From chemistry-request@server.ccl.net Thu Dec 10 05:01:05 1998 Received: from www.ccl.net (www.ccl.net [192.148.249.5]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id FAA06048 for ; Thu, 10 Dec 1998 05:01:05 -0500 Received: from sg1503.chemie.uni-marburg.de (root@sg1503.Chemie.Uni-Marburg.DE [137.248.151.215]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id EAA10958 Thu, 10 Dec 1998 04:55:17 -0500 (EST) Received: from pc15105 (pc15105.Chemie.Uni-Marburg.DE [137.248.151.180]) by sg1503.chemie.uni-marburg.de (8.9.1a/8.9.0/schn) with SMTP id KAA27798 for ; Thu, 10 Dec 1998 10:55:11 +0100 (MET) From: "Stefan Fau" To: "CCL" Subject: addendum: RE: Energy value for a specific initial orbital set Date: Thu, 10 Dec 1998 10:56:07 +0100 Message-ID: <000801be2423$4ef3d310$b497f889@pc15105.chemie.uni-marburg.de> MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" X-Priority: 3 (Normal) X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook 8.5, Build 4.71.2173.0 In-Reply-To: <000201be229a$9904a900$b497f889@pc15105.chemie.uni-marburg.de> X-MimeOLE: Produced By Microsoft MimeOLE V4.72.3110.3 Importance: Normal Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id FAA06049 Dear CClers, I think I should improve the strongly misleading expression of some days ago: Obviously the line E=... does not contain the SCF energy but the electronic energy, which must be added to the "nuclear repulsion energy" of link 301 (.5291772490 Hartrees) to yield the SCF energy given with the label "after 2 cycles". > Cycle 1 Pass 1 IDiag 1: > E= -.159893374700988D+01 > DIIS: error= 6.15D-02 at cycle 1. > T= 669. NK=0 NO(<0.9)= 0 NV(>0.1)= 0 1.00e < EF .00e > >EF Err=0.0D+00 > RMSDP=1.26D-02 MaxDP=5.12D-02 > > >>>>>>>>>> Convergence criterion not met. > SCF Done: E(RHF) = -1.06975649801 A.U. after 2 cycles > Convg = .1261D-01 -V/T = 2.1068 > S**2 = .0000 > KE= 9.665348275766D-01 PE=-3.192567796550D+00 EE= 6.270992219632D-01 > Convergence failure -- run terminated. Apologies, Stefan ___________________________________ Dr. Stefan Fau Fachbereich Chemie, AK Frenking Philipps-Universität Marburg 35032 Marburg, Germany fau@chemie.uni-marburg.de > -----Original Message----- > From: chemistry-request@www.ccl.net > [mailto:chemistry-request@www.ccl.net]On Behalf Of Stefan Fau > Sent: Tuesday, December 08, 1998 12:05 PM > To: Marta Forés i Bocsh > Cc: CCL > Subject: CCL:Re: Energy value for a specific initial orbital set > > > > > Dear Marta, > > you can get the SCF-energy of your guess from any SCF-method > using the #p command line option. In the case of direct SCF (with > maxcyc=1 for the sake of speed), you get some lines like the following; > > Cycle 1 Pass 1 IDiag 1: > E= -.159893374700988D+01 > DIIS: error= 6.15D-02 at cycle 1. > T= 669. NK=0 NO(<0.9)= 0 NV(>0.1)= 0 1.00e < EF .00e > >EF Err=0.0D+00 > RMSDP=1.26D-02 MaxDP=5.12D-02 > > >>>>>>>>>> Convergence criterion not met. > SCF Done: E(RHF) = -1.06975649801 A.U. after 2 cycles > Convg = .1261D-01 -V/T = 2.1068 > S**2 = .0000 > KE= 9.665348275766D-01 PE=-3.192567796550D+00 EE= 6.270992219632D-01 > Convergence failure -- run terminated. > > The line E=... gives you the SCF-energy. It is the same value > with all SCF-methods and sometimes labeled EE=... > > Stefan > ___________________________________ > Dr. Stefan Fau > Fachbereich Chemie, AK Frenking > Philipps-Universität Marburg > 35032 Marburg, Germany > fau@chemie.uni-marburg.de > > > > --- > Administrivia: This message is automatically appended by the mail > exploder: > CHEMISTRY@www.ccl.net: Everybody | CHEMISTRY-REQUEST@www.ccl.net: > Coordinator > MAILSERV@www.ccl.net: HELP CHEMISTRY or HELP SEARCH | Gopher: > www.ccl.net 73 > Anon. ftp: www.ccl.net | CHEMISTRY-SEARCH@www.ccl.net -- archive search > Web: http://www.ccl.net/chemistry.html > --- > From chemistry-request@server.ccl.net Thu Dec 10 16:24:26 1998 Received: from www.ccl.net (www.ccl.net [192.148.249.5]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id