From mcblimts@leonis.nus.sg Sat Sep 30 03:21:05 1995 Received: from sable.nus.sg for mcblimts@leonis.nus.sg by www.ccl.net (8.6.10/950822.1) id DAA28558; Sat, 30 Sep 1995 03:12:38 -0400 Received: from leonis.nus.sg (mcblimts@leonis.nus.sg [137.132.1.18]) by sable.nus.sg (8.6.10/8.6.9) with ESMTP id PAA05107; Sat, 30 Sep 1995 15:08:26 +0800 Received: (from mcblimts@localhost) by leonis.nus.sg (8.6.10/8.6.9/CNS-3.5) id PAA15080; Sat, 30 Sep 1995 15:08:25 +0800 Date: Sat, 30 Sep 1995 15:08:25 +0800 (SST) From: Lim Teck Sin To: ccl cc: tshehla@hoopoe.und.ac.za Subject: summary on flexible docking - partII Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi everyone There are only 2 additional postings on software that perform flexible docking.(please see summary below) Best regards - teck sin ------------------Start of summary------------------------------- Date: Tue, 12 Sep 1995 09:00:45 +0300 From: "Andreas P. Heiner" To: mcblimts@leonis.nus.sg Subject: soft docking Dear dr. Sin, you may want to test the SCULPT-package, which in a way is interactive flexible docking. For academics relatively cheap (<$USD 2000), you can obtain a demo-version of it via WWW at http://www.intsim.com/~isigen. If you get other more info, I would be pleased to stay informed. Sincerely, Andrepeter Heiner ================================================================= | Andreas P. Heiner | voice : +358-0-456 5105 | | VTT/Biotechnology and | fax : +358-0-455 2103 | | Food Research | e-mail: andrepeter.heiner@vtt.fi | | Biologinkuja 1, Espoo | | | FIN-02044 VTT Finland | | ================================================================= -------------------------------------------------------------------- Date: Sat, 16 Sep 1995 19:30:41 -0400 From: "Wayne C. Guida" To: mcblimts@leonis.nus.sg Cc: wcg@ussu.Ciba.Com Subject: flexible docking Dear Teck-sin: We have used the BatchMin program (available from Columbia University - Clark Still's group) for flexible conformational searches in enzyme binding sites and full flexible docking (positional and conformational sampling) as well. A pointer to our work appears in a review we have written for Current Opinion in Structural Biology: "Software for Structure-based Drug Design", W. C. Guida, Current Opinion in Structural Biology, 1994, 777-781. -Wayne C. Guida ========================================================================= Wayne C. Guida Pharmaceuticals Division Ciba 556 Morris Ave. Summit, New Jersey 07901 Phone: 908-277-7954 FAX: 908-277-2405 Internet: wcg@ussu.ciba.com ========================================================================= ----------------------------------------------------end of summary-------- From ccluser@chu.chem.nthu.edu.tw Sat Sep 30 07:21:08 1995 Received: from chu.chem.nthu.edu.tw for ccluser@chu.chem.nthu.edu.tw by www.ccl.net (8.6.10/950822.1) id HAA29337; Sat, 30 Sep 1995 07:08:21 -0400 From: Received: by chu.chem.nthu.edu.tw (AIX 3.2/UCB 5.64/4.03) id AA14002; Sat, 30 Sep 1995 19:05:16 +0900 Message-Id: <9509301005.AA14002@chu.chem.nthu.edu.tw> Subject: PCM and SCI-PCM models in G94 ? To: chemistry@www.ccl.net Date: Sat, 30 Sep 95 19:05:15 TAIDT X-Mailer: ELM [version 2.4dev PL17] Dear list members, I have two problems about PCM and SCI-PCM models in G94: (1) Can we calculation ions with these two models? (2) How do we estimste the isodensity value in SCI-PCM? Any response will be