From chemistry-request@server.ccl.net Tue Jul 9 03:56:42 2002 Received: from tigris.klte.hu ([193.6.138.33]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g697ufp32669 for ; Tue, 9 Jul 2002 03:56:41 -0400 Received: from cthulhu (193.6.133.59) by tigris.klte.hu (MX V5.1-A Vn6f) with SMTP; Tue, 9 Jul 2002 09:54:39 +0200 Message-ID: <004e01c2271e$35083e30$3b8506c1@cthulhu> From: "Tamas E. Gunda" To: "Luciana Marinelli" , References: <3D29C50E.CCD1338F@novel7.farmacia.unina.it> Subject: Re: CCL:problem with mol2topdb script Date: Tue, 9 Jul 2002 09:57:00 +0200 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 5.50.4522.1200 X-MimeOLE: Produced By Microsoft MimeOLE V5.50.4522.1200 Luciana, The sybyl2 file looks quite strange - I mean the atoms and residues are scrambled, bonds between chains etc. The sum of partial charges is -104.18. Is it surely correct? The file was produced by Sybyl, if I understood well. Have you tried to re-read the file into Sybyl? Is it OK then? Regards Dr. Tamas E. Gunda Research Group for Antibiotics Hungarian Academy of Sciences University of Debrecen, POBox 36 H-4010 Debrecen, Hungary tamasgunda@tigris.klte.hu ----- Original Message ----- From: "Luciana Marinelli" To: Sent: Monday, July 08, 2002 18:59 Subject: CCL:problem with mol2topdb script > hallo, > I am a new AUTODOCK user, I have problem with mol2topdb script. > I am working on a silicon graphics with an operating system: IRIX64 > Release 6. I have download the new one version of autodock. > I have downloaded my protein from PDB and I have added H and charges by > sybyl as you explain in the user guide, than I saved it as mol2 file, > but when I try to run the script that should convert the mol2 file into > the pdbq I have this output: > % mol2topdbq 1L5G.pdb > gawk - Command not found > % > > From chemistry-request@server.ccl.net Tue Jul 9 04:16:08 2002 Received: from zeus.ruca.ua.ac.be (avalo@[143.129.201.210]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g698G8p01747 for ; Tue, 9 Jul 2002 04:16:08 -0400 Received: from localhost (avalo@localhost) by zeus.ruca.ua.ac.be (8.9.3 (PHNE_22672)/8.9.3) with ESMTP id KAA26136 for ; Tue, 9 Jul 2002 10:16:03 +0200 (METDST) Date: Tue, 9 Jul 2002 10:16:03 +0200 (METDST) From: An Van Looy To: chemistry@ccl.net Subject: distributed multiopole analysis of the molecule NF3 Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hello I have a problem. I want to do a distributed multipole analysis with the program GAMESS for the molecule NF3, but what do I do with the free electronpair: ingnore, dummy ... I tried to do it the same way as for example CF4, SiF4 (this means ignore the free electronpair) First I optimize the structure of the molecule with G98. Then I make my Gamess inputfile. in $data, I give a C1 symmetry and the (G98) coordinates of the molecule. This is then my Gamess inputfile ... $contrl scftyp=rhf mplevl=2 $end $system memory=4000000 $end $basis gbasis=n311 ngauss=6 ndfunc=1 diffsp=.true. $end $guess guess=huckel $end $stone ATOMS $end $data distributed multipole C1 N 7 0.000000 0.477297 0.000000 F 9 -1.230673 -0.124400 0.000000 F 9 0.615337 -0.123416 1.066030 F 9 0.615337 -0.123416 -1.066030 $end I tried to use a dummy in the structure for the free electronpair. To me it seems that I have to do something with the free electronpair. But the calculation does not do anything with the dummy It gets no multipoles at all. This was the used input-file ... $stone ATOMS POINT 0.000000 0.000000 1.000000 DUMMY ... C1 N 7 0.000000 0.000000 0.000000 F 9 1.197378 0.000000 -0.573989 F 9 -0.598689 -1.036960 -0.573989 F 9 -0.598689 1.036960 -0.573989 $end How can I calculate