From chemistry-request@server.ccl.net Wed Mar 8 18:11:21 2000 Received: from lrz.uni-muenchen.de (lsanca1-ar99-078-106.biz.dsl.gtei.net [4.3.78.106]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id SAA13593 for ; Wed, 8 Mar 2000 18:11:20 -0500 Received: (from eugene.leitl@localhost) by lrz.uni-muenchen.de (8.8.8/8.8.8) id PAA08761; Wed, 8 Mar 2000 15:09:25 -0800 From: Eugene Leitl MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Message-ID: <14534.56736.528206.501146@lrz.uni-muenchen.de> Date: Wed, 8 Mar 2000 15:09:20 -0800 (PST) To: "Jochen K?pper" Cc: PEROTT@if.ufrgs.br, chemistry@server.ccl.net Subject: CCL:Mass storage devices In-Reply-To: <14534.31327.676223.394080@yogi.pc1.uni-duesseldorf.de> References: <01JMRABWR2GI0012M7@if1.if.ufrgs.br> <14534.31327.676223.394080@yogi.pc1.uni-duesseldorf.de> X-Mailer: VM 6.71 under 21.1 (patch 4) "Arches" XEmacs Lucid Jochen K?pper writes: > Use RAID. That defers the first problem back to OS' or hardware > designers. Striping should give you best average performance. I would add to this very good advice the following: 1) use modern, large EIDE drives (currently, 40 GBytes for ~$250: http://www.pricewatch.com/1/26/2119-1.htm ). If money is not an issue at all, use 10 k rpm (UW..etc)SCSI drives: http://www.pricewatch.com/1/26/2150-1.htm If you have a money printing press, use hardware RAID with them: http://www.pricewatch.com/1/26/1537-1.htm http://www.linuxdoc.org/HOWTO/mini/DPT-Hardware-RAID.html 2) Use several of large, modern EIDE drives as soft or hard RAID. http://www.linuxdoc.org/HOWTO/Software-RAID-HOWTO.html if you use EIDE drives, put them on individual EIDE host adapter interface. These are ~$30 apiece, for instance: http://www.buy.com/comp/product.asp?sku=10023443 3) if you're using Linux, use lots of RAM. 512 MByte-1 GByte or more (make sure it is being recognized, you might have to supply options at boot, though probably not with newer kernels). Linux utilizes extra memory for file caching, which can speed up things dramatically. 4) use a recent (preferably, cutting, not bleeding edge) kernel, because sometimes improvements in caching algorithms/drivers translate in very noticeable improvement in overall performance. 5) if you have large files (>2 GByte) you'll need 64 bit clean file systems (patches for Linux vanilla ext2 are available). Also, look around on http://www.beowulf-underground.org/ , there are patches/software to be found there which also might improve performance even for nonparallel systems. Regards, Eugene Leitl > Many OS's allow software RAID without any additional hardware, but > then if you are willing to spend the cash, you could use hardware RAID > as well :-) > Fail-safety is something else to be considered, but probably not for > your "scratch"-files. From chemistry-request@server.ccl.net Thu Mar 9 05:11:44 2000 Received: from balder.nilu.no (balder.nilu.no [128.39.104.34]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id FAA16073 for ; Thu, 9 Mar 2000 05:11:44 -0500 Received: from afrodite.no. (afrodite.nilu.no) by balder.nilu.no (Sun Internet Mail Server sims.3.5.2000.01.05.12.18.p9) with ESMTP id <0FR5000CAGB2HR@balder.nilu.no> for chemistry@ccl.net; Thu, 9 Mar 2000 11:11:26 +0100 (MET) Received: from eshpc (eshpc.nilu.no. [128.39.66.15]) by afrodite.no. (8.9.1b+Sun/8.9.1) with SMTP id LAA17807 for ; Thu, 09 Mar 2000 11:13:04 +0100 (MET) Date: Thu, 09 Mar 2000 11:11:19 +0100 From: =?iso-8859-1?Q?Eldbj=F8rg_Sofie_Heimstad?