha1; q=dns; c=nofws; s=beta; d=gmail.com; h=received:message-id:date:from:reply-to:to:subject:mime-version:content-type:content-transfer-encoding:content-disposition; b=Qo5g+1qfaJ8IXDV3CUrFoL2r9/MDvij2a7XE8FLWD9g9hh6Mzeugv3c4OvdaMfWxGjU98Zhmrzz71vxCYGtj5EoVfmRpx4Tl33r/sIQfQ78V10juq5cyhHLjnrJdL9D/DNw2qFbX4oCY56HGpaPRxj79ZKAE930XJGbHDlZKWys= Received: by 10.38.9.72 with SMTP id 72mr434956rni; Wed, 18 May 2005 08:26:58 -0700 (PDT) Received: by 10.38.86.63 with HTTP; Wed, 18 May 2005 08:26:58 -0700 (PDT) Message-ID: Date: Wed, 18 May 2005 10:26:58 -0500 From: sunnylele Reply-To: sunnylele To: CHEMISTRY [] ccl.net Subject: CCL:Hi, all, How to find the updated experimental structure parameters of molecules in solution? Mime-Version: 1.0 Content-Type: text/plain; charset=ISO-8859-1 Content-Disposition: inline X-Spam-Status: No, score=0.4 required=5.0 tests=DNS_FROM_RFC_ABUSE,RCVD_BY_IP autolearn=no version=3.0.3 X-Spam-Checker-Version: SpamAssassin 3.0.3 (2005-04-27) on server.ccl.net Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id j4IFR0sR010357 I want to compare the structure calculated with the one measured by experiment. But I can only find the data in gas phase on CRC handbook, even they are from 1960s' reference. Thanks. Jing Song From chemistry-request@ccl.net Wed May 18 17:30:52 2005 Received: from azah.fccc.edu ([131.249.4.237]) by server.ccl.net (8.13.1/8.13.1) with ESMTP id j4ILUdkA032464 for ; Wed, 18 May 2005 17:30:41 -0400 Received: from [192.168.1.45] ([131.249.104.72]) by azah.fccc.edu (8.12.11/8.12.11) with ESMTP id j4IKInLj019110; Wed, 18 May 2005 16:18:49 -0400 (EDT) In-Reply-To: <000801c1e487$24c8c5a0$424f959f@Villa> References: <000801c1e487$24c8c5a0$424f959f@Villa> Mime-Version: 1.0 (Apple Message framework v622) Content-Type: multipart/alternative; boundary=Apple-Mail-7-701381094 Message-Id: <54e79a4a8db1c3ec4497dc5aa53c9985 |a| fccc.edu> From: Roland Dunbrack Subject: MolIDE -- an open-source graphical environment for homology modeling Date: Wed, 18 May 2005 16:18:54 -0400 To: CCL X-Mailer: Apple Mail (2.622) X-Spam-Status: No, score=0.0 required=5.0 tests=none autolearn=failed version=3.0.3 X-Spam-Checker-Version: SpamAssassin 3.0.3 (2005-04-27) on server.ccl.net --Apple-Mail-7-701381094 Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=US-ASCII; delsp=yes; format=flowed We would like to introduce MolIDE, an open-source cross-platform graphical environment for homology modeling. It implements the most frequently used steps involved in basic homology modeling: -- multiple-round PSI-BLAST search of the non-redundant sequence database -- secondary structure prediction based on PSI-BLAST results with PSIPRED -- PSI-BLAST of PDB sequences with profiles generated in search of non-redundant database -- sortable table of PDB results to aid selection of templates for homology modeling -- assisted alignment editing, integrating a template structure viewer and secondary structure prediction -- model construction, including handling of SEQRES/coordinate residue numbering issues -- side-chain replacement with SCWRL -- loop building, with visually-assisted selection of anchor residues MolIDE is currently available for Windows and Linux. The program is freely available to both non-profit and commercial users. More information is available on this site: http://dunbrack.fccc.edu/molide The paper is available online: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi? cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=15845657 Adrian Canutescu and Roland Dunbrack **************************************** * Roland