the DMA for NF3, which way is the right one ? Is there someone who can help me ? Thanks ! An --- *** --- An Van Looy avalo@ruca.ua.ac.be Ph.D student researchgroup Prof B.J. van der Veken RUCA - University of Antwerp BELGIUM From chemistry-request@server.ccl.net Tue Jul 9 07:45:31 2002 Received: from mailer.gwdg.de ([134.76.10.26]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g69BjUp10953 for ; Tue, 9 Jul 2002 07:45:30 -0400 Received: from vrlab03.mpibpc.gwdg.de ([134.76.211.99] helo=mpi-bpc.mpg.de) by mailer.gwdg.de with esmtp (Exim 3.33 #11) id 17RtQw-0002hX-00 for chemistry@ccl.net; Tue, 09 Jul 2002 13:45:30 +0200 Message-ID: <3D2ACBE9.1060504@mpi-bpc.mpg.de> Date: Tue, 09 Jul 2002 13:41:29 +0200 From: Vlad Cojocaru User-Agent: Mozilla/5.0 (X11; U; Linux i686; en-US; rv:0.9.4) Gecko/20011126 Netscape6/6.2.1 X-Accept-Language: en-us MIME-Version: 1.0 To: CCL list Subject: differences between hydrogen bonding Content-Type: text/plain; charset=us-ascii; format=flowed Content-Transfer-Encoding: 7bit Hi! I am trying (using Gaussian 94) to estimate the differences between hydrogen bonding between A-T and 2-amino purine-T. I also have other base analogues with which I want to do the same. Would you please indicate me some references or some advices about the approach for such kind of studies? Thanks a lot in advance, vlad -- Vlad Cojocaru Max Planck Institut for Biophysical Chemistry Deparment: 060 Am Fassberg 11, 37077 Goettingen, Germany tel: ++49-551-201.1389 e-mail: Vlad.Cojocaru@mpi-bpc.mpg.de From chemistry-request@server.ccl.net Tue Jul 9 09:14:05 2002 Received: from mr2.cc.ic.ac.uk ([155.198.5.112]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g69DE5p15288 for ; Tue, 9 Jul 2002 09:14:05 -0400 Received: from origin.ch.ic.ac.uk ([155.198.224.252] helo=chcmga.ch.ic.ac.uk) by mr2.cc.ic.ac.uk with esmtp (Exim 3.35 #1) id 17RuoZ-0001V2-02 for chemistry@ccl.net; Tue, 09 Jul 2002 14:13:59 +0100 Received: from hbtower.ch.ic.ac.uk ([155.198.226.132] helo=ic.ac.uk) by chcmga.ch.ic.ac.uk with esmtp (Exim 2.02 #1) id 17Ruq2-004yw5-00; Tue, 9 Jul 2002 14:15:30 +0100 Sender: krzys@ic.ac.uk Message-ID: <3D2AE185.499E2254@ic.ac.uk> Date: Tue, 09 Jul 2002 14:13:41 +0100 From: Krzysztof Radacki Organization: Imperial College, London X-Mailer: Mozilla 4.78 [en] (X11; U; Linux 2.4.7-10smp i686) X-Accept-Language: en MIME-Version: 1.0 To: CCL Subject: gaussian problems Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Dear all, I have two question and one information concerning gaussian. 1) I wanted to perform an optimization with possibly slowest changing of geometry. The command line was as: #P OPT=(Redundant,CalcAll,StepSize=1,TIGHT) INT=(GRID=99590) I got an error: QPERR --- A SYNTAX ERROR WAS DETECTED IN THE INPUT LINE. #P OPT=(REDUNDANT,CALCALL,STEPSIZE=1,TIG ' What's wrong? On p.129 of User's reference one can find description of StepSize in Opt and I can't see why it shouldn't work. 2) However calculation of IR was already sometimes discussed on CCL I still have uneasy feeling. An example. I have a molecule with trigonal bipiramide (D3h) structure. I know however that minimum is distorted - both axial ligands are moved out of Z-axis in direction of one equatorial ligand (f.e.: ax-ax angle 160) and the equatorial are still co-planar (C2v). (I hope that you can imagin it from my description). Now: If I would distorte D3h structure to C2v with ax-ax angle 175 deg and optimized geometry with frozen ax-ax, should IR calculation have a one imaginary freq. narrowing ax-ax angle or not? If it gives me no Imag - hwat does it mean? One can find in books that vibrational analysis should be performed only on stationary point - if not it's meaningless. What sense has it if one makes such restriction? If I want to be sure that I'm in minimum should I repaet all symmetry bounded calculation (like above D3h) with NoSymm? 