= Subject: PDB files: Adding (polar) H and atomic charges - free software? To: CCL Reply-to: =?iso-8859-1?Q?Eldbj=F8rg_Sofie_Heimstad?= Message-id: <007301bf89af$d3472340$0f422780@nilu.no> MIME-version: 1.0 X-Mailer: Microsoft Outlook Express 5.00.2314.1300 Content-type: text/plain; charset=iso-8859-1 Content-transfer-encoding: 8BIT X-MSMail-Priority: Normal X-MimeOLE: Produced By Microsoft MimeOLE V5.00.2314.1300 X-Priority: 3 Dear CCLers, I apologise if this question has been asked before. Does there exist any simple free available (Unix or windows) software which is able to add hydrogens and/or atomic charges to PDB files? I have tried 'babel', but the program does not seem to manage to add the hydrogens correctly. I have used the following command and the program adds atoms without any ID to the output file. babel -v -ip 'input.pdb' -h -op 'output.pdb' Thanks in advance, ######################################### Eldbjørg S. Heimstad NILU Norwegian Institute for Air Research The Polar Environmental Centre N-9296 Tromsø, Norway Tel. +47-77 75 03 75 Fax. +47-77 75 03 76 E-mail: Eldbjorg.Sofie.Heimstad@nilu.no Web: http://www.nilu.no ######################################### From chemistry-request@server.ccl.net Thu Mar 9 06:48:34 2000 Received: from mailgw.barc.ernet.in ([202.54.18.131]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id GAA16953 for ; Thu, 9 Mar 2000 06:48:25 -0500 Received: from apsara.barc.ernet.in (apsara.barc.ernet.in [10.0.0.3]) by mailgw.barc.ernet.in (8.9.1/8.9.1) with ESMTP id SAA11423 for ; Thu, 9 Mar 2000 18:26:24 +0530 Received: from localhost (tapang@localhost) by apsara.barc.ernet.in (8.9.3/8.9.3) with SMTP id QAA25030 for ; Thu, 9 Mar 2000 16:53:51 +0530 Date: Thu, 9 Mar 2000 16:53:51 +0530 (IST) From: "Dr.Tapan K.Ghanty" Reply-To: "Dr.Tapan K.Ghanty" To: CHEMISTRY@CCL.net Subject: MOLPRO & MOLCAS Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi All, Can anybody tell me the approximate price of MOLPRO and MOLCAS softwares, and the address for correspondence for buying those softwares? I am also interested to know if there are other efficient packages (commercial or free) for doing configuration interaction and CASSCF calculations which can be used for close shell as well as open shell molecule excited state geometry optimization and other excited state property calculations. With thanks, Sincerely, Dr. Tapan K. Ghanty From chemistry-request@server.ccl.net Thu Mar 9 09:32:49 2000 Received: from sos1.chem.iupui.edu ([134.68.137.53]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id JAA18124 for ; Thu, 9 Mar 2000 09:32:49 -0500 Received: from localhost (dgao@localhost) by sos1.chem.iupui.edu (980427.SGI.8.8.8/980728.SGI.AUTOCF) via ESMTP id JAA79592 for ; Thu, 9 Mar 2000 09:33:06 -0500 (EST) Date: Thu, 9 Mar 2000 09:33:05 -0500 From: Daquan Gao To: chemistry@ccl.net Subject: empirical partial charges Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi all, I apologize if this is an FAQ. But I need opinions about empirical charge methods such as Gasteiger, QEq, and Del Re. Are there others? How do they perform? Thanks for any info. Regards. Daquan Gao From