From chemistry-request@server.ccl.net Fri Jun 7 09:02:37 2002 Received: from ned1.sims.nrc.ca ([132.246.108.2]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g57D2bL31455 for ; Fri, 7 Jun 2002 09:02:37 -0400 Received: from localhost (ps@localhost) by ned1.sims.nrc.ca (8.8.8/8.8.8) with ESMTP id JAA09326; Fri, 7 Jun 2002 09:02:33 -0400 (EDT) Date: Fri, 7 Jun 2002 09:02:33 -0400 From: Serguei Patchkovskii Reply-To: Serguei.Patchkovskii@nrc.ca To: Malcolm Gillies cc: chemistry@ccl.net, "Peterson,Brian K." Subject: Re: CCL:EIDE vs SCSI & backup in Linux clusters In-Reply-To: <20020606102115.K301@tr4.ok.dtu.dk> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII On Thu, 6 Jun 2002, Malcolm Gillies wrote: > The remaining advantage of SCSI for me is the ability to swap drives > easily, and to connect drives in an external enclosure. As far as I > know, hot-swapping of IDE drives is currently impossible. A number of vendors (e.g. http://www.promise.com/) will gladly sell you hot-swap enclosures for IDE/ATA drives, often used with RAID controllers. They are not particularly uncommon, or expensive. Serguei From chemistry-request@server.ccl.net Fri Jun 7 04:41:27 2002 Received: from mhub2.bbsrc.ac.uk ([149.155.202.2]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g578fQL27162 for ; Fri, 7 Jun 2002 04:41:26 -0400 Received: from exrout.cc.bbsrc.ac.uk ([149.155.100.88]) by mhub2.bbsrc.ac.uk with esmtp (Exim 3.31 #1) id 17GFDb-0002vD-04; Fri, 07 Jun 2002 09:35:35 +0100 Received: from bits-exch1.bits.bbsrc.ac.uk ([149.155.108.13]) by exrout.cc.bbsrc.ac.uk with SMTP (Microsoft Exchange Internet Mail Service Version 5.5.2653.13) id ML4P04HD; Fri, 7 Jun 2002 09:36:04 +0100 Received: by bits-exch1.bits.bbsrc.ac.uk with Internet Mail Service (5.5.2653.19) id ; Fri, 7 Jun 2002 09:36:03 +0100 Message-ID: <41773CEF2B8FD411920200508BDCDC12BE1427@bits-exch1.bits.bbsrc.ac.uk> From: "michael hanlon (BITS)" To: "'Parthiban Srinivasan'" , chemistry@ccl.net Subject: RE: Freeware for drug design Date: Fri, 7 Jun 2002 09:36:02 +0100 MIME-Version: 1.0 X-Mailer: Internet Mail Service (5.5.2653.19) Content-Type: multipart/alternative; boundary="----_=_NextPart_001_01C20DFE.5B751810" X-ECS-MailScanner-BBSRC: Found to be clean This message is in MIME format. Since your mail reader does not understand this format, some or all of this message may not be legible. ------_=_NextPart_001_01C20DFE.5B751810 Content-Type: text/plain; charset="iso-8859-1" MODELLER is popular for protein modelling, including within the drug discovery sector. It's free to academics: http://tatiana.rockefeller.edu/modeller/ Autodock is pretty widely used for molecular docking, and comes up on this list a fair bit: http://www.scripps.edu/pub/olson-web/doc/autodock/ Mike -----Original Message----- From: Parthiban Srinivasan [mailto:parthi.s@jubilantbiosys.com] Sent: 06 June 2002 07:54 To: chemistry@ccl.net Subject: CCL:Freeware for drug design Dear Friends: I am looking for downloadable programs (trivial to sophisticated) applicable in various stages of drug discovery pipeline. Kindly send me the URL and/or any other helpful info. As an useful prcatice, I will summarise the replies. Thanks and Regards S Parthiban Jubilant Biosys ------_=_NextPart_001_01C20DFE.5B751810 Content-Type: text/html; charset="iso-8859-1"
MODELLER is popular for protein modelling, including within the drug discovery sector. It's free to academics:
 
 
Autodock is pretty widely used for molecular docking, and comes up on this list a fair bit:
 
 
Mike
-----Original Message-----
From: Parthiban Srinivasan [mailto:parthi.s@jubilantbiosys.com]
Sent: 06 June 2002 07:54
To: chemistry@ccl.net
Subject: CCL:Freeware for drug design

Dear Friends:
I am looking for downloadable programs (trivial to sophisticated) applicable in
various stages of drug discovery pipeline. Kindly send me the URL and/or
any other helpful info. As an useful prcatice, I will summarise the replies.