appreciated! Sincerely, ===================================================================== Chiu-Ling Lin | E-mail: ccluser@chu.chem.nthu.edu.tw Department of chemistry | National Tsing Hua University | Phone: 886-35-721634 Hsinchu, Taiwan 30043 | Fax: 886-35-711082 ===================================================================== From cpeng@scripps.edu Sat Sep 30 12:51:12 1995 Received: from scripps.edu for cpeng@scripps.edu by www.ccl.net (8.6.10/950822.1) id MAA01013; Sat, 30 Sep 1995 12:36:22 -0400 Received: from pauli.scripps.edu by scripps.edu (5.61/1.34) id AA07708; Sat, 30 Sep 95 09:36:20 -0700 Received: by pauli.Scripps.EDU (4.1/SMI-4.1/TSRI1.0) id AA08550; Sat, 30 Sep 95 09:28:22 PDT Date: Sat, 30 Sep 95 09:28:22 PDT From: cpeng@scripps.edu (Chun Yang) Message-Id: <9509301628.AA08550@pauli.Scripps.EDU> To: CHEMISTRY@www.ccl.net Subject: Spartan and Z-matrix The default optimization method in Gaussian 94 is the redundant geometry optimization. You can use Cartesian, Z-matrix or mixed coordinate in the input, However, if you use the default optimization keyword, Gaussian will direct it to the redundant geometry optimization. In acyclic molecules, its worst performance is about the same as Z-matrix. In cyclic molecules, its performance is much better than Z-matrix. So that's why Gaussian use it as a default optimization method. One of the references is: CY Peng, Schlegel HB., Isr. Journal of Chemistry, 33(4):449-454, 1993 You can also see some of Baker's papers. ChunYang Peng -------------------------------------------` begin included message: ------------------------------------------------- From tgray@post.cis.smu.edu Sat Sep 30 08:44:37 1995 Date: Sat, 30 Sep 1995 10:52:30 -0500 (CDT) From: Thomas Gray Subject: Re:CCL:G:Spartan and Z-matrix (fwd) To: cpeng@riscsm Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Content-Length: 1122 X-Lines: 39 Status: RO Dear Sir, Would you cite a reference for the statement below, that cartesian optimizations outperform optimizations in internal coordinates in Gaussian 94? Many thanks. ---------------------- Thomas Gray tgray@post.cis.smu.edu ---------------------- ---------- Forwarded message ---------- Date: Wed, 27 Sep 95 21:23:04 PDT From: Chun Yang To: CHEMISTRY@www.ccl.net Subject: CCL:G:Spartan and Z-matrix You can use the Cartesian coordinate generated by Spartan directly in your Gaussian 94 input, use the default optimization method in g94 which even performs better than Z-matrix. ChunYang Peng The Scripps Research Institute -------This is added Automatically by the Software-------- -- Original Sender Envelope Address: cpeng@scripps.edu -- Original Sender From: Address: cpeng@scripps.edu 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 mcblimts@leonis.nus.sg Sat Sep 30 03:12:42 1995 Received: from sable.nus.sg for mcblimts@leonis.nus.sg by www.ccl.net (8.6.10/950822.1) id DAA28558; Sat, 30 Sep 1995 03:12:38 -0400 Received: from leonis.nus.sg (mcblimts@leonis.nus.sg [137.132.1.18]) by sable.nus.sg (8.6.10/8.6.9) with ESMTP id PAA05107; Sat, 30 Sep 1995 15:08:26 +0800 Received: (from mcblimts@localhost) by leonis.nus.sg (8.6.10/8.6.9/CNS-3.5) id PAA15080; Sat, 30 Sep 1995 15:08:25 +0800 Date: Sat, 30 Sep 1995 15:08:25 +0800 (SST) From: Lim Teck Sin To: ccl cc: tshehla@hoopoe.und.ac.za Subject: summary on flexible docking - partII Message-ID: Hi everyone There are only 2 additional postings on software that perform flexible docking.