3) Last week I wanted to calculated some quite complicated molecules like CO or CCH2 and various level of theory. Everything was fine with DFT and MP2 but the same inputs didn't work for CCSD and CCSD(T). The input like: %MEM=1000MB %NPROC=2 %SAVE %CHK=CO-CCSD #P OPT=(CART,TIGHT) POP=FULL CCSD/6-311G(D,P) Gues=Read carbon monoxid 0 1 C 0.000000000000 0.000000000000 0.000000000000 O 0.000000000000 0.000000000000 1.126962524921 produced an error: Symbolic Z-matrix: Charge = 0 Multiplicity = 1 C 0. 0. 0. O 0. 0. 1.12696 Leave Link 101 at Fri Jul 5 17:23:43 2002, MaxMem= 13107200 cpu: 0.2 (Enter /usr/local/SW/g98/l114.exe) NEF-NEF-NEF-NEF-NEF-NEF-NEF-NEF-NEF-NEF-NEF-NEF-NEF-NEF-NEF-NEF-NEF-NEF- NUMERICAL EIGENVECTOR FOLLOWING MINIMUM SEARCH INITIALIZATION PASS ************************************************ ** ERROR IN INITNF. NUMBER OF VARIABLES ( 0) ** ** INCORRECT (SHOULD BE BETWEEN 1 AND 50) ** ************************************************ Error termination via Lnk1e in /usr/local/SW/g98/l114.exe. I was supprised that gaussian was looking for z-matrix even if I wrote opt=cart. I've repeated the calculation with opt=z-matrix and geometry: C O 1 r1 r1 = 1.126962524921 and gaussian succeed with Normal Termination. So probably I've found small bug. Thanks a lot in advance and best reagrds Krzysztof -- Dr. K.Radacki Department of Chemistry Catalysis and Advanced Materials Section Imperial College, London From chemistry-request@server.ccl.net Tue Jul 9 09:40:32 2002 Received: from tfplx12.tfp.uni-karlsruhe.de ([129.13.73.109]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g69DeWp16648 for ; Tue, 9 Jul 2002 09:40:32 -0400 Received: from localhost (heurich@localhost) by tfplx12.tfp.uni-karlsruhe.de (8.9.3/8.9.3/Debian 8.9.3-6) with ESMTP id PAA04332 for ; Tue, 9 Jul 2002 15:40:31 +0200 X-Authentication-Warning: tfplx12.tfp.uni-karlsruhe.de: heurich owned process doing -bs Date: Tue, 9 Jul 2002 15:40:31 +0200 (CEST) From: Jan Heurich X-X-Sender: To: Subject: gold basis set Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi everybody, I am planning to carry out some electronic structure calculations including gold atoms. In particular it would be great if ehty could be carried out with a minimal basis set in the sense that the inner 68 electrons are all lumped into an ECP and only the "valence" s,p,d-shells are treated on the level of a gaussian basis set. The only basis set which I have found and which fulfills these requirements has a maximum angular momentul lmax of 4 in its ECP. However, unfortunately TURBOMOLE (which I would like to use) cannot deal with this apparently so I wonder if there are any other basis sets for gold out there which could do the job...? Thanks in advance Jan Heurich ********************************************************************* Jan Heurich mail: heurich@tfp.physik.uni-karlsruhe.de Adlerstr. 18a Tel: ++49 (0)721/3504774 (privat) 76133 Karlsruhe Tel: ++49 (0)721/608-6363 (Uni) WWW: http://www-tfp.physik.uni-karlsruhe.de/~heurich From chemistry-request@server.ccl.net Tue Jul 9 10:35:45 2002 Received: from postal.sdsc.edu (IDENT:vsXklq6gNqrAYAoN5+zfQQ45hoaZlhxk@[132.249.20.114]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g69EZjp18032 for ; Tue, 9 Jul 2002 10:35:45 -0400 Received: from fragment.sdsc.edu (IDENT:G4VEtLus9/zgVMdgd65KWHTnKX5efeDQ@fragment.sdsc.edu [132.249.21.128]) by postal.sdsc.edu (8.11.6/8.11.6/server/40) with ESMTP id g69EZdw19902; Tue, 9 