From chemistry-request@server.ccl.net Tue Jul 30 21:54:12 2002 Received: from gandalf.cber.nih.gov ([128.231.52.5]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g6V1sBf25801 for ; Tue, 30 Jul 2002 21:54:11 -0400 Received: from localhost (rvenable@localhost) by gandalf.cber.nih.gov (980427.SGI.8.8.8/980728.SGI.AUTOCF) via ESMTP id VAA27762; Tue, 30 Jul 2002 21:56:12 -0400 (EDT) Date: Tue, 30 Jul 2002 21:56:12 -0400 From: Rick Venable To: amor san juan cc: CHEMISTRY@ccl.net, Marcel Swart Subject: Re: CCL:Hint geometry optimization In-Reply-To: Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=X-UNKNOWN Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from QUOTED-PRINTABLE to 8bit by server.ccl.net id g6V1sCf25802 At first I thought this question was about the file format (what program produced this file?), but I think it's both more subtle and more obvious than that. I think the real answer is that the molecule has been translated in space and is no longer centered at the origin. That's why "these 2 commercial packages generated small cartesian coordinates"; the molecule was at/near the origin in those cases, and the benzamidine coords in the original message (below) have obviously been translated about 15 A or so in Y and Z. If you want to compare Cartesian coords, you must put the molecule in the same position and orientation. You may want to compare internal coordinates instead, i.e. molecular geometries such as bond lengths, bond angles, and single bond torsions for bonded heavy atoms. On Tue, 30 Jul 2002, Marcel Swart wrote: > This is straightforward.. > The numbers you see on the lines are the Cartesian coordinates in > Angstroms !! > I know cuz I tried to convert them into a C3D file (with my own > program), and succeeded: > 18 title > C 1 -1.853000 14.311000 16.658000 63 2 10 12 > C 2 -2.107000 15.653000 16.758000 63 1 3 4 > H 3 -2.573000 16.191000 15.916000 11 2 [lines deleted] > Any chemistry package can probably read the above coordinate set. > If you want I can generate the coordinates also in another format. > > As for the hints on conversion of file formats, look for the Babel > program; > links to it can be found in the CCL archives. > ––––––––––––––––––––––––––––––––––––– > Marcel Swart > Organische en Anorganische Chemie > Faculteit der Exacte Wetenschappen > Vrije Universiteit Amsterdam > On Monday, July 29, 2002, at 11:23 , amor san juan wrote: > > This had been a problem to me many months. Hope > > somebody patient enough to point out what molecular > > package can give cartesian coordinates for benzamidine > > as follows: > > > > ATOM1 C1 BEN 1 -1.853 14.311 16.658 ben C > > ATOM2 C2 BEN 1 -2.107 15.653 16.758 ben C > > ATOM3 H2 BEN 1 -2.573 16.191 15.916 ben H > > ATOM4 C3 BEN 1 -1.774 16.341 17.932 ben C > > ATOM5 H3 BEN 1 -1.983 17.421 18.014 ben H > > ATOM6 C4 BEN 1 -1.175 15.662 19.005 ben C > > ATOM7 H4 BEN 1 -0.914 16.201 19.931 ben H > > ATOM8 C5 BEN 1 -0.914 14.295 18.885 ben C > > ATOM9 H5 BEN 1 -0.441 13.744 19.715 ben H > > ATOM10 C6 BEN 1 -1.257 13.634 17.708 ben C > > ATOM11 H6 BEN 1 -1.051 12.555 17.611 ben H > > ATOM12 C7 BEN 1 -2.193 13.627 15.496 ben C > > ATOM13 N1 BEN 1 -2.797 14.235 14.491 ben N > > ATOM14 N2 BEN 1 -1.762 12.391 15.309 ben N > > ATOM15 H11 BEN 1 -3.039 13.707 13.640 ben H > > ATOM16 H12 BEN 1 -3.026 15.237 14.558 ben H > > ATOM17 H21 BEN 1 -1.287 11.890 16.073 ben H > > ATOM18 H22 BEN 1 -1.901 11.929 14.399 ben H > > > > I tried 2 different commercial molecular modeling > > package both have MM & semiempirical yet, I cant find > > result of conformation as above. Based from what I did > > these 2 commercial packages generated small cartesian > > coordinates. > > > > Would someone please show where is the > > problem.....advice some reading journals.....or even > > give any ideas. =+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+= Rick Venable 29/500 FDA/CBER/OVRR Biophysics Lab 1401 Rockville Pike HFM-419 Rockville, MD 20852-1448 U.S.A. (301) 496-1905 Rick_Venable@nih.gov ALT email: rvenable@speakeasy.org =+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+= From chemistry-request@server.ccl.net Wed Jul 31 07:51:07 2002 Received: from