L. Dunbrack, Jr. * Member * Institute for Cancer Research * Fox Chase Cancer Center * 333 Cottman Avenue * Philadelphia PA 19111 * (215) 728-2434 * (215) 728-2412 (fax) * Roland.Dunbrack @ fccc.edu * http://dunbrack.fccc.edu (research) * http://dunbrack.org (genealogy) **************************************** --Apple-Mail-7-701381094 Content-Transfer-Encoding: 7bit Content-Type: text/enriched; charset=US-ASCII Times0000,0000,0000We would like to introduce MolIDE, an open-source cross-platform graphical environment for homology modeling. It implements the most frequently used steps involved in basic homology modeling: -- multiple-round PSI-BLAST search of the non-redundant sequence database -- secondary structure prediction based on PSI-BLAST results with PSIPRED -- PSI-BLAST of PDB sequences with profiles generated in search of non-redundant database -- sortable table of PDB results to aid selection of templates for homology modeling -- assisted alignment editing, integrating a template structure viewer and secondary structure prediction -- model construction, including handling of SEQRES/coordinate residue numbering issues -- side-chain replacement with SCWRL -- loop building, with visually-assisted selection of anchor residues MolIDE is currently available for Windows and Linux. The program is freely available to both non-profit and commercial users. More information is available on this site: http://dunbrack.fccc.edu/molide The paper is available online: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=15845657 Adrian Canutescu and Roland Dunbrack0000,0000,0000 **************************************** * Roland L. Dunbrack, Jr. * Member * Institute for Cancer Research * Fox Chase Cancer Center * 333 Cottman Avenue * Philadelphia PA 19111 * (215) 728-2434 * (215) 728-2412 (fax) * Roland.Dunbrack @ fccc.edu * http://dunbrack.fccc.edu (research) * http://dunbrack.org (genealogy) **************************************** --Apple-Mail-7-701381094-- From chemistry-request@ccl.net Wed May 18 14:34:47 2005 Received: from rproxy.gmail.com (rproxy.gmail.com [64.233.170.196]) by server.ccl.net (8.13.1/8.13.1) with ESMTP id j4IIYkwW022201 for ; Wed, 18 May 2005 14:34:46 -0400 Received: by rproxy.gmail.com with SMTP id r35so116574rna for ; Wed, 18 May 2005 11:34:45 -0700 (PDT) DomainKey-Signature: a=rsa-sha1; q=dns; c=nofws; s=beta; d=gmail.com; h=received:message-id:date:from:reply-to:to:subject:in-reply-to:mime-version:content-type:content-transfer-encoding:content-disposition:references; b=ObNE3EMi9vCccQGihzoqDgpg8HuO34q9aTWNhB7b4p9cWb2XiQoESwDlnIBk0awU+vmcSF0j8RByCWVZ+qKRvAKJbbWIhNCeDENVKy2IOF8Hj77PrJ96+ubmJFIWi4kGs09+mzXSQ7P4DoT+x2EAoJu17fBSusomrziGrMjU4Wo= Received: by 10.38.24.41 with SMTP id 41mr545283rnx; Wed, 18 May 2005 11:34:45 -0700 (PDT) Received: by 10.38.86.63 with HTTP; Wed, 18 May 2005 11:34:44 -0700 (PDT) Message-ID: Date: Wed, 18 May 2005 13:34:44 -0500 From: sunnylele Reply-To: sunnylele To: CHEMISTRY /a\ ccl.net Subject: CCL:Hi, all, How to find the updated experimental structure parameters of molecules in solution? In-Reply-To: Mime-Version: 1.0 Content-Type: text/plain; charset=ISO-8859-1 Content-Disposition: inline References: X-Spam-Status: No, score=0.4 required=5.0 tests=DNS_FROM_RFC_ABUSE,RCVD_BY_IP autolearn=no version=3.0.3 X-Spam-Checker-Version: SpamAssassin 3.0.3 (2005-04-27) on server.ccl.net Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id j4IIYlwW022205 I want to compare the structure calculated with the one measured by experiment. But I can only find the data in gas phase on CRC handbook, even those data are