From chemistry-request@server.ccl.net Tue Nov 30 08:27:37 1999 Received: from mail-b.bcc.ac.uk (mail-b.bcc.ac.uk [144.82.100.22]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id IAA07784 for ; Tue, 30 Nov 1999 08:27:36 -0500 Received: from biochem.ucl.ac.uk (actually host bsmori1.biochem.ucl.ac.uk) by mail-b.bcc.ac.uk with SMTP (XT-PP) with ESMTP; Tue, 30 Nov 1999 12:20:41 +0000 Received: from bsmir18.biochem.ucl.ac.uk (bsmir18 [128.40.46.21]) by biochem.ucl.ac.uk (8.9.2/8.9.1) with ESMTP id MAA15250 for ; Tue, 30 Nov 1999 12:20:52 GMT Received: from localhost (nobeli@localhost) by bsmir18.biochem.ucl.ac.uk (8.9.3/8.9.3) with SMTP id MAA00896 for ; Tue, 30 Nov 1999 12:20:51 GMT X-Authentication-Warning: bsmir18.biochem.ucl.ac.uk: nobeli owned process doing -bs Date: Tue, 30 Nov 1999 12:20:51 +0000 ("GMT) From: Irene Nobeli X-Sender: nobeli@bsmir18 To: Computational Chemistry List Subject: Another DOCK question Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear CCL readers Can anyone help with the following? I did a rigid docking calculation using DOCK4.0 with the following parameters for the ranking of the resulting orientations: total_orientations 500 rank_orientations yes rank_orientation_total 100 This resulted -correctly- in 100 orientations being ranked in the output file. Then I tried to dock the same ligand to the same receptor using a conformation search for the ligand. I used an anchor search and the same parameters for the ranking of orientations. However, this time I only get 10 ranked orientations in the output and I don't seem to be able to increase that. Is there some parameter I should change, or is this a limit for docking combined with conformational search? Many thanks, I will report back the answers, if any. Irilenia ------------------------------------------------ Irene (Irilenia) Nobeli Biomolecular Structure and Modelling Unit Department of Biochemistry and Molecular Biology University College London Darwin Building Gower Street London WC1E 6BT nobeli@biochem.ucl.ac.uk 0171-419 3890 0171 504 2171 >>> I wanted to go out and change the world but... I couldn't find a babysitter <<< From chemistry-request@server.ccl.net Tue Nov 30 09:58:14 1999 Received: from mailhost.univ-orleans.fr (dns.univ-orleans.fr [194.167.30.130]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id JAA08196 for ; Tue, 30 Nov 1999 09:58:13 -0500 Received: from univ-orleans.fr (IDENT:postdoc@gremi73.univ-orleans.fr [193.49.77.73]) by mailhost.univ-orleans.fr (8.9.3/jtpda-5.3.1p) with ESMTP id OAA29508 for ; Tue, 30 Nov 1999 14:51:23 +0100 (MET) Sender: postdoc@univ-orleans.fr Message-ID: <3843D6D0.14C85133@univ-orleans.fr> Date: Tue, 30 Nov 1999 14:53:20 +0100 From: Xiangyun GUO X-Mailer: Mozilla 4.61 [en] (X11; I; Linux 2.2.12-20 i686) X-Accept-Language: en MIME-Version: 1.0 To: chemistry@ccl.net Subject: L-J potential parameters Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Hello, everyone I am doing Molecular Dynamics simulations about Si3N4 decomposition, could anyone tell me the energy and length parameters of Si atom in Lennard-Jones 12-6 potential ? Please reply to : Xiangyun.Guo@univ-orleans.fr Thank you in advance. With best regards Xiangyun GUO From chemistry-request@server.ccl.net Tue Nov 30 09:48:28 1999 Received: from pegasus.lnls.br ([200.18.249.72]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id JAA08167 for ; Tue, 30 Nov 1999 09:48:21 -0500 Received: from lnls.br (MMO1 [200.136.164.51]) by