Jul 2002 07:35:40 -0700 (PDT) Received: from localhost by fragment.sdsc.edu (980427.SGI.8.8.8/1.11-IRIXclient) with ESMTP id HAA13686; Tue, 9 Jul 2002 07:35:39 -0700 (PDT) Date: Tue, 9 Jul 2002 07:35:39 -0700 From: Laura Brovold To: Krzysztof Radacki cc: CCL Subject: Re: CCL:gaussian problems In-Reply-To: <3D2AE185.499E2254@ic.ac.uk> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII I can answer the first one - as I had the same problem recently. The ability to use a reduced step size is present in the program, but the keyword is not properly connected. To use a reduced step size, use "IOp(1/8=N)", where N has the same meaning as the N in stepsize=N. Additionally, you should add the option "NoTrustUpdate" to the opt keyword. So, your input should contain "#p opt=(Redundant,CalcAll,TIGHT,notrustupdate) iop(1/8=1)"... Cheers, Laura --------------------------------------------------------------------------------- Laura Gregerson (Brovold) UCSD/SDSC MC-0505 9500 Gilman Dr. La Jolla, CA 92093-0505 (858)531-2172 fax: http://www.sdsc.edu/~lgregers/laura.html On Tue, 9 Jul 2002, Krzysztof Radacki wrote: > Dear all, > I have two question and one information concerning gaussian. > > 1) > I wanted to perform an optimization with possibly slowest changing > of geometry. The command line was as: > #P OPT=(Redundant,CalcAll,StepSize=1,TIGHT) INT=(GRID=99590) > > I got an error: > > QPERR --- A SYNTAX ERROR WAS DETECTED IN THE INPUT LINE. > #P OPT=(REDUNDANT,CALCALL,STEPSIZE=1,TIG > ' > > What's wrong? On p.129 of User's reference one can find description > of StepSize in Opt and I can't see why it shouldn't work. > > > > 2) > However calculation of IR was already sometimes discussed on CCL I > still have uneasy feeling. An example. > I have a molecule with trigonal bipiramide (D3h) structure. I know > however that minimum is distorted - both axial ligands are moved out > of Z-axis in direction of one equatorial ligand (f.e.: ax-ax angle 160) > and the equatorial are still co-planar (C2v). > (I hope that you can imagin it from my description). > > Now: If I would distorte D3h structure to C2v with ax-ax angle 175 deg > and optimized geometry with frozen ax-ax, should IR calculation have > a one imaginary freq. narrowing ax-ax angle or not? If it gives me no > Imag - hwat does it mean? > > One can find in books that vibrational analysis should be performed > only on stationary point - if not it's meaningless. What sense has it > if one makes such restriction? If I want to be sure that I'm in minimum > should I repaet all symmetry bounded calculation (like above D3h) > with NoSymm? > > > > 3) > Last week I wanted to calculated some quite complicated > molecules like CO or CCH2 and various level of theory. > Everything was fine with DFT and MP2 but the same inputs > didn't work for CCSD and CCSD(T). > The input like: > > %MEM=1000MB > %NPROC=2 > %SAVE > %CHK=CO-CCSD > > #P OPT=(CART,TIGHT) POP=FULL CCSD/6-311G(D,P) Gues=Read > > carbon monoxid > > 0 1 > C 0.000000000000 0.000000000000 0.000000000000 > O 0.000000000000 0.000000000000 1.126962524921 > > produced an error: > > Symbolic Z-matrix: > Charge = 0 Multiplicity = 1 > C 0. 0. 0. > O 0. 0. 