chemistry-request@server.ccl.net Thu Mar 9 08:50:49 2000 Received: from hydra.chem.rug.nl (hydra.chem.rug.nl [129.125.35.229]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id IAA17880 for ; Thu, 9 Mar 2000 08:50:49 -0500 Received: from [129.125.7.13] (theochem1.chem.rug.nl [129.125.7.13]) by hydra.chem.rug.nl (AIX4.2/UCB 8.7/8.7) with ESMTP id OAA21418 for ; Thu, 9 Mar 2000 14:50:38 +0100 (MET) Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" X-Sender: swart@hydra.chem.rug.nl Message-Id: In-Reply-To: Date: Thu, 9 Mar 2000 14:55:02 +0100 To: CHEMISTRY@ccl.net From: Marcel Swart Subject: Re: CCL:MOLPRO & MOLCAS Dear Dr. Ghanty, I only know the Web-address of the MOLCAS program: http://www.teokem.lu.se/molcas/ Regards, M. Swart. ------------------------------------------------ drs. Marcel Swart Theoretical Chemistry (MSC) Molecular Dynamics (GBB) Rijksuniversiteit Groningen Chemistry Department Nijenborgh 4 9747 AG Groningen The Netherlands tel : +31 - (0)50 - 3634377 fax : +31 - (0)50 - 3634441 E-mail : m.swart@chem.rug.nl WWW: http://theochem.chem.rug.nl/~marcel/ ------------------------------------------------ From chemistry-request@server.ccl.net Thu Mar 9 10:32:47 2000 Received: from envy.med.harvard.edu (envy.med.harvard.edu [134.174.146.162]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id KAA18596 for ; Thu, 9 Mar 2000 10:32:45 -0500 Received: from localhost (joseph@localhost) by envy.med.harvard.edu (980427.SGI.8.8.8/970903.SGI.AUTOCF) via SMTP id KAA74969 for ; Thu, 9 Mar 2000 10:30:33 -0500 (EST) Date: Thu, 9 Mar 2000 10:30:32 -0500 (EST) From: Diane Joseph-McCarthy To: chemistry@ccl.net Subject: DOCK4.0.1 on an alpha Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi. Has anyone compiled DOCK4.0.1 on a dec alpha running linux and with digital unix compilers. Thanks. Diane ------------------------------------------------------------------- Dr. Diane Joseph-McCarthy joseph@vp2.med.harvard.edu Biological Chemistry Department Genetics Institute phone: (617) 665-8933 87 CambridgePark Drive Cambridge, MA 02140 FAX: (617) 665-8993 ------------------------------------------------------------------- From chemistry-request@server.ccl.net Thu Mar 9 11:56:48 2000 Received: from unomail.unomaha.edu (unomail.unomaha.edu [137.48.1.6]) by server.ccl.net (8.8.7/8.8.7) with SMTP id LAA19064 for ; Thu, 9 Mar 2000 11:56:46 -0500 From: Douglas_Stack/CAS/UNO/UNEBR@unomail.unomaha.edu Received: by unomail.unomaha.edu(Lotus SMTP MTA v4.6.4 (830.2 3-23-1999)) id 8625689D.005C9880 ; Thu, 9 Mar 2000 10:51:23 -0600 X-Lotus-FromDomain: UNIVERSITY OF NEBRASKA To: "Dr.Tapan K.Ghanty" cc: CHEMISTRY@CCL.net Message-ID: <8625689D.005C9671.00@unomail.unomaha.edu> Date: Thu, 9 Mar 2000 10:51:17 -0600 Subject: Re: CCL:MOLPRO & MOLCAS Mime-Version: 1.0 Content-type: text/plain; charset=us-ascii Content-Disposition: inline Take a t look at : http://www.tc.bham.ac.uk/molpro How did I find this information? I simply type "MOLPRO" into the first internet search engine that appear on my Netscape browser. I sometimes wonder why, in this age of "the information superhighway" , so many simple queries like this are needed on the CCL. Douglas E. Stack Assistant Professor Department of Chemistry University of Nebraska at Omaha Omaha, NE 68182-0109 (402) 554-3647 (402) 554-3888 (fax) destack@unomaha.edu