(please see summary below) Best regards - teck sin ------------------Start of summary------------------------------- Date: Tue, 12 Sep 1995 09:00:45 +0300 From: "Andreas P. Heiner" To: mcblimts@leonis.nus.sg Subject: soft docking Dear dr. Sin, you may want to test the SCULPT-package, which in a way is interactive flexible docking. For academics relatively cheap (<$USD 2000), you can obtain a demo-version of it via WWW at http://www.intsim.com/~isigen. If you get other more info, I would be pleased to stay informed. Sincerely, Andrepeter Heiner ================================================================= | Andreas P. Heiner | voice : +358-0-456 5105 | | VTT/Biotechnology and | fax : +358-0-455 2103 | | Food Research | e-mail: andrepeter.heiner@vtt.fi | | Biologinkuja 1, Espoo | | | FIN-02044 VTT Finland | | ================================================================= -------------------------------------------------------------------- Date: Sat, 16 Sep 1995 19:30:41 -0400 From: "Wayne C. Guida" To: mcblimts@leonis.nus.sg Cc: wcg@ussu.Ciba.Com Subject: flexible docking Dear Teck-sin: We have used the BatchMin program (available from Columbia University - Clark Still's group) for flexible conformational searches in enzyme binding sites and full flexible docking (positional and conformational sampling) as well. A pointer to our work appears in a review we have written for Current Opinion in Structural Biology: "Software for Structure-based Drug Design", W. C. Guida, Current Opinion in Structural Biology, 1994, 777-781. -Wayne C. Guida ========================================================================= Wayne C. Guida Pharmaceuticals Division Ciba 556 Morris Ave. Summit, New Jersey 07901 Phone: 908-277-7954 FAX: 908-277-2405 Internet: wcg@ussu.ciba.com ========================================================================= ----------------------------------------------------end of summary-------- From ccluser@chu.chem.nthu.edu.tw Sat Sep 30 07:08:29 1995 Received: from chu.chem.nthu.edu.tw for ccluser@chu.chem.nthu.edu.tw by www.ccl.net (8.6.10/950822.1) id HAA29337; Sat, 30 Sep 1995 07:08:21 -0400 From: Received: by chu.chem.nthu.edu.tw (AIX 3.2/UCB 5.64/4.03) id AA14002; Sat, 30 Sep 1995 19:05:16 +0900 Message-Id: <9509301005.AA14002@chu.chem.nthu.edu.tw> Subject: PCM and SCI-PCM models in G94 ? To: chemistry@www.ccl.net Date: Sat, 30 Sep 95 19:05:15 TAIDT X-Mailer: ELM [version 2.4dev PL17] Dear list members, I have two problems about PCM and SCI-PCM models in G94: (1) Can we calculation ions with these two models? (2) How do we estimste the isodensity value in SCI-PCM? Any response will be appreciated! Sincerely, ===================================================================== Chiu-Ling Lin | E-mail: ccluser@chu.chem.nthu.edu.tw Department of chemistry | National Tsing Hua University | Phone: 886-35-721634 Hsinchu, Taiwan 30043 | Fax: 886-35-711082 ===================================================================== From jkl@ccl.net Sat Sep 30 18:51:17 1995 Received: from bedrock.ccl.net for jkl@ccl.net by www.ccl.net (8.6.10/950822.1) id SAA03976; Sat, 30 Sep 1995 18:43:20 -0400 Received: from krakow.ccl.net for jkl@ccl.net by bedrock.ccl.net (8.6.10/950822.1) id SAA10052; Sat, 30 Sep 1995 18:43:19 -0400 From: Jan Labanowski Received: for jkl@ccl.net by krakow.ccl.net (8.6.10/920428.1525) id SAA11717; Sat, 30 Sep 1995 18:43:19 -0400 Date: Sat, 30 Sep 