1.12696 > Leave Link 101 at Fri Jul 5 17:23:43 2002, MaxMem= 13107200 cpu: 0.2 > (Enter /usr/local/SW/g98/l114.exe) > > NEF-NEF-NEF-NEF-NEF-NEF-NEF-NEF-NEF-NEF-NEF-NEF-NEF-NEF-NEF-NEF-NEF-NEF- > NUMERICAL EIGENVECTOR FOLLOWING MINIMUM SEARCH > INITIALIZATION PASS > > > ************************************************ > ** ERROR IN INITNF. NUMBER OF VARIABLES ( 0) ** > ** INCORRECT (SHOULD BE BETWEEN 1 AND 50) ** > ************************************************ > > > Error termination via Lnk1e in /usr/local/SW/g98/l114.exe. > > > I was supprised that gaussian was looking for z-matrix even if I wrote > opt=cart. I've repeated the calculation with opt=z-matrix and geometry: > > C > O 1 r1 > > r1 = 1.126962524921 > > and gaussian succeed with Normal Termination. So probably I've found small > bug. > > > Thanks a lot in advance and best reagrds > Krzysztof > > > -- > Dr. K.Radacki > Department of Chemistry > Catalysis and Advanced Materials Section > Imperial College, London > > -= 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 Tue Jul 9 11:40:25 2002 Received: from chinon.cnrs-orleans.fr ([163.9.6.107]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g69FePp21581 for ; Tue, 9 Jul 2002 11:40:25 -0400 Received: (from hinsen@localhost) by chinon.cnrs-orleans.fr (8.11.2/8.11.2) id g69FbC831342; Tue, 9 Jul 2002 17:37:12 +0200 Date: Tue, 9 Jul 2002 17:37:12 +0200 Message-Id: <200207091537.g69FbC831342@chinon.cnrs-orleans.fr> X-Authentication-Warning: chinon.cnrs-orleans.fr: hinsen set sender to hinsen@cnrs-orleans.fr using -f From: Konrad Hinsen To: chemistry@ccl.net Subject: Annoucement: nMOLDYN 2.0 nMOLDYN 2.0 =========== nMOLDYN is an interactive analysis program for Molecular Dynamics simulations. It is especially designed for the computation and decomposition of neutron scattering spectra, but also computes other quantities. The current release 2.0 of nMOLDYN can compute the following quantities: Quantities related to neutron scattering: * coherent intermediate scattering function * memory function for coherent scattering function * dynamic structure factor * incoherent intermediate scattering function * elastic incoherent structure factor Other quantities: * mean-square displacement * velocity autocorrelation function * memory function for velocity autocorrelation function * density of states * angular velocity autocorrelation function (and its spectrum) * reorientational correlation function nMOLDYN has both a graphical user interface that is easy to use, and a command-line interface for experienced users. The latter is also appropriate for situations in which the graphical interface cannot be used for technical reasons (network restrictions etc.) For more information and for downloading nMOLDYN, see http://dirac.cnrs-orleans.fr/nMOLDYN/ -- ------------------------------------------------------------------------------- Konrad Hinsen | E-Mail: hinsen@cnrs-orleans.fr Centre de Biophysique Moleculaire (CNRS) | Tel.: +33-2.38.25.56.24 Rue Charles Sadron | Fax: +33-2.38.63.15.17 45071 Orleans Cedex 2 | Deutsch/Esperanto/English/ France | Nederlands/Francais ------------------------------------------------------------------------------- From chemistry-request@server.ccl.net Tue Jul 9 13:10:15 2002 Received: from ciril.fr ([193.50.27.66]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g69HAEp27049 for ; Tue, 9 Jul 2002 13:10:14 -0400 Received: from lctn.uhp-nancy.fr (cm.mpi.univie.ac.at [131.130.14.100]) (authenticated bits=0) by ciril.fr (8.12.4/8.12.4/Guy-23-01-2002) with ESMTP id g69HAAFx001318; Tue, 9 Jul 2002 19:10:11 +0200 (METDST) Message-ID: <3D2B1933.2CCCD46@lctn.uhp-nancy.fr> Date: Tue, 09 Jul 2002 19:11:15 +0200 From: =?iso-8859-1?Q?=C1ngy=E1n=20J=E1nos?