QAA06947 for ; Thu, 10 Dec 1998 16:24:26 -0500 Received: from bohr.quimica.ufpr.br (bohr.quimica.ufpr.br [200.17.215.142]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id QAA17211 Thu, 10 Dec 1998 16:18:37 -0500 (EST) Received: from localhost by bohr.quimica.ufpr.br with smtp id m0zoDTH-000P3HC (Debian Smail-3.2.0.101 1997-Dec-17 #2); Thu, 10 Dec 1998 19:18:03 -0200 (EDT) Date: Thu, 10 Dec 1998 19:18:01 -0200 (EDT) From: Eduardo Lemos de Sa To: chemistry@www.ccl.net Subject: fortran sources to ampac2.1 version Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=ISO-8859-1 Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from QUOTED-PRINTABLE to 8bit by server.ccl.net id QAA06948 Dear netters Does somebody, please, know where I can find a ampac2.1 (or higher) sources to compiling at UNIX (FreeBSD or Linux) enviroment? I've tried to use these from ccl.osc, but I can't to solve the problem from SIZES/NOLIST file (isn't have any file with this name in the package) thanks a lot Eduardo edulsa@quimica.ufpr.br Univ. Feder. Paraná - Curitiba - Brazil From chemistry-request@server.ccl.net Thu Dec 10 21:08:27 1998 Received: from www.ccl.net (www.ccl.net [192.148.249.5]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id VAA07230 for ; Thu, 10 Dec 1998 21:08:26 -0500 Received: from csb0.IPC.PKU.EDU.CN (csb0.ipc.pku.edu.cn [162.105.177.12]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with SMTP id VAA00295 Thu, 10 Dec 1998 21:02:32 -0500 (EST) Received: by csb0.IPC.PKU.EDU.CN (920330.SGI/940406.SGI.AUTO) for chemistry@www.ccl.net id AA13666; Fri, 11 Dec 98 10:00:40 -0800 Date: Fri, 11 Dec 1998 10:00:39 -0800 (PST) From: Arthur Wang To: CCL Subject: Free program release: predict the binding affinity Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII --------------------------------------------------------------- SCORE: Predict the Binding Affinity of a Protein-Ligand Complex --------------------------------------------------------------- SCORE is an empirical method developed for estimating the binding affinity of a protein-ligand complex with known three-dimensional structure. It uses a linear scoring function to describe the binding free energy, which includes terms to account for van der Waals contact, metal-ligand bonding, hydrogen bonding, hydrophobic effect, and deformational change upon the binding process. The coefficients of each term are obtained by multivariate regressional analysis of 170 protein-ligand complexes. The scoring function reproduces the binding free energies of the whole training set with a cross-validated deviation of only 6.3 kJ/mol. Although SCORE follows the pioneering idea of H.J.Bohm, it gives considerably better result. It may be applied to screening the hits given by database searching or ranking the results of de novo design programs. An innovation of this method is the introduction of atomic binding score, which allows the researcher to inspect and optimize the lead compound rationally in a structure-based drug design procedure. For more details, you can come to: Renxiao Wang, Liang Liu, Luhua Lai, and Youqi Tang "SCORE: A New Empirical Method for Estimating the Binding Affinity of a Protein-Ligand Complex", Journal of Molecular Modeling, 1998, 4, 379-394. The program, SCORE, is now released to the public. You can get it via WWW or anonymous FTP to ftp.ipc.pku.edu.cn (162.105.177.12) /pub/software/score/. The electronic reprint of the paper is available by contacting the following address. Best wishes, Arthur _/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/ _/ Renxiao Wang Doctoral Candidate _/ _/ Molecular Design Laboratory _/ _/ Institute of Physical Chemistry, Peking University _/ _/ Beijing 100871, P.R.China _/ _/ _/ _/ E-mail: arthur@ipc.pku.edu.cn _/ _/ Tel: 86-10-62751490 Fax: 86-10-62751725 _/ _/ WWW: http://www.ipc.pku.edu.cn/~arthur/arthur.html _/ _/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/