from 1960s' references. Thanks. Jing Song From chemistry-request@ccl.net Wed May 18 17:22:35 2005 Received: from prserv.net (asmtp1.prserv.net [32.97.166.51]) by server.ccl.net (8.13.1/8.13.1) with ESMTP id j4ILMWMG032044 for ; Wed, 18 May 2005 17:22:32 -0400 Received: from [127.0.0.1] (cpe-65-26-182-65.indy.res.rr.com[65.26.182.65]) by prserv.net (asmtp1) with ESMTP id <20050518202248251053p2sde> (Authid: jmmckel); Wed, 18 May 2005 20:22:48 +0000 Message-ID: <428BA454.5030208 /a\ attglobal.net> Date: Wed, 18 May 2005 15:23:48 -0500 From: John McKelvey User-Agent: Mozilla Thunderbird 1.0.2 (Windows/20050317) X-Accept-Language: en-us, en MIME-Version: 1.0 To: chemistry /a\ ccl.net Subject: FTP ... Content-Type: text/plain; charset=ISO-8859-1; format=flowed Content-Transfer-Encoding: 7bit X-Spam-Status: No, score=0.0 required=5.0 tests=none autolearn=failed version=3.0.3 X-Spam-Checker-Version: SpamAssassin 3.0.3 (2005-04-27) on server.ccl.net Folks, This is off topic, but I simply am not a system guru, and need a suggestion as to where to go off-line from CCL for a solution. I have a W2K and a Linux box on an LAN each of which can ping the other correctly, but I can not get FTP to work either way. Though on a hub, the hub is connected to a VPN Router which the two boxes share as a gateway [192.168.1.1], and both bozes can ping the gateway. I can readily go from the W2K box to the internet [to write this.] Apologies for the bandwidth. Best regards, John McKelvey From chemistry-request@ccl.net Wed May 18 22:19:14 2005 Received: from mx5.net.nih.gov (mailfwd.nih.gov [165.112.130.36]) by server.ccl.net (8.13.1/8.13.1) with ESMTP id j4J2JAKF015409 for ; Wed, 18 May 2005 22:19:10 -0400 Received: from mx5.net.nih.gov (localhost [127.0.0.1]) by mx5.net.nih.gov (8.12.10/8.11.6) with ESMTP id j4J0wuas007646 for ; Wed, 18 May 2005 20:58:56 -0400 Received: from pollux.cber.nih.gov (pollux.cber.nih.gov [128.231.52.5]) by mx5.net.nih.gov (8.12.10/8.11.6) with ESMTP id j4J0wuKe007643; Wed, 18 May 2005 20:58:56 -0400 Date: Wed, 18 May 2005 20:19:13 -0400 From: Rick Venable To: John McKelvey cc: chemistry~at~ccl.net Subject: Re: CCL:FTP ... In-Reply-To: <428BA454.5030208~at~attglobal.net> Message-ID: References: <428BA454.5030208~at~attglobal.net> ReplyTo: Rick_Venable~at~nih.gov MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII X-Spam-Status: No, score=0.0 required=5.0 tests=none autolearn=failed version=3.0.3 X-Spam-Checker-Version: SpamAssassin 3.0.3 (2005-04-27) on server.ccl.net On Wed, 18 May 2005, John McKelvey wrote: > This is off topic, but I simply am not a system guru, and need a > suggestion as to where to go off-line from CCL for a solution. > > I have a W2K and a Linux box on an LAN each of which can ping the other > correctly, but I can not get FTP to work either way. Though on a hub, > the hub is connected to a VPN Router which the two boxes share as a > gateway [192.168.1.1], and both bozes can ping the gateway. I can > readily go from the W2K box to the internet [to write this.] One of the machines needs to be running an ftp server, which is usually not set up by default. Setting up ftpd on the Linux box ought to be straightforward, and may need to be done. =+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+= Rick Venable 29/500 FDA/CBER/OVRR Biophysics Lab 1401 Rockville Pike HFM-419 Rockville, MD 20852-1448 U.S.A. (301) 496-1905 Rick_Venable~at~nih.gov ALT email: rvenable~at~speakeasy.org ------------------------------------- "Don't blame me, I voted for Kang." Homer =+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=