= Reply-To: angyan@lctn.uhp-nancy.fr Organization: LCTN X-Mailer: Mozilla 4.79 [en] (Win98; U) X-Accept-Language: en MIME-Version: 1.0 To: chemistry@ccl.net Subject: Announcement: Optimally Partitioned Electric Properties - OPEP Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit X-Virus-Scanned: by amavisd-milter arcturus (http://amavis.org/) =============================================== OPEP: Optimally Partitioned Electric Properties =============================================== OPEP (Optimal Partitioning of Electric Properties) is a suite of Fortran programs, featuring a Tcl/Tk graphical user interface to facilitate the fit of electric charges and multipoles, as well as models of distributed polarizabilities. It relies upon two alternative fitting procedures, a least-squares approach and a statistical analysis of the distributed electric components. The goal of OPEP is to provide compact and flexible models of distributed multipoles and polarizabilities, that can be used in a variety of applications, among which the design of molecular mechanical force fields. OPEP main functionalities include: - handle molecular symmetry; - allow to constrain the molecular charge, or the charge borne by user-defined fragments; - automated generation of local frames of reference for fitting multipolar properties; - models of distributed polarizabilities, including charge-flow polarizabilities; - visualization of both the molecular structures and their local frames of reference through an interface with XMakemol; - automated generation of input files for Gaussian computations of electrostatic potential and induction energy grids. OPEP is a free software, distributed under the GNU General Public License. For more information and download, refer to: http://www.lctn.uhp-nancy.fr/Opep/ Comments and requests for additional information can be addressed to: mailto:opep@lctn.uhp-nancy.fr ----------------------------------------------------------------- ÁNGYÁN János SRSMC UMR 7565 Directeur de Recherche au CNRS Laboratoire de Chimie théorique Janos.Angyan@lctn.uhp-nancy.fr BP. 239 tel: +33-(0)3.83.68.43.80 Université Henri Poincaré fax: +33-(0)3.83.68.43.71 54506 Vandoeuvre-lès-Nancy FRANCE ----------------------------------------------------------------- From chemistry-request@server.ccl.net Tue Jul 9 10:21:02 2002 Received: from hotmail.com ([64.4.9.223]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g69EL1p17805 for ; Tue, 9 Jul 2002 10:21:02 -0400 Received: from mail pickup service by hotmail.com with Microsoft SMTPSVC; Tue, 9 Jul 2002 07:20:56 -0700 Received: from 134.184.24.98 by lw9fd.law9.hotmail.msn.com with HTTP; Tue, 09 Jul 2002 14:20:56 GMT X-Originating-IP: [134.184.24.98] From: "George Hall" To: chemistry@ccl.net Subject: CHELPG Date: Tue, 09 Jul 2002 14:20:56 +0000 Mime-Version: 1.0 Content-Type: text/plain; format=flowed Message-ID: X-OriginalArrivalTime: 09 Jul 2002 14:20:56.0548 (UTC) FILETIME=[D72AF240:01C22753] Hi everybody, I wonder if some could point me out what are the differences between Chelpg charges and Mulliken. Would you please indicate me some references or some advices about the aproach for these kind of charges. Thanks a lot in advance. George Hall. _________________________________________________________________ Chat with friends online, try MSN Messenger: http://messenger.msn.com From chemistry-request@server.ccl.net Tue Jul 9 15:50:44 2002 Received: from mail.rpi.edu ([128.113.22.40]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g69Joip02931 for ; Tue, 9 Jul 2002 15:50:44 -0400 Received: from webmail.rpi.edu (webmail.rpi.edu [128.113.26.21]) by mail.rpi.edu (8.12.1/8.12.1) with ESMTP id g69JoeU9129906; Tue, 9 Jul 2002 15:50:40 -0400 Message-Id: <200207091950.g69JoeU9129906@mail.rpi.edu> Content-Type: text/plain Content-Disposition: inline To: georgehalli@hotmail.com From: "Dr. N. SUKUMAR" Organization: Rensselaer Polytechnic Institute Cc: chemistry@ccl.net X-Originating-Ip: 128.113.135.209 Mime-Version: 1.0 Reply-To: "Dr. N. SUKUMAR" Date: Tue, 09 Jul 2002 15:50:39 EDT X-Mailer: EMUmail 4.00 Subject: Re: CCL:CHELPG X-Scanned-By: MIMEDefang 2.3 (www dot roaringpenguin dot com slash mimedefang) Mulliken charges are asigned by apportioning the electrons in the overlap region between two atoms (two center overlap integrals) equally between the atoms, which are then added to the net atomic populations (from the one-center overlap integrals). Like most such schemes, it is an arbitrary scheme for assigning charges (since "atomic charges" are not unambiguously defined, at least outside of Bader's AIM theory). If one wants to reproduce the electrostatic effects of the electron charge distribution in a molecule with reasonable accuracy, without arbitrary parametrization, one can employ either: * a distribution of point charges (i.e. monopoles) fitted to the electrostatic potential -- this is exactly what the CHELPG procedure does; or * a distribution of monopoles, dipoles, quadrupoles and higher-order multipoles -- we have implemented this in a version of our RECON algorithm: Whitehead, Sukumar and Breneman, submitted to J. Comp. Chem. The original reference for CHELPG (CHarges from ELectrostatic Potentials Grid) is: "Determining Atom-Centered Monopoles from Molecular Electrostatic Potentials. The Need for High Sampling Density in Formamide Conformational Analysis" J. Comput. Chem., 11, 361-373 (1990) Curt M. Breneman and Kenneth B. Wiberg Dr. N. Sukumar http://www.drugmining.com/ Rensselaer Department of Chemistry On Tue, 09 Jul 2002 14:20:56 +0000 "George Hall" wrote: > > Hi everybody, > > I wonder if some could point me out what are the differences between > Chelpg > charges and Mulliken. > > Would you please indicate me some references or some advices about the > aproach for these kind of charges. > > Thanks a lot in advance. > > George Hall. > > > _________________________________________________________________ > Chat with friends online, try MSN Messenger: http://messenger.msn.com > > > > -= 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 Tue Jul 9 14:26:59 2002 Received: from toni.schrodinger.com ([192.156.98.56]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g69IQxp31239 for ; Tue, 9 Jul 2002 14:26:59 -0400 Received: (from announce@localhost) by toni.schrodinger.com (8.8.8/8.8.5) id LAA10405 for chemistry@ccl.net; Tue, 9 Jul 2002 11:26:50 -0700 Message-Id: <200207091826.LAA10405@toni.schrodinger.com> Subject: In silico solutions for drug discovery To: chemistry@ccl.net Date: Tue, 9 Jul 2002 11:26:50 -0700 (PDT) From: Schrodinger Announce Account Reply-To: Schrodinger Information Account X-Mailer: ELM [version 2.5 PL0b2] MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Schrodinger is pleased to announce the release of FirstDiscovery 2.0, which contains breakthrough technology designed to accelerate the drug-discovery process and reduce development costs. 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From chemistry-request@server.ccl.net Tue Jul 9 15:14:10 2002 Received: from ucidoor.unitedcatalysts.com ([208.23.162.2]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g69JEAp01678 for ; Tue, 9 Jul 2002 15:14:10 -0400 Received: by ucidoor.unitedcatalysts.com; (8.8.8/1.3/10May95) id PAA20828; Tue, 9 Jul 2002 15:14:09 -0400 (EDT) Received: from 10.1.0.50 by ucismtp02.unitedcatalysts.com (InterScan E-Mail VirusWall NT); Tue, 09 Jul 2002 15:11:57 -0400 Received: from lvlxch01.unitedcatalysts.com ([10.16.100.88]) by lvlmail.unitedcatalysts.com (PMDF V6.0-24 #41777) with ESMTP id <0GYZ00EERX5D0Q@lvlmail.unitedcatalysts.com>; Tue, 09 Jul 2002 15:08:01 -0400 (EDT) Received: by lvlxch01.unitedcatalysts.com with Internet Mail Service (5.5.2653.19) id <31QX4X55>; Tue, 