From chp1aa@surrey.ac.uk Wed Aug 25 07:13:27 1993 Received: from sun2.nsfnet-relay.ac.uk for chp1aa@surrey.ac.uk by oscsunb.ccl.net (5.65c+KVa/930601.1506) id AA26421; Wed, 25 Aug 1993 06:18:36 -0400 Via: uk.ac.surrey; Wed, 25 Aug 1993 11:17:39 +0100 Via: central.surrey.ac.uk; Wed, 25 Aug 93 11:17:34 BST Received: by central.surrey.ac.uk (16.6/16.2) id AA20420; Wed, 25 Aug 93 11:17:33 +0100 From: Mr Andrew D Allen Message-Id: <9308251017.AA20420@central.surrey.ac.uk> Subject: AMSOL To: chemistry@ccl.net Date: Wed, 25 Aug 93 11:17:33 BST Mailer: Elm [revision: 66.25] > Dear netters: > > Does anyone have information on how to get AM1-SM1 program running on SGI > machine and how much it will cost? > > Thank you in advance! > > Shaomeng Wang > LMC,NCI,NIH > Bethesda, MD20892 AMSOL (QCPE #606) does AM1-SM1, AM2-SM2, PM3-SM3 as well as the AM1a etc... Price QCPE for a quote, though ours was approximately $300 or 175 pounds. Fairly cheap anyway. Cramer - Truhlar has released Vers 3.5, and there was some talk of QCPE setting up an ftp server for downloading software, so the price may be different now. Andy. From skeinath@ncsa.uiuc.edu Wed Aug 25 03:27:03 1993 Received: from newton.ncsa.uiuc.edu for skeinath@ncsa.uiuc.edu by oscsunb.ccl.net (5.65c+KVa/930601.1506) id AA28606; Wed, 25 Aug 1993 09:27:06 -0400 Received: from saturn.ncsa.uiuc.edu by newton.ncsa.uiuc.edu with SMTP id AA28540 (5.65a/IDA-1.4.2 for CHEMISTRY@ccl.net); Wed, 25 Aug 93 08:27:04 -0500 Return-Path: Received: by saturn.ncsa.uiuc.edu (4.1/NCSA-4.1) id AA29716; Wed, 25 Aug 93 08:27:03 CDT Date: Wed, 25 Aug 93 08:27:03 CDT From: skeinath@ncsa.uiuc.edu (Steven E. Keinath) Message-Id: <9308251327.AA29716@saturn.ncsa.uiuc.edu> To: CHEMISTRY@ccl.net Subject: Protein database Cc: skeinath@ncsa.uiuc.edu CCL Netters -- We have heard that there is a database in existence that contains the molecular structures, i.e., atomic coordinates, of the native structures of practically all of the proteins for which structures have been determined. Specifically, we are interested in the native structures, i.e., the 3D placement of all of the amino acid residues, and not just the sequence of amino acids. Can anyone identify this database resource for us? Thanks in advance. -- Steve Keinath and Marc Mansfield Michigan Molecular Institute Midland, Michigan 48640 U.S.A. From d3f012@pellucidar.pnl.gov Wed Aug 25 01:06:35 1993 Received: from pnlg.pnl.gov for d3f012@pellucidar.pnl.gov by oscsunb.ccl.net (5.65c+KVa/930601.1506) id AA29992; Wed, 25 Aug 1993 11:08:40 -0400 Received: from pellucidar.pnl.gov (130.20.182.74) by pnlg.pnl.gov; Wed, 25 Aug 93 08:09 PDT Received: by pellucidar.pnl.gov (920330.SGI/920502.SGI) for @pnlg.pnl.gov:chemistry@ccl.net id AA06373; Wed, 25 Aug 93 08:06:35 -0700 Date: Wed, 25 Aug 93 08:06:35 -0700 From: d3f012@pellucidar.pnl.gov Subject: Biosym Water To: dibug@comp.bioz.unibas.ch, chemistry@ccl.net Message-Id: <9308251506.AA06373@pellucidar.pnl.gov> X-Envelope-To: chemistry@ccl.net JORGE M. SEMINARIO writes: Dear Friends, Regarding the following post by Mark Thompson: >Just as a reminder, Biosym uses: > >1) flexible water. >2) SPC LJ parameters for Oxygen. >3) TIP3P internal geometry. >4) LJ "A" param for hydrogen of 10^-8 (kcal Ang^12)/mol. I recall that sometime ago I took a look to the force field available in DISCOVER and found out, just by looking at the manuals, that the force field for water contains also nondiagonal terms like: ... + SUM SUM F[b,theta]*(b-bo)(theta-thetao) b theta + SUM SUM F[b,b']*(b-bo)*(b'-bo') + ... b b' I even found the parameters on a Table explicitely stated for for water to be F[b,b']= -14.5 F[b,theta]= 31.3 Are those terms considered in your calculation? Can someone comment on those nondiagonal terms. ************* I did not use cross-terms in my water simulations. I doubt they would have a significant effect on the rdf's. I was not aware that cross terms would be used in Biosym water...does the "full" Biosym water model include cross terms? Mark Thompson ************************************************************************** Mark A. Thompson Sr. Research Scientist email: d3f012@pnlg.pnl.gov Molecular Science Research Center FAX : 509-375-6631 Pacific Northwest Laboratory voice: 509-375-6734 PO Box 999, Mail Stop K1-90 Richland, WA. 99352 Disclaimer: The views expressed in this message are solely my own and do not represent Battelle Memorial Institute, Pacific Northwest Laboratory, or any of its clients. ************************************************************************** From zellmer@sodium.mps.ohio-state.edu Wed Aug 25 