ws4-4.us4.outblaze.com ([205.158.62.105]) by server.ccl.net (8.11.6/8.11.0) with SMTP id g6VBp7f24982 for ; Wed, 31 Jul 2002 07:51:07 -0400 Received: (qmail 3298 invoked by uid 1001); 31 Jul 2002 10:04:22 -0000 Message-ID: <20020731100422.3297.qmail@linuxmail.org> Content-Type: text/plain; charset="iso-8859-1" Content-Disposition: inline Content-Transfer-Encoding: 7bit MIME-Version: 1.0 X-Mailer: MIME-tools 5.41 (Entity 5.404) Received: from [129.69.145.79] by ws4-4.us4.outblaze.com with http for bimo7@linuxmail.org; Wed, 31 Jul 2002 12:04:22 +0200 From: "Bimo Ario Tejo" To: CHEMISTRY@ccl.net Date: Wed, 31 Jul 2002 12:04:22 +0200 Subject: CCL:proton transfer X-Originating-Ip: 129.69.145.79 X-Originating-Server: ws4-4.us4.outblaze.com Dear CCLers, I'm trying to minimise an ester with its transition state using hf/sto-3g (g98). Total charge is -1 because of one O atom is unprotonated (to mimic the transition state of serine hydrolase). However, optimised structure shows proton transfer from neighbouring N to O. The structure is not valid anymore to mimic the transition state because O atom now is protonated and can't create an oxyanion hole anymore. Any suggestion how to solve this problem? Thank you, Bimo Stuttgart -- Get your free email from www.linuxmail.org Powered by Outblaze From chemistry-request@server.ccl.net Wed Jul 31 08:09:33 2002 Received: from ws4-4.us4.outblaze.com ([205.158.62.105]) by server.ccl.net (8.11.6/8.11.0) with SMTP id g6VC9Xf25493 for ; Wed, 31 Jul 2002 08:09:33 -0400 Received: (qmail 12263 invoked by uid 1001); 31 Jul 2002 10:22:47 -0000 Message-ID: <20020731102247.12262.qmail@linuxmail.org> Content-Type: text/plain; charset="iso-8859-1" Content-Disposition: inline Content-Transfer-Encoding: 7bit MIME-Version: 1.0 X-Mailer: MIME-tools 5.41 (Entity 5.404) Received: from [129.69.145.79] by ws4-4.us4.outblaze.com with http for bimo7@linuxmail.org; Wed, 31 Jul 2002 12:22:47 +0200 From: "Bimo Ario Tejo" To: chemistry@ccl.net Cc: jkl@ccl.net Date: Wed, 31 Jul 2002 12:22:47 +0200 Subject: CCL:proton transfer X-Originating-Ip: 129.69.145.79 X-Originating-Server: ws4-4.us4.outblaze.com Dear CCLers, I'm trying to minimise an ester with its transition state using hf/sto-3g (g98). Total charge is -1 because of one O atom is unprotonated (to mimic the transition state of serine hydrolase). However, optimised structure shows proton transfer from neighbouring N to O. The structure is not valid anymore to mimic the transition state because O atom now is protonated and can't create an oxyanion hole anymore. Any suggestion how to solve this problem? Thank you, Bimo Stuttgart -- Get your free email from www.linuxmail.org Powered by Outblaze From chemistry-request@server.ccl.net Wed Jul 31 06:16:00 2002 Received: from tungsten.chem.vu.nl ([130.37.144.65]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g6VAG0f21916 for ; Wed, 31 Jul 2002 06:16:00 -0400 Received: from tungsten.chem.vu.nl (LOCALHOST [127.0.0.1]) by tungsten.chem.vu.nl (8.10.0/8.10.0) with ESMTP id g6VBHx706124 for ; Wed, 31 Jul 2002 13:17:59 +0200 (MET DST) Message-Id: <200207311117.g6VBHx706124@tungsten.chem.vu.nl> X-Mailer: exmh version 2.0.2 2/24/98 To: chemistry@ccl.net From: Stan van Gisbergen Subject: ADF and ADFview available for Windows and Mac Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Date: Wed, 31 Jul 2002 13:17:59 +0200 Sender: vgisberg@tungsten.chem.vu.nl Dear CCL-list member, SCM announces the 2002.02 release of ADF, the complete density functional software package for chemists. For the first time, ADF is available on Windows and Mac OS X, in addition to the Linux and Unix platforms. ADF2002.02 also features the first module of the ADF-GUI: ADFview. ADFview enables you to visualize ADF output in 3D, such as orbitals, densities and electrostatic potentials. For further information on ADF, the ADF-GUI, or our band structure program BAND, visit our website http://www.scm.com or ask for a free copy of the ADF brochure (E-mail: admin@scm.com). Alternatively, you can meet us next week at the WATOC'02 conference for a live demonstration of ADFview or ADF. Best regards, Stan van Gisbergen, CEO of Scientific Computing & Modelling NV (SCM)