From chemistry-request@server.ccl.net Fri Sep 6 14:22:28 2002 Received: from xsmtp.ethz.ch ([129.132.97.6]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g86IMR305578 for ; Fri, 6 Sep 2002 14:22:27 -0400 Received: from xfe1.d.ethz.ch ([192.168.36.10]) by xsmtp.ethz.ch with Microsoft SMTPSVC(5.0.2195.4905); Fri, 6 Sep 2002 20:22:27 +0200 Received: from laplinux ([129.132.118.154]) by xfe1.d.ethz.ch with Microsoft SMTPSVC(5.0.2195.4905); Fri, 6 Sep 2002 20:22:26 +0200 Content-Type: text/plain; charset="iso-8859-1" From: Alessandro Contini Organization: Istituto di Chimica Organica To: Zhang Xiaodong , "michael hanlon (BITS)" Subject: Re: CCL:dock Date: Fri, 6 Sep 2002 20:22:54 +0200 X-Mailer: KMail [version 1.4] Cc: "'chemistry@ccl.net'" References: In-Reply-To: MIME-Version: 1.0 Message-Id: <200209062022.54755.alessandro.contini@unimi.it> X-OriginalArrivalTime: 06 Sep 2002 18:22:26.0394 (UTC) FILETIME=[5A293BA0:01C255D2] Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id g86IMS305579 For small molecule charges you can use any QM program as MOPAC or GAMESS to calculate charges, then convert it in mol2 with MOLDEN or VEGA. For proteins you can assigne Kollman charges with ADT. For software visit http://zeus.polsl.gliwice.pl/~nikodem/linux4chemistry.html Bye Alessandro Alle 19:38, venerdì 6 settembre 2002, Zhang Xiaodong ha scritto: > hi, DOCK or Autodock users > > if no sybyl, How to get the charge which is calculated by SYBYL for > dock (ALL ) or autodock program? > > > -= This is automatically added to each message by mailing script =- > CHEMISTRY@ccl.net -- To Everybody | CHEMISTRY-REQUEST@ccl.net -- To Admins > Ftp: ftp.ccl.net | WWW: http://www.ccl.net/chemistry/ | Jan: > jkl@ccl.net -- Dott. Alessandro Contini Istituto di Chimica Organica, Facoltà di Farmacia Università degli Studi di Milano Via Venezian, 21 20133 Milano Tel. +390250314480 Fax +390250314476 http://users.unimi.it/istchimorg/pagconthtm.htm From chemistry-request@server.ccl.net Fri Sep 6 16:05:44 2002 Received: from xsmtp.ethz.ch ([129.132.97.6]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g86K5h308083 for ; Fri, 6 Sep 2002 16:05:44 -0400 Received: from xfe1.d.ethz.ch ([192.168.36.10]) by xsmtp.ethz.ch with Microsoft SMTPSVC(5.0.2195.4905); Fri, 6 Sep 2002 22:05:43 +0200 Received: from laplinux ([129.132.118.154]) by xfe1.d.ethz.ch with Microsoft SMTPSVC(5.0.2195.4905); Fri, 6 Sep 2002 22:05:43 +0200 Content-Type: text/plain; charset="iso-8859-15" From: Alessandro Contini Organization: Istituto di Chimica Organica To: chemistry@ccl.net Subject: summary of Water in Autodock Date: Fri, 6 Sep 2002 22:06:11 +0200 X-Mailer: KMail [version 1.4] MIME-Version: 1.0 Message-Id: <200209062206.11756.alessandro.contini@unimi.it> X-OriginalArrivalTime: 06 Sep 2002 20:05:43.0169 (UTC) FILETIME=[C7BA0F10:01C255E0] Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id g86K5i308089 Hi CCLers, I summarize tips given for considering water in docking: 1. Yes it's possible. Sometimes it makes the difference between success and no success: from Dr. David van der Spoel who suggest the reading of the very exhaustive paper reported below 2.It is very simple: just give hydrogens (e.g. with GROMACS or REDUCE) and partial charges (q.kollua scriptof AD) and you can make the grid, as if waters were part of the protein; from Csaba that suggest the same paper: Efficient docking of peptides to proteins without prior knowledge of the binding site Protein Sci 2002 11: 1729-1737 3. Try to read The Role of Water in Drug Design: Thymidine Kinase as Case Study Pavel Pospisil, Leonardo Scapozza and Gerd Folkers Rational Approaches to Drug Design - book of 13th European Symposium on Quantitative Structure-Activity Relationship, 08/2000, printed 3/2001 Alessandro -- Dott. Alessandro Contini Istituto di Chimica Organica, Facoltà di Farmacia Università degli Studi di Milano Via Venezian, 21 20133 Milano Tel. +390250314480 Fax +390250314476 http://users.unimi.it/istchimorg/pagconthtm.htm From chemistry-request@server.ccl.net Fri Sep 6 14:54:38 2002 Received: from postal.sdsc.edu (IDENT:Zwg+COjiWTDaalaZp8Ev+PM8/LCq5A6a@[132.249.20.114]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g86Isc306168 for ; Fri, 6 Sep 2002 14:54:38 -0400 Received: from koa.sdsc.edu (IDENT:M4ZKfi5znSgHV/tuhVVdGLzicr3eJ1c6@koa.sdsc.edu [132.249.23.116]) by postal.sdsc.edu (8.11.6/8.11.6/server/46) with ESMTP id g86IsP028486; Fri, 6 Sep 2002 11:54:26 -0700 (PDT) Received: from localhost by koa.sdsc.edu (SGI-8.9.3/1.11-IRIXclient) with ESMTP id LAA13802; Fri, 6 Sep 2002 11:54:25 -0700 (PDT) Date: Fri, 6 Sep 2002 11:54:24 -0700 From: Wibke Sudholt To: DanMajor cc: Subject: Re: CCL:CIS np* minimization In-Reply-To: <3D78430F.28CA5C7B@mail.biu.ac.il> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi, this