07:15:47 1993 Received: from sodium.mps.ohio-state.edu for zellmer@sodium.mps.ohio-state.edu by oscsunb.ccl.net (5.65c+KVa/930601.1506) id AA00218; Wed, 25 Aug 1993 11:15:50 -0400 Received: from phosphorus.mps.ohio-state.edu.theorychem by sodium.mps.ohio-state.edu (4.1/1.890401) id AA20553; Wed, 25 Aug 93 11:15:47 EDT Date: Wed, 25 Aug 93 11:15:47 EDT From: Bob Zellmer Message-Id: <9308251515.AA20553@sodium.mps.ohio-state.edu> To: CHEMISTRY@ccl.net Subject: Re: Seeking words of wisdom <199308172144.AA08056@oscsunb.ccl.net> It appears that the C90fr (% of C90) is based on the test jobs running on a single processor on the C90. Wouldn't the timings for the multiprocessor SGI jobs be more "consistent" if they were compared to C90 times based on the same number of processors (where possible). Robert Zellmer Ohio State Un. zellmer@sodium.mps.ohio-state.edu From abby@mercury.aichem.arizona.edu Wed Aug 25 04:36:46 1993 Received: from mercury.aichem.Arizona.EDU for abby@mercury.aichem.arizona.edu by oscsunb.ccl.net (5.65c+KVa/930601.1506) id AA03194; Wed, 25 Aug 1993 14:49:55 -0400 Received: by mercury.aichem.arizona.edu (5.57/Ultrix3.0-C) id AA15421; Wed, 25 Aug 93 11:44:00 -0700 Date: Wed, 25 Aug 1993 11:36:46 -0700 (MST) From: Abby Parrill Subject: Re: Protein database To: "Steven E. Keinath" Cc: CHEMISTRY@ccl.net, skeinath@ncsa.uiuc.edu In-Reply-To: <9308251327.AA29716@saturn.ncsa.uiuc.edu> Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII On Wed, 25 Aug 1993, Steven E. Keinath wrote: > > CCL Netters -- > > Specifically, we are interested in the native structures, > i.e., the 3D placement of all of the amino acid residues. What you are interested is the Protein Data Bank (PDB) which can be accessed by anonymous ftp (pdb.pdb.bnl.gov). The PDB can be contacted by the following: Protein Data Bank Chemistry Department, Building 555 Brookhaven National Laboratory Upton, NY 11973 U.S.A. 516-282-3629 FAX: 516-282-5751 e-mail:pdb@bnlchm.bitnet pdb@chm.chm.bnl.gov > > -- Steve Keinath and Marc Mansfield > Michigan Molecular Institute > Midland, Michigan 48640 U.S.A. From bak@isadora.albany.edu Wed Aug 25 14:53:59 1993 Received: from uacsc2.albany.edu for bak@isadora.albany.edu by oscsunb.ccl.net (5.65c+KVa/930601.1506) id AA06300; Wed, 25 Aug 1993 18:54:03 -0400 Received: from isadora.albany.edu by UACSC2.ALBANY.EDU (IBM VM SMTP V2R2) with TCP; Wed, 25 Aug 93 18:52:49 EDT Received: by isadora.albany.edu (920330.SGI/920502.SGI) for @uacsc2.albany.edu:chemistry@ccl.net id AA25944; Wed, 25 Aug 93 18:53:59 -0400 From: bak@isadora.albany.edu (Brian A. Kell) Message-Id: <9308252253.AA25944@isadora.albany.edu> Subject: Re: Protein database To: skeinath@ncsa.uiuc.edu (Steven E. Keinath) Date: Wed, 25 Aug 93 18:53:59 EDT Cc: chemistry@ccl.net In-Reply-To: <9308251327.AA29716@saturn.ncsa.uiuc.edu>; from "Steven E. Keinath" at Aug 25, 93 8:27 am X-Mailer: ELM [version 2.3 PL11] Steven E. Keinath writes: > > We have heard that there is a database in existence that contains the > molecular structures, i.e., atomic coordinates, of the native structures > of practically all of the proteins for which structures have been > determined. Specifically, we are interested in the native structures, > i.e., the 3D placement of all of the amino acid residues, and not just > the sequence of amino acids. Can anyone identify this database resource > for us? Thanks in advance. > You are referring to The Protein Data Bank ("PDB"), which is administered by the Brookhaven National Laboratory. Three-D protein structures can be obtained in a number of ways, including tape, CD-ROM, e-mail file server, and anonymous FTP. The following information was taken directly from the April 1993 version of the PDB Newsletter: > ----------------------------------------------------------------------- > To Contact the PDB: > > Protein Data Bank > Chemistry Department, Building 555 > Brookhaven National Laboratory > Upton, NY 11973 USA > > Telephone: +1 516-282-3629 > Facsimile: +1 516-282-5751 > e-mail:pdb@bnl.bitnet > or pdb@bnl.gov > > Please include your telephone number, facsimile number, mailing > address, and e-mail address in all correspondence. > ----------------------------------------------------------------------- You can also reach their file server via anonymous ftp at pdb.pdb.bnl.gov [130.199.144.1]. (Disclaimer: I'm not affiliated with the PDB nor BNL.) ------------------------------------------------------------------ Brian A. Kell Applications Support Specialist bak@biosym.com Biosym Technologies, Inc. ------------------------------------------------------------------