From chemistry-request@server.ccl.net Fri Sep 8 03:04:54 2000 Received: from cns.FTA-Berlin.de (root@cns.FTA-Berlin.de [141.16.244.4]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id DAA08391 for ; Fri, 8 Sep 2000 03:04:53 -0400 Received: from cs1.FTA-Berlin.de (root@cs1.FTA-Berlin.de [194.25.98.134]) by cns.FTA-Berlin.de (8.9.3/8.9.3) with ESMTP id IAA03233; Fri, 8 Sep 2000 08:06:04 +0200 Received: from langmuir.aca-berlin.de (hofmann@langmuir.ACA-Berlin.de [141.16.16.120]) by cs1.FTA-Berlin.de (8.9.3/8.9.3) with ESMTP id JAA30352; Fri, 8 Sep 2000 09:04:45 +0200 Date: Fri, 8 Sep 2000 09:05:21 +0200 (CEST) From: Alexander Hofmann To: Kiniu WONG Kin-Yiu cc: chemistry@ccl.net Subject: Re: CCL:one more questions about an error in Gaussian In-Reply-To: <001e01c018f2$89863480$14d3bd89@l> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi, I think you've got two problems. > Estimate disk for full transformation 76475988068 words. 1. You need 76 GW disk space, this are about 0.5 TeraBytes! > LAS= 19899475200 but cannot sort more than 2147483647 items. 2. This looks likt you're using a 32 bit machine. So variables are limited to 2**32-1 bytes. Hope this helps Alex --- Dr. Alexander Hofmann Institut fuer Angewandte Chemie Berlin-Adlershof e.V. Richard-Willstaetter-Str. 12 D-12489 Berlin hofmann@aca-berlin.de Tel.: +49-30-6392-4408 Fax.: +49-30-6392-4350 http://www.aca-berlin.de PGP-Private key: http://www.uni-leipzig.de/~quant/hofmann/alexander.hofmann.pubkey.asc From chemistry-request@server.ccl.net Fri Sep 8 04:36:21 2000 Received: from rzumail2.unizh.ch (rzumail2.unizh.ch [130.60.128.10]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id EAA08977 for ; Fri, 8 Sep 2000 04:36:20 -0400 Received: from zisp0303.unizh.ch (zisp0303.unizh.ch [130.60.7.175]) by rzumail2.unizh.ch (8.9.3/8.9.3/07) with ESMTP id KAA17962; Fri, 8 Sep 2000 10:36:11 +0200 (MET DST) Received: (from toukie@localhost) by zisp0303.unizh.ch (AIX4.3/8.9.3/8.8.8) id KAA26662; Fri, 8 Sep 2000 10:36:11 +0200 From: "Dr. S. Shapiro" Message-Id: <200009080836.KAA26662@zisp0303.unizh.ch> Subject: ? re E of solvation/desolvation To: chemistry@ccl.net Date: Fri, 8 Sep 2000 10:36:11 +0200 (MEST) Cc: toukie@zui.unizh.ch X-Mailer: ELM [version 2.4 PL25 PGP2] Content-Type: text Dear Colleagues; Is anyone aware of any approximate "algebraic" formulae for estimating in a rough way the energy of aqueous solvation/desolvation for small molecular weight organic molecules? If so, please share this information with me, including any relevant citations/references. Thanks in advance to all responders, S. Shapiro toukie@zui.unizh.ch From chemistry-request@server.ccl.net Fri Sep 8 04:10:59 2000 Received: from server.biokemi.su.se (server.biokemi.su.se [130.237.179.5]) by server.ccl.net (8.8.7/8.8.7) with SMTP id EAA08872 for ; Fri, 8 Sep 2000 04:10:59 -0400 Received: from mail.biokemi.su.se (unverified [130.237.179.175]) by server.biokemi.su.se (EMWAC SMTPRS 0.83) with SMTP id ; Fri, 08 Sep 2000 10:12:34 +0200 Sender: zhang@ccl.net Message-ID: <39B89E09.5F88F12C@mail.biokemi.su.se> Date: Fri, 08 Sep 2000 10:06:33 +0200 From: Xiao-Ping Zhang Reply-To: zhang@biokemi.su.se X-Mailer: Mozilla 4.72 [en] (X11; U; Linux 2.2.14-12 i686) X-Accept-Language: en MIME-Version: 1.0 To: "Garrett M. Morris" , chemistry@ccl.net Subject: Re: CCL:ligand broken after docking in autodock 3.0 References: Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit Dear Morris, Thank you for your reply on Aug 31. I have sent you my ligand pdbq files (before and after autotors) and log file of autodock3. If you got my mail, please give me an hit. Thank you for your kind help. Best regards, Xiao-Ping Zhang "Garrett M. Morris" wrote: > > Dear Zhang, > > On Thu, 31 Aug 2000, Xiao-Ping Zhang wrote: > > > Hi, > > > > I have another problems for peptide docking with autodock > > 3.0. > > > > (1) If I define tortions for the peptide ligand, I got a > > docked peptide which contains a broken backbone (displayed > > in molecular modeling programs). The distance between the > > atoms where the bond broken was about 4.0 - 4.5 Å. > > > > This sounds like you have a bad PDBQ file for your peptide... > > I would suggest you check this, and if necessary run your peptide > through AutoTors again. > > > (2) I always get a docked peptide with many missed atoms. > > How could we keep a peptide ligand intact during