Thanks and Regards
S Parthiban
Jubilant Biosys
 
------_=_NextPart_001_01C20DFE.5B751810-- From chemistry-request@server.ccl.net Fri Jun 7 13:00:22 2002 Received: from denali.biochem.missouri.edu ([128.206.91.240]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g57H0ML03134 for ; Fri, 7 Jun 2002 13:00:22 -0400 Received: from localhost (berjanskii@localhost) by denali.biochem.missouri.edu (SGI-SGI-8.9.3/8.9.3) with SMTP id LAA52688 for ; Fri, 7 Jun 2002 11:40:03 -0500 (CDT) Date: Fri, 7 Jun 2002 11:40:02 -0500 (CDT) From: Mark Berjanskii To: chemistry@ccl.net Subject: TEMP from CORREL in CHARMM Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear CHARMM users, Could you please help me to find answers for some of the following questions related to the TEMP routine in CORREL module of CHARMM? 1) Should I use coordinate trajectories (IUNCRD files from Dynamics routine) or velocity files (IUNVEL files from Dynamics routine) to determine temperature with CORREL? 2) If I should use velocity files, does the temperature determined by CORREL with coordinate trajectories have any meaning? 3) If I should use velocity files, is there a procedure in CHARMM to convert coordinate trajectories into velocity files? 4) Are there other ways to determine temperature / kinetic energy of a part of your system (not the whole system) from an already collected coordinate trajectory? Thank you, Mark Berjanskii Department of Biochemistry University of Missouri-Columbia 117 Schweitzer Hall Columbia, MO 65211 email: mberjans@coin.org From chemistry-request@server.ccl.net Fri Jun 7 16:20:49 2002 Received: from research.dfci.harvard.edu ([155.52.50.28]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g57KKmL05490 for ; Fri, 7 Jun 2002 16:20:49 -0400 Received: from [155.52.22.78] (account reche HELO research.dfci.harvard.edu) by research.dfci.harvard.edu (CommuniGate Pro SMTP 3.5.9) with ESMTP-TLS id 684108 for chemistry@ccl.net; Fri, 07 Jun 2002 16:22:42 -0400 Sender: par@ccl.net Message-ID: <3D011467.FF7753ED@research.dfci.harvard.edu> Date: Fri, 07 Jun 2002 16:15:35 -0400 From: Pedro A Reche Reply-To: reche@research.dfci.harvard.edu Organization: Dana-Farber Cancer Institute X-Mailer: Mozilla 4.7C-SGI [en] (X11; I; IRIX64 6.5 IP28) X-Accept-Language: en MIME-Version: 1.0 To: chemistry@ccl.net Subject: solvent accessibility Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Hi all, does anyone know of a good unix program to calculate the percentage of the area that is accessible/buried for every residue/side chain in a pdb file? Cheers ******************************************************************* PEDRO A. RECHE , pHD TL: 617 632 3824 Dana-Farber Cancer Institute, FX: 617 632 4569 Harvard Medical School, EM: reche@research.dfci.harvard.edu 44 Binney Street, D1510A, EM: reche@mifoundation.org Boston, MA 02115 URL: http://www.reche.org ******************************************************************* From chemistry-request@server.ccl.net Fri Jun 7 10:17:26 2002 Received: from f04n07.cac.psu.edu ([128.118.141.35]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g57EHQL00665 for ; Fri, 7 Jun 2002 10:17:26 -0400 Received: from ra.chem.psu.edu (ra.chem.psu.edu [128.118.199.40]) by f04n07.cac.psu.edu (8.9.3/8.9.3) with ESMTP id KAA80280 for ; Fri, 7 Jun 2002 10:17:22 -0400 Content-Type: text/plain; charset="us-ascii" From: Rajarshi Guha Reply-To: rajarshi@presidency.com To: chemistry@ccl.net Subject: a question regarding Mopac & polarizabilities Date: Fri, 7 Jun 