From chemistry-request@server.ccl.net Wed May 30 03:32:18 2001 Received: from hartree.chem.kuleuven.ac.be ([134.58.49.1]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f4U7WHS06328 for ; Wed, 30 May 2001 03:32:17 -0400 Received: from localhost (kiran@localhost) by hartree.chem.kuleuven.ac.be (8.9.0/8.9.0) with ESMTP id JAA47910 for ; Wed, 30 May 2001 09:33:28 +0100 Date: Wed, 30 May 2001 09:33:27 +0100 (NFT) From: Kiran Boggavarapu To: chemistry@ccl.net Subject: Turbomole Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear Netters, We are using Turbomole quite extensively. But we are handicapped by not having good public domain, Graphical Interface (I know MSI has but that is too expensive for academics). Are there any utility programmes for converting turbomole MOS and moloch output to be viewed with either Molden or someother programme. I am running huge calcualtions on openshell systems (with the limitations we have, Gaussian fails to do a single point on them!). So, i am looking for some utility which can handle opehshell systems. If someone has the informatiom pl. let me know, It would be of great help to me. Thanks in advance cheers kiran ------------------------------------------------------------------------ Kiran Boggavarapu Labo for Quantumchemistry kiran.boggavarapu@chem.kuleuven.ac.be Celestijnenlaan 200F Tel. : (32) 16 327599 B-3001 Heverlee Fax. : (32) 16 327992 Belgium Cell : (32) 16 0486792143 From chemistry-request@server.ccl.net Wed May 30 05:16:01 2001 Received: from rzumail2.unizh.ch ([130.60.128.10]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f4U9G0S19699 for ; Wed, 30 May 2001 05:16:00 -0400 Received: from zisgi.unizh.ch (zisgi.unizh.ch [130.60.19.17]) by rzumail2.unizh.ch (8.9.3/8.9.3/08) with ESMTP id LAA04718; Wed, 30 May 2001 11:15:59 +0200 (MET DST) From: "Dr. Peter Burger" Received: [(chburger@localhost) by zisgi.unizh.ch (SGI-8.9.3/SMI-IRIX6.2/USAR_MAIL_V2) id LAA56911; Wed, 30 May 2001 11:15:59 +0200 (MDT)] Message-Id: <200105300915.LAA56911@zisgi.unizh.ch> Subject: Re: CCL:Turbomole To: Kiran.Boggavarapu@chem.kuleuven.ac.be (Kiran Boggavarapu) Date: Wed, 30 May 2001 11:15:59 +0200 (CEST) Cc: CHEMISTRY@ccl.net In-Reply-To: from "Kiran Boggavarapu" at May 30, 1 09:33:27 am X-Mailer: ELM [version 2.4 PL25 PGP2] MIME-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit Well, 1) the latest version has a turbo2molden program just ask the Ahlrichs group about it. 2) Also, you can use gopenmol which has some small pearl script programs to convert moloch grid.dat files. (That's what I prefer) 3) Finally, there is viewmol (ver. 2) from Joerg-Ruediger Hill. Hope this helps Peter ------------------------------------------------------ Peter Burger Anorg.-chem. Institut Universitaet Zuerich chburger@aci.unizh.ch > Dear Netters, > > We are using Turbomole quite extensively. But we are handicapped by not > having good public domain, Graphical Interface (I know MSI has but that is > too expensive for academics). > > Are there any utility programmes for converting turbomole MOS and moloch > output to be viewed with either Molden or someother programme. > > I am running huge calcualtions on openshell systems (with the limitations > we have, Gaussian fails to do a single point on them!). So, i am looking > for some utility which can handle opehshell systems. > > If someone has the informatiom pl. let me know, It would be of great > help to me. > > Thanks in advance > cheers > kiran > > ------------------------------------------------------------------------ > Kiran Boggavarapu > Labo for Quantumchemistry kiran.boggavarapu@chem.kuleuven.ac.be > Celestijnenlaan 200F Tel. : (32) 16 327599 > B-3001 Heverlee Fax. : (32) 16 327992 > Belgium Cell : (32) 16 0486792143 > > > -= This is automatically added to each message by mailing script =- > CHEMISTRY@ccl.net -- To Everybody | CHEMISTRY-REQUEST@ccl.net -- To Admins > MAILSERV@ccl.net -- HELP CHEMISTRY or HELP SEARCH > CHEMISTRY-SEARCH@ccl.net -- archive search | Gopher: gopher.ccl.net 70 > Ftp: ftp.ccl.net | WWW: http://www.ccl.net/chemistry/ | Jan: jkl@ccl.net > > > > > From chemistry-request@server.ccl.net Wed May 30 04:13:18 2001 Received: from melia.qut.edu.au ([131.181.127.2]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f4U8DFS27555 for ; Wed, 30 May 2001 04:13:16 -0400 Received: from tu02m2.qut.edu.au ([131.181.127.148]) by melia.qut.edu.au (PMDF V5.2-33 #40788) with ESMTP id <0GE5072BL2TU2O@melia.qut.edu.au> for chemistry@ccl.net; Wed, 30 May 2001 18:13:06 +1000 (EST) Received: by tu02m2.qut.edu.au id SAA1412660; Wed, 30 May 2001 18:12:55 +1000 (EST) Date: Wed, 30 May 2001 18:12:54 +1000 (EST) From: Sergio Manzetti Subject: MOPAC for WIndows To: chemistry@ccl.net Message-id: <991210374.3b14ab86b410b@email.qut.edu.au> MIME-version: 1.0 Content-type: text/plain; charset=ISO-8859-1 Content-transfer-encoding: 8bit User-Agent: IMP/PHP IMAP webmail program 2.2.3 X-IMP-User: n2618117 X-Originating-IP: 131.181.120.220 Hi all. How can I convert a *PDB file, or *mol file to a MOPAC input (*.mpn or *.dat) . Babel can outpu MOPAC internal and cartesian files, but