docking? > > > > This sounds like it is related to the bad peptide PDBQ file > > If you cannot solve this problem, send me the peptide and the PDBQ > file you have been using, I will try to help repair it. > > > (3) Concerning the flexibility of peptide ligand, we can > > find the following information in autodock homepage: > > > > "Testing the side chain flexibility in AutoDock 4.0 > > We have now added side chain flexibility to AutoDock, and we > > are now in the process of testing this." > > This is side chain flexibility in the protein! You have always been > able to have flexibility anywhere in the ligand. > > > > > Does that mean that autodock3 can not handle the side chain > > tortions even if you can define the tortions for side chain > > with "autotors3"? > > No. > > > > > (4) What is the best program for peptide docking, > > commercial and free? > > > > My answer is bound to be biased, so I won't answer this! > > :) > > > Thank you advance for your reply. > > You are welcome. > > > > > Sincerely, > > > > Xiao-Ping Zhang > > > > ****************************** > > Xiao-Ping Zhang > > Department of Biochemistry > > Arrhenius Laboratories of Natural Sciences > > Stockholm Universities > > 106 91 Stockholm > > Sweden > > > > Phone: 046-08-162472 /162582 > > Fax: 046-08-153679 > > e-mail: zhang@biokemi.su.se > > > > > > -= This is automatically added to each message by mailing script =- > > CHEMISTRY@ccl.net -- To Everybody | CHEMISTRY-REQUEST@ccl.net -- To Admins > > MAILSERV@ccl.net -- HELP CHEMISTRY or HELP SEARCH > > CHEMISTRY-SEARCH@ccl.net -- archive search | Gopher: gopher.ccl.net 70 > > Ftp: ftp.ccl.net | WWW: http://www.ccl.net/chemistry/ | Jan: jkl@ccl.net > > Best wishes, > > Garrett > > ___ > Dr Garrett M. Morris, MA, DPhil > The Scripps Research Institute, tel: (858) 784-2292 > Dept. Molecular Biology, MB-5, fax: (858) 784-2860 > 10550 North Torrey Pines Road, email: garrett@scripps.edu > La Jolla, CA 92037-1000, USA. www.scripps.edu/pub/olson-web/gmm -- ****************************** Xiao-Ping Zhang Department of Biochemistry Arrhenius Laboratories of Natural Sciences Stockholm Universities 106 91 Stockholm Sweden Phone: 046-08-162472 /162582 Fax: 046-08-153679 e-mail: zhang@biokemi.su.se From chemistry-request@server.ccl.net Fri Sep 8 12:13:10 2000 Received: from poptop.llnl.gov (poptop.llnl.gov [128.115.41.70]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id MAA12043 for ; Fri, 8 Sep 2000 12:13:10 -0400 Received: from [128.115.204.4] (grogers.llnl.gov [128.115.204.4]) by poptop.llnl.gov (8.8.8/LLNL-3.0.2/pop.llnl.gov-5.1) with ESMTP id JAA27136 for ; Fri, 8 Sep 2000 09:10:57 -0700 (PDT) Date: Fri, 8 Sep 2000 09:10:57 -0700 (PDT) X-Sender: e001642@poptop.llnl.gov Message-Id: Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" To: chemistry@ccl.net From: Jennifer Young Subject: Ligand .rtf files Does anyone have tested/published residue topology files for the various estrogen receptor ligands (tamoxifen, raloxifene,estradiol ect.) for use in the academic version of CHARMM? Thanks in advance, Jennifer Young ************************************ Jennifer Young Lawrence Livermore National Laboratory Chemistry and Chemical Engineering Division P.O. Box 808, L 474 Livermore, CA 94550 phone: (925) 422-3673 fax: (925) 424-6333 jyoung@llnl.gov From chemistry-request@server.ccl.net Fri Sep 8 14:39:05 2000 Received: from cariari.ucr.ac.cr (cariari.ucr.ac.cr [163.178.101.5]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id OAA12652 for ; Fri, 8 Sep 2000 14:39:00 -0400 Received: from [163.178.91.171] (eitikias.equi.ucr.ac.cr [163.178.91.171]) by cariari.ucr.ac.cr (8.9.3/8.9.3) with ESMTP id MAA20169 for ; Fri, 8 Sep 2000 12:20:23 -0600 Mime-Version: 1.0 Message-Id: Date: Fri, 8 Sep 2000 12:21:10 -0600 To: chemistry@ccl.net From: "Guy V. Lamoureux" Subject: Solvation of Anions Content-Type: text/plain; charset="us-ascii" ; format="flowed" Hello, We are looking for information about the solvation of anions in water and how the solvation shell changes with the size of the anion. Are there any recent references or reviews that discuss the difference in calculated solvation from F- to I-? Does the number of solvation molecules change or does the cage only expand as the ion size increases? Thank you for any replies and I will summarize the reponses to the list. Guy Lamoureux email: glamoure@cariari.ucr.ac.cr