1995 18:43:19 -0400 Message-Id: <199509302243.SAA11717@krakow.ccl.net> To: chemistry@www.ccl.net Subject: Spin Contamination in DFT -- How to compute? Forwarding: Mail from 'Jan Labanowski ' dated: Sat, 30 Sep 1995 18:21:10 -0400 Cc: jkl@ccl.net Dear Netters, I am trying to compute spin contamination in DFT. My starting point is the A. Szabo, N.S. Ostlund -- Modern Quantum Chemistry", pp. 104-107, McGraw-Hill, New York, 1989. Background: Multiplicity is MULT = 2*S + 1 where S is the total spin quantum number having possible values 0.0, 0.5, 1.0, 1.5, .... S is simply 0.5 times the number of unpaired electrons. Assuming that NALPHA is the number of electrons with spin alpha, and NBETA is the number of electrons with spin beta, S = 0.5 * (NALPHA - NBETA) if we assume that NALPHA >= NBETA. The eigenvalue of the operator of square of total spin is denoted by S2, and is NOT EQUAL to S*S but is equal to: S2 = S * (S + 1) To calculate S from S2 the following formula (solution of quadratic equation) can be used: S = 0.5*(SQRT(1.0 + 4.0*S2) - 1.0) Another quantum number: MS = -S, -S+1, ... S-1, S is the quantum number (and also the eigenvalue) of the z-component of the total spin. Now, S2 = 0.5*(NALPHA-NBETA)*(0.5*(NALPHA-NBETA) + 1) i.e., the "exact value" of eigenvalue of square of spin (SEXCT) should be: S2EXCT = S2 = 0.25*(NALPHA - NBETA)(NALPHA - NBETA + 2) and the "exact" multiplictity should be: MULTEX = NALPHA - NBETA + 1 I assume that the formula for the expectation value of S2 (S2EXPT), given on page 107 of Szabo & Ostlund as: S2EXPT = S2EXCT + NBETA - sum{i=1,N} sum{j=1,N} |(SAB[i,j])|^2 for the case of NALPHA >= NBETA (the meaning of N is not defined), can be extended to fractional occupation numbers as: S2EXPT = S2EXCT + NBETA - sum{i=1,NLA} sum{j=1,NLB} DOCA[i] * DOCB[j] * |(SAB[i,j])^2| where NLA is the number of occupied (possibly with fractional occupation numbers) ALPHA MO's, NLB is the number of occupied (possibly fractionally) BETA MO's, DOCA[i] is the (fractional) occupation number on i-th ALPHA orbital, DOCB[j] is the (possibly) fractional occupation number on j-th orbital, SAB[i,j] = is the overlap integral between PSIA[i] (the i-th MO for spin ALPHA) and PSIB[j] (the j-th MO for spin BETA). Taking this into account that PSIA[i] = sum{k=1,NCNTRT} CALPHA[k,i]*PHI[k] PSIB[j] = sum{k'=1,NCNTRT} CBETA[k',j]*PHI[k'] where NCNTRT is the number of basis functions (contractions), CALPHA[k,i] is the MO coefficient in the i-th ALPHA MO for k-th basis function, CBETA[k',j] is the MO coefficient in the j-th BETA MO for k'-th basis function, and PHI[k] is the k-th basis function; one gets: SAB[i,j] = sum{k=1,NCNTRT} sum{k'=1,NCNTRT} CALPHA[k,i]*CBETA[k',j]*S[k,k'] and hence: S2EXPT = S2EXCT + NBETA - sum{i=1,NLA} sum{j=1,NLB} sum{k=1,NCNTRT} sum{k'=1,NCNTRT} DOCA[i] * CALPHA[k,i] * DOCB[j] * CBETA[k',j] * S[k,k'] where S[k,k'] is the oridinary overlap integral between k-th and k'-th basis function: S[k,k'] = . Now, is this formula correct? Or I messed it up... Yes, I understand that fractional occupation numbers are suspect, and I really should not have them when my SCF converges. However, I need to calculate SOMETHING for the case when I do level smearing. On the other hand, I am not that sure if the formula is even correct for the intergal occupation numbers. Can you help? Jan Labanowski jkl@ccl.net P.S. Sorry, to some who got a portion of this message on my first try.