From chemistry-request@server.ccl.net Fri Feb 15 23:58:32 2002 Received: from sd.accelrys.com ([146.202.0.254]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g1G4wVZ31365 for ; Fri, 15 Feb 2002 23:58:31 -0500 Received: (from dgregory@localhost) by sd.accelrys.com (8.11.0/8.11.0) id g1G64nH16881 for CHEMISTRY@ccl.net; Fri, 15 Feb 2002 22:04:49 -0800 Received: from loaner22.accelrys.com (dp-dhcp158.sd.accelrys.com [172.30.199.158] (may be forged)) by sd.accelrys.com (8.11.0/8.11.0) with ESMTP id g1G64m916872 for ; Fri, 15 Feb 2002 22:04:48 -0800 Message-Id: <5.1.0.14.2.20020215205436.01b211b0@sparky2.sd.accelrys.com> X-Sender: dgregory@sparky2.sd.accelrys.com X-Mailer: QUALCOMM Windows Eudora Version 5.1 Date: Fri, 15 Feb 2002 21:01:47 -0800 To: CHEMISTRY@ccl.net From: Don Gregory Subject: Re: CCL:SBOUND and MMFP In-Reply-To: <3C6D2D97.6BC72D4B@cornell.edu> Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii"; format=flowed Hi Richard, I'd suggest having a good look at the MMFP doc files. (Miscellaneous Mean Field Potential) I think Charlie Brooks has revamped the sbound potentials, and included them in the MMFP toolset. These include not only spherical potentials, but cylindrical as well as planar. Hope this helps! Don Gregory At 2/15/2002 -0500, you wrote: >Hi all > >A colleague of mine has a slight problem that I have been brought in to >help with and I am stumped. > >Apparently, there was a subroutine developed in CHARMm called SBOUND >which is supposed to allow the user to specify the use of a spherical, >cubic, or >plane potential. > >Well, we have learned (we think) that SBOUND contains an "undefined" >variable >called IBOUND, which is what allows the choice of spherical (IBOUND=1), >cubic >(IBOUND=2) or planar (IBOUND=3) potentials. Thus, since IBOUND is not >defined >anywhere in the program (at least as far as SBOUND is concerned; there >is an IBOUND >used in an unrelated subroutine as an array) we cannot use "SBOUND", >so we have to input the potential in another way. > >The question I have is this. We have a "file" that defines a spherical >potential. >Does anyone out there know how we can generate a file having a planar >potential, >or does someone have a palnar potential file in the "correct" format >that we could use? > >I would think that since there are many users of CHARMm out there that >someone >has encountered this problem before so that we don't have to reinvent >the wheel. >(BTW, I have seen Brooks' and Karplus's paper in J. Chem. Phys, vol. 79, >pp 6312 - >6325.) > >Thanks in advance, >Richard > >-- >Richard L. Wood, Ph. D. >Physical/Computational Chemist >Post-doctoral Associate >Department of Food Science >120 Stocking Hall >Cornell University, Ithaca, NY 14853 > > > > > >-= 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 Dr. Don Gregory (dgregory@accelrys.com) Manager, Macromolecular Application Science; US & Asia/Pacific Accelrys (http://www.accelrys.com) 9685 Scranton Rd. San Diego, CA 92121 Office Phone: (858) 799-5331 Office Fax : (858) 799-5100 Mobile Phone: (619) 200-3613 From chemistry-request@server.ccl.net Fri Feb 15 21:25:39 2002 Received: from schrodinger.com ([192.156.98.99]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g1G2PdZ29190 for ; Fri, 15 Feb 2002 21:25:39 -0500 Received: from schrodinger.com (amaris.schrodinger.com [192.156.98.121]) by schrodinger.com (8.8.5/8.8.5) with ESMTP id SAA07643; Fri, 15 Feb 2002 18:25:11 -0800 Message-ID: <3C6DC4AA.63272296@schrodinger.com> Date: Fri, 15 Feb 2002 18:32:10 -0800 From: George Vacek Reply-To: info@schrodinger.com Organization: Schrodinger, Inc. X-Mailer: Mozilla 4.75 [en] (Windows NT 5.0; U) X-Accept-Language: en MIME-Version: 1.0 To: Christian.Pilger@bc.boehringer-ingelheim.com, chemistry@ccl.net Subject: Re: CCL:aqueous solubilities of organic compounds References: <5.1.0.14.0.20020215120213.02a7aaf0@pop3.norton.antivirus> Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit QikProp predicts a variety of pharmaceutical properties, including solubility, that are important in determining ADME characteristics for drug candidates. The complete set of properties predicted by QikProp, methods, data and literature references are available at http://www.schrodinger.com For the specific case of solubility, the data set and descriptors are detailed in the article W. L. Jorgensen and E. M. Duffy, Bioorg. Med. Chem. Lett., 10 (2000) 1155-8. > At 02:25 PM 2/15/2002 +0100, Christian.Pilger@bc.boehringer-ingelheim.com > wrote: > > currently I'm looking for methods and datasets for the prediction of > >aqueous solubilities of organic (preferrably drug like) compounds. > >Thus I would like to ask for your advice: are you > >aware of methods to predict solubility ? Did you ever come across > >databases with experimentally determined solubilities, which might be > >accessible ? Regards, George Vacek =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=- vacek@schrodinger.com (503) 299-1150 http://www.schrodinger.com/ Schrodinger, Inc., 1500 SW First Ave., Suite 1180, Portland, OR 97201 Every culture that has lost myth has lost, by the same token, its natural, healthy creativity. -- Friedrich Nietzsche "The Birth of Tragedy" 1872 =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=- From chemistry-request@server.ccl.net Sat Feb 16 09:24:40 2002 Received: from serenity.mcc.ac.uk ([130.88.200.93]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g1GEOeZ10223 for ; Sat, 16 Feb 2002 09:24:40 -0500 Received: from pm2-60.mcc.ac.uk ([194.66.22.120] helo=pirx) by serenity.mcc.ac.uk with smtp (Exim 2.05 #6) id 16c5lF-000Bv4-00 for chemistry@ccl.net; Sat, 16 Feb 2002 14:24:21 +0000 Message-ID: <000801c1b6f5$64d1d340$781642c2@ch.man.ac.uk> From: "Matthias Mohr" To: Subject: Autodock - near misses Date: Sat, 16 Feb 2002 01:48:16 -0000 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 6.00.2600.0000 X-MimeOLE: Produced By Microsoft MimeOLE V6.00.2600.0000 Dear CCLers, currently i am trying to improve the autodock scoring function. I would be interested in any unpublished "near misses", that is, the proper binding mode is found by autodock, but not ranked in the lowest cluster. Regards, Matthias --- Dr. Matthias Mohr University of Manchester Department of Chemistry Brunswick Street M13 9PL Manchester Tel: +44 (0)161 275 4683 Fax: +44 (0)161 275 4598 email:Matthias.Mohr@man.ac.uk