09 Jul 2002 15:11:24 -0400 Content-return: allowed Date: Tue, 09 Jul 2002 15:11:18 -0400 From: "Shobe, Dave" Subject: RE: CHELPG To: "'George Hall'" , "'CCL'" Message-id: <157A51F55AAAD3119CD70008C7B1629D01C15E4F@lvlxch01.unitedcatalysts.com> MIME-version: 1.0 X-Mailer: Internet Mail Service (5.5.2653.19) 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 g69JEAp01679 Mulliken charges are assigned to atoms based on the "usage" of the atoms' basis functions in the molecular orbitals that are calculated. It is known as a quick-and-dirty way of assigning charges, but one that doesn't necessarily have any physical meaning. Mulliken charges are notoriously basis-set dependent. CHELPG charges are based on the electrostatic field generated by the molecule. It is a best-fit method; the set of charges produced by the CHELPG method are the point charges that would produce an electric field which is as similar as possible to the molecule's. Accordingly, if you need the charges for molecular-mechanics calculations which include electrostatic interactions, CHELPG is arguably the best for that purpose. There are other methods of assigning atomic charges. GAPT charges are based on the derivative of the molecular dipole moment WRT the atomic positions. AIM charges are based on the division of 3-dimensional space among the atoms in the molecule, according to a surface that has certain mathematical properties. NBO charges are similar to Mulliken charges, but the orbitals are transformed into "natural" orbitals, which fixes some of the basis-set dependency of the Mulliken method. --David Shobe Süd-Chemie Inc. phone (502) 634-7409 fax (502) 634-7724 email dshobe@sud-chemieinc.com Don't bother flaming me: I'm behind a firewall. -----Original Message----- From: George Hall [mailto:georgehalli@hotmail.com] Sent: Tuesday, July 09, 2002 10:21 AM To: chemistry@ccl.net Subject: CCL:CHELPG Hi everybody, I wonder if some could point me out what are the differences between Chelpg charges and Mulliken. Would you please indicate me some references or some advices about the aproach for these kind of charges. Thanks a lot in advance. George Hall. _________________________________________________________________ Chat with friends online, try MSN Messenger: http://messenger.msn.com -= 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 Tue Jul 9 16:56:17 2002 Received: from cse.nd.edu (root@[129.74.25.101]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g69KuHp06790 for ; Tue, 9 Jul 2002 16:56:17 -0400 Received: from dylan.cse.nd.edu (ako@dylan.cse.nd.edu [129.74.32.170]) by cse.nd.edu (8.11.2/8.11.2) with ESMTP id g69KuDx13892 for ; Tue, 9 Jul 2002 15:56:13 -0500 (EST) Received: from localhost (ako@localhost) by dylan.cse.nd.edu (8.11.2/8.10.1) with ESMTP id g69KuAp25600 for ; Tue, 9 Jul 2002 15:56:10 -0500 (EST) Date: Tue, 9 Jul 2002 15:56:10 -0500 (EST) From: Alice NgarKit Ko To: chemistry@ccl.net Subject: charmm IO error Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi, I generated a equil1.trj file and wanted to extract some information from it. But I got the following error. eor/uio: [1010] off end of record logical unit 11, named 'equil1.trj' lately: reading sequential unformatted external IO Abort My input file is: ... ! Convert the files open unit 11 read file name equil1.trj open unit 1 write file name equil1A_1.dcd merge coor firstu 11 nunit 1 skip 1 outputu 1 begin 21000 stop 25000 sele segid A .and. resid 1:180 end Anyone knows what that error means? My trajectory file is about 6MB large. When I ran the simulation, the energy file was written out okay and the output of charmm said normal termination. Thanks Alice