2002 10:15:53 -0400 X-Mailer: KMail [version 1.4] MIME-Version: 1.0 Content-Transfer-Encoding: 8bit Message-Id: <200206071015.53785.rajarshi@presidency.com> -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 Hi, I'm using Mopac 7.01 and am trying to calculate polarizabilities. I am a little confused by the instructions in the manual - does the end of the deck mean the end of the mopac input file or the line after the keyword line. Further more I only need the linear polarizability (alpha) - and I am unsure of what values I need to fill up for Nfreq etc. I would be very grateful if somebody could provide an example of the setup for a polarizability calculation TIA, - -- - ------------------------------------------------------------------- Rajarshi Guha | email: rajarshi@presidency.com 417 Davey Laboratory | web : http:// www.jijo.cjb.net Dept. Of Chemistry | ICQ : 123242928 Pennsylvania State University | AIM : LoverOfPanda - ------------------------------------------------------------------- GPG Fingerprint: DCCB 4D1A 5A8B 2F5A B5F6 1F9E CDC4 5574 9017 AF2A Public Key : http://pgp.mit.edu/ - ------------------------------------------------------------------- After a number of decimal places, nobody gives a damn. -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.0.6 (GNU/Linux) Comment: For info see http://www.gnupg.org iD8DBQE9AMAZzcRVdJAXryoRAo4oAKC6r3ZTtHwtlt1+HMx7FrUcGGsRQwCgzg02 fsBIvjE33NhgadIn1g5sfzk= =Oy00 -----END PGP SIGNATURE----- From chemistry-request@server.ccl.net Fri Jun 7 20:56:08 2002 Received: from ns1.scripps.edu ([192.42.82.59]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g580u7L20515 for ; Fri, 7 Jun 2002 20:56:07 -0400 Received: from antigen.scripps.edu (antigen.scripps.edu [137.131.200.100]) by ns1.scripps.edu (8.11.6/TSRI-4.2rx) with SMTP id g580u6V06680 for ; Fri, 7 Jun 2002 17:56:06 -0700 (PDT) Received: from relay2.scripps.edu(137.131.200.30) by antigen.scripps.edu via csmap id 25747; Fri, 07 Jun 2002 17:52:00 -0700 (PDT) Received: from goliath.scripps.edu (goliath.scripps.edu [137.131.108.88]) by relay2.scripps.edu (8.11.6/TSRI-4.2.1rAV) with ESMTP id g580ttc04836; Fri, 7 Jun 2002 17:55:55 -0700 (PDT) Received: from aaron (aaron [137.131.108.91]) by goliath.scripps.edu (SGI-8.9.3/TSRI-3.0.1) with SMTP id RAA66216; Fri, 7 Jun 2002 17:55:54 -0700 (PDT) Message-Id: <200206080055.RAA66216@goliath.scripps.edu> Date: Fri, 7 Jun 2002 17:55:54 -0700 (PDT) From: Michel Sanner Reply-To: Michel Sanner Subject: CCL:solvent accessibility To: reche@research.dfci.harvard.edu, garrett@scripps.edu Cc: chemistry@ccl.net MIME-Version: 1.0 Content-Type: TEXT/plain; charset=us-ascii Content-MD5: /TE4WzxCx2w6JE8nMSW5mw== X-Mailer: dtmail 1.3.0 @(#)CDE Version 1.4.2 SunOS 5.8 sun4u sparc > Hi all, > does anyone know of a good unix program to calculate the percentage of > the area that is accessible/buried for every residue/side chain in a pdb > file? are you interested in the percentage of the area buried by atoms in the same molecule on the total surface of the residue ? or by the percentage of the accessible area buried by another molecule ? ----------------------------------------------------------------------- Michel F. Sanner Ph.D. The Scripps Research Institute Assistant Professor Department of Molecular Biology 10550 North Torrey Pines Road Tel. (858) 784-2341 La Jolla, CA 92037 Fax. (858) 784-2860 sanner@scripps.edu http://www.scripps.edu/sanner -----------------------------------------------------------------------