pegasus.lnls.br with SMTP (Microsoft Exchange Internet Mail Service Version 5.5.1960.3) id X8MXKHW1; Tue, 30 Nov 1999 11:41:19 -0300 Message-ID: <3843E216.889DF734@lnls.br> Date: Tue, 30 Nov 1999 11:41:26 -0300 From: Osmar Norberto de Souza Reply-To: osmarns@lnls.br Organization: LNLS X-Mailer: Mozilla 4.61 [en] (WinNT; I) X-Accept-Language: en MIME-Version: 1.0 To: CCL Subject: heme parameters Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit Dear CCLers, Are there all-atom oxy- and deoxy-heme parameters for the AMBER force field? Many thanks. Best wishes, Osmar ----------------------------------------------------------- Osmar NORBERTO DE SOUZA, Ph.D. Group Leader: Modelagem Molecular & Simulação Laboratório Nacional de Luz Síncrotron (LNLS) P.O. Box 6192 Campinas 13087-970, São Paulo Brasil ----------------------------------------------------------- Tel: +55 19 287-4520 Fax: +55 19 287-4632 E-mail: osmarns@lnls.br ----------------------------------------------------------- From chemistry-request@server.ccl.net Tue Nov 30 10:03:13 1999 Received: from mail-b.bcc.ac.uk (mail-b.bcc.ac.uk [144.82.100.22]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id KAA08236 for ; Tue, 30 Nov 1999 10:03:08 -0500 Received: from biochem.ucl.ac.uk (actually host bsmori1.biochem.ucl.ac.uk) by mail-b.bcc.ac.uk with SMTP (XT-PP) with ESMTP; Tue, 30 Nov 1999 13:56:01 +0000 Received: from bsmir18.biochem.ucl.ac.uk (bsmir18 [128.40.46.21]) by biochem.ucl.ac.uk (8.9.2/8.9.1) with ESMTP id NAA17973 for ; Tue, 30 Nov 1999 13:56:13 GMT Received: from localhost (nobeli@localhost) by bsmir18.biochem.ucl.ac.uk (8.9.3/8.9.3) with SMTP id NAA01073 for ; Tue, 30 Nov 1999 13:56:12 GMT X-Authentication-Warning: bsmir18.biochem.ucl.ac.uk: nobeli owned process doing -bs Date: Tue, 30 Nov 1999 13:56:12 +0000 ("GMT) From: Irene Nobeli X-Sender: nobeli@bsmir18 To: Computational Chemistry List Subject: Re: CCL:Another DOCK question (fwd) Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Many thanks to Jon Erickson for providing a very prompt answer to my recent question (in fact I received his answer BEFORE I received a copy of my question at the CCL!). He identified the "number of peripheral seeds" parameter as the one responsible for DOCK4 outputting only 10 ranked orientations. I. ------------------------------------------------ Irene (Irilenia) Nobeli Biomolecular Structure and Modelling Unit Department of Biochemistry and Molecular Biology University College London Darwin Building Gower Street London WC1E 6BT nobeli@biochem.ucl.ac.uk 0171-419 3890 0171 504 2171 >>> I wanted to go out and change the world but... I couldn't find a babysitter <<< From chemistry-request@server.ccl.net Tue Nov 30 13:14:18 1999 Received: from arnold.chem.uoa.gr (arnold.chem.uoa.gr [195.134.76.50]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id NAA10057 for ; Tue, 30 Nov 1999 13:14:16 -0500 Received: from localhost (jkerk@localhost) by arnold.chem.uoa.gr (8.8.8/8.8.8) with SMTP id TAA09627 for ; Tue, 30 Nov 1999 19:06:42 +0200 (EET) Date: Tue, 30 Nov 1999 19:06:42 +0200 (EET) From: John Kerkines To: chemistry@ccl.net Subject: Molpro Output Visualization Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi, Does anybody know if there exist any programs for visualization or processing of the Molpro output? I am only aware of MOLDEN and for Molpro98.1 version. Regards, John Kerkines University of Athens Greece From chemistry-request@server.ccl.net Tue Nov 