sounds like the usual "root flipping" problem to me. If you are not very lucky (meaning the exited state minima are quite separated electronically and geometrically), you will only be able to optimize the energetically lowest excited state in each given symmetry. This is due to the fact that the system relaxes simultaneously electronically and geometrically, finally mostly leading to the roots "flipping" (meaning the state characters interchange) so that the overall lowest excited state is represented (states of one symmetry mix when they are close). So if you have Cs symmetry and you are only interested in states of one multiplicity, you will only be able to optimize the 2A' and 1A'' states (when 1A' is the ground state). When you have no (C1) symmetry, however, you can usually only optimize the 2A excited state (1A is the ground state). In my experience, this holds for CIS as well as MCSCF, although their respective "overall lowest" excited state may be a different one due to the influence of electron correlation. I hope this helps, Wibke Sudholt University of California, San Diego wibke@sdsc.edu On Fri, 6 Sep 2002, DanMajor wrote: > Hi, > I'm minimizing the geometry of np* excited states of heterocycles using > CIS in Gaussian98 (I'm not using MCSCF due to the size of > the molecules investigated). > In Cs symmetry the geometry minimization of these states converge > nicely, but they are not local minima. > When I remove symmetry restrictions the nature of the CIS root changes > to pp* for most molecules. > I've tried to restart the minimization from the previous steps with the > new geometry and correct root, but this doesn't always help. I've > also tried adding the normal mode (corresponding to the imaginary freq.) > > of the symmetric np* excited states as a perturbation to the > initial structure and this does help in some cases, but not all. > Does anyone have any other ideas how to minimize excited np* states ? > Why does the excited states minimization of np* states often > collapse to pp* states ? > > Sincerely, > Dan > > > > > > -= This is automatically added to each message by mailing script =- > CHEMISTRY@ccl.net -- To Everybody | CHEMISTRY-REQUEST@ccl.net -- To Admins > Ftp: ftp.ccl.net | WWW: http://www.ccl.net/chemistry/ | Jan: jkl@ccl.net > > > > > From chemistry-request@server.ccl.net Sat Sep 7 10:46:13 2002 Received: from ptp.fki.dtu.dk ([130.225.67.169]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g87EkC310389 for ; Sat, 7 Sep 2002 10:46:13 -0400 Received: (from ghp@localhost) by ptp.fki.dtu.dk (8.11.6/8.11.0) id g87F4I603488 for chemistry@ccl.net; Sat, 7 Sep 2002 17:04:18 +0200 Date: Sat, 7 Sep 2002 17:04:18 +0200 From: Guenther Peters Message-Id: <200209071504.g87F4I603488@ptp.fki.dtu.dk> To: chemistry@ccl.net Subject: Autodock - compilation error Dear "autodock" users, I try to install autodock 3.0.3 and encountered three error messages listed below. One error occurred when compiling 'atmtobnd.c' and two errors occurred when running 'make' in 'autodock'. I was wondering if anybody has encountered the same problem before and could provide me with some hints how to proceed. Thanks in advance for any help. Guenther COMPILATION ERROR: 1) cc -bnoquiet -o atmtobnd atmtobnd.c ld: 0711-318 ERROR: Undefined symbols were found. The following symbols are in error: Symbol Inpndx TY CL Source-File(Object-File) OR Import-File{Shared-object} RLD: Address Section Rld-type Referencing Symbol ---------------------------------------------------------------------------------------------- .hypot [98] ER PR atmtobnd.c(atmtobnd.o) 000002dc .text R_RBR [14] .do_dist 000002ec .text R_RBR [14] .do_dist 2) c++ -DNDEBUG -O3 -IPA -LNO:auto_dist=ON:gather_scatter=2 -c -DWRITEPDBQSTATE main.cc main.cc:60: declaration of C function `int gethostname(char *, int)' conflicts with /usr/include/unistd.h:579: previous declaration `int gethostname(char *, long unsigned int)' here 3) c++ -DNDEBUG -O3 -IPA -LNO:auto_dist=ON:gather_scatter=2 -c support.cc In file included from support.cc:19: support.h:53: syntax error before `&' support.h:84: syntax error before `&' support.h:113: syntax error before `&' support.h:143: syntax error before `&' support.h:242: definition of implicitly-declared `Individual::operator =(const Individual &)' support.cc:281: definition of implicitly-declared `Genotype::operator =(const Genotype &)' support.cc:437: definition of implicitly-declared `Phenotype::operator =(const Phenotype &)' support.cc: In method `struct Molecule * Individual::getMol()': support.cc:626: warning: address of local variable `returnedMol' returned support.cc: At top level: support.cc:648: definition of implicitly-declared `Population::operator =(const Population &)' make: 1254-004 The error code from the last command is 1.