30 13:39:31 1999 Received: from aquarius.ime.eb.br (aquarius.ime.eb.br [200.20.120.44]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id NAA10541 for ; Tue, 30 Nov 1999 13:39:28 -0500 Received: from epq.ime.eb.br (epq.ime.eb.br [200.20.121.33]) by aquarius.ime.eb.br (8.9.1a/8.9.1) with ESMTP id PAA30868; Tue, 30 Nov 1999 15:45:37 -0200 Received: from EPQ/SpoolDir by epq.ime.eb.br (Mercury 1.44); 30 Nov 99 15:31:23 -0200 Received: from SpoolDir by EPQ (Mercury 1.44); 30 Nov 99 15:31:01 -0200 Received: from sdio (200.20.123.210) by epq.ime.eb.br (Mercury 1.44); 30 Nov 99 15:30:52 -0200 Message-ID: <004b01bf3b58$a62d2300$d27b14c8@ime.eb.br> From: "Teodorico Ramalho" To: , References: <9911291415.ZM23527@wavefun.com> Subject: Re: CCL:RE:boron PM3 parameters Date: Tue, 30 Nov 1999 15:30:51 -0200 MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 7bit X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 5.00.2314.1300 X-MimeOLE: Produced By Microsoft MimeOLE V5.00.2314.1300 Hi Yu, There is the PM3 parametrs to boron, and boron-magnesium. There is a software: Spartan Pro. It use the PM3(tm). Good luck, Teodorico C. Ramalho From chemistry-request@server.ccl.net Tue Nov 30 15:03:46 1999 Received: from aleph.net.uniovi.es (aleph.net.uniovi.es [156.35.11.1]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id PAA11301 for ; Tue, 30 Nov 1999 15:03:39 -0500 Received: from pinon.ccu.uniovi.es (pinon.ccu.uniovi.es [156.35.31.1]) by aleph.net.uniovi.es (PMDF V5.2-32 #38866) with ESMTP id <01JIYLCPRON2002O20@aleph.net.uniovi.es> for CHEMISTRY@ccl.net; Tue, 30 Nov 1999 19:56:42 +0100 (MET) Received: (from pueyo@localhost) by pinon.ccu.uniovi.es (8.9.2/8.9.2) id TAA17285 for CHEMISTRY@ccl.net; Tue, 30 Nov 1999 19:56:41 +0100 (MET) Date: Tue, 30 Nov 1999 19:56:41 +0100 (MET) From: Victor Lua~na Subject: On He2(+) To: CHEMISTRY@ccl.net Message-id: <199911301856.TAA17285@pinon.ccu.uniovi.es> MIME-version: 1.0 Content-type: text/plain; charset=us-ascii Content-transfer-encoding: 7BIT Some one asked today about the experimental detection of He2 ions. The reference L Coman et al, Phys. Rev. Lett. 83 (1999) 2715--2717 provides binding energy and rotational constants for He_2(+). Some more data appears on the NIST's webbook: http://webbook.nist.gov/ As for He_2(+2), the webbook cites only the results of theoretical calculations. Best regards, Victor Lua~na -- HomePage %%http://www3.uniovi.es/~quimica.fisica/qcg/vlc/luana.html%% Free software %%http://www3.uniovi.es/~quimica.fisica/qcg/%% +----------------------------------------------+ +---^---/ / ! Victor Lua~na ! | ~ / Just in case ! Departamento de Quimica Fisica y Analitica ! | | you don't ! Universidad de Oviedo, 33006-Oviedo, Spain ! < / remember ! e-mail: %%victor@carbono.quimica.uniovi.es%% ! | / where Oviedo ! phone: +34-985-103491 fax: +34-985-103125 ! |____ ___/ is ;-) +----------------------------------------------+ \/ From chemistry-request@server.ccl.net Tue Nov 30 17:25:45 1999 Received: from mailbox.syr.edu (root@mailbox.syr.edu [128.230.18.5]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id RAA12083 for ; Tue, 30 Nov 1999 17:25:44 -0500 Received: from syr.edu (curie.syr.edu [128.230.187.116]) by mailbox.syr.edu (8.9.2/8.9.2) with ESMTP id QAA14063 for ; Tue, 30 Nov 1999 16:18:56 -0500 (EST) Sender: desingh@mailbox.syr.edu Message-ID: <3844405E.CE9B3EE1@syr.edu> Date: Tue, 30 Nov 1999 16:23:42 -0500 From: Deepak Singh Organization: Dept. of Chemistry, Syracuse University X-Mailer: Mozilla 4.61C-SGI [en] (X11; I; IRIX64 6.5 IP30) X-Accept-Language: en MIME-Version: 1.0 To: Computational Chemistry List Subject: ab initio/vs PM3 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Hi, I have been using G98 for some calculations on retinal (ab-initio and semi-empirical) and I get some strange results. Could anyone familiar with ab-initio calculations on similar molecules please email me? Thanks Deepak. -- ********************************************************************** Deepak Singh Tel : (315)443 1739 (w) Graduate Student (315)472 9659 (h) Dept. of Chemistry Fax : (315)443 4070 Syracuse University email : desingh@syr.edu 1-014 CST, Syracuse URL : http://web.syr.edu/~desingh NY 13244 "Violence is the last refuge of the incompetent." --- Salvor Hardin ********************************************************************** From chemistry-request@server.ccl.net Tue Nov 30 17:56:11 1999 Received: from medicor.wustl.edu (medicor.wustl.edu [128.252.223.195]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id RAA12236 for ; Tue, 30 Nov 1999 17:56:10 -0500 From: ReichertD@mir.wustl.edu Subject: Calculating lipophilicity To: chemistry@ccl.net X-Mailer: Lotus Notes Release 5.0 March 30, 1999 Message-ID: Date: Tue, 30 Nov 1999 15:45:29 -0600 X-Priority: 3 (Normal) X-MIMETrack: Serialize by Router on Medicor/Washington University(Release 5.0.1a|August 17, 1999) at 11/30/99 03:45:34 PM MIME-Version: 1.0 Content-type: text/plain; charset=us-ascii Hi, I apologize for the broad topic in the subject. I'm trying to find references to calculating the lipophilicity (specifically logP) for metal coordination compounds, not normal organic molecules. Any leads would be greatly appreciated. thanks, Dave Reichert David Reichert, Ph.D. Washington University School of Medicine 510 S. Kingshighway, Campus Box 8225 St Louis, MO 63110 e-mail: reichertd@mir.wustl.edu voice: (314) 362-8461 fax: (314) 362-9940 From chemistry-request@server.ccl.net Tue Nov 30 20:42:45 1999 Received: from dragon.inha.ac.kr (dragon.inha.ac.kr [165.246.10.3]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id UAA13007 for ; Tue, 30 Nov 1999 20:42:39 -0500 Received: from dragon.inha.ac.kr ([165.246.154.77]) by dragon.inha.ac.kr (8.9.1a-H1/8.9.1) with ESMTP id JAA07407 for ; Wed, 1 Dec 1999 09:34:54 +0900 (KST) Message-ID: <38446DED.B098F353@dragon.inha.ac.kr> Date: Wed, 01 Dec 1999 09:38:05 +0900 From: "Prof. Chan Kyung Kim" Organization: Dept. of Chem., Inha Univerity X-Mailer: Mozilla 4.51 [ko] (Win98; I) X-Accept-Language: ko MIME-Version: 1.0 To: chemistry@ccl.net Subject: Experimental proton affinity of Br anion (Br-) Content-Type: text/plain; charset=EUC-KR Content-Transfer-Encoding: 8bit Dear Computational Chemists: Sorry for the question not directly related to the computational topic. I am looking for an experimental proton affinity of Br anion(Br-). I can not find it from the NIST (webbook.nist.gov) nor any references I searched. If it does not exist, is there any reason for this? Thank you for your help in advance. Chan -- =============================================================================== Prof.Chan Kyung Kim (Tel) +82-32-860-7684 Department of Chemistry (Fax) +82-32-867-5604 or +82-32-873-9333 Inha University (e-mail) kckyung@dragon.inha.ac.kr Inchon, 402-751, Korea (homepage) http://dragon.inha.ac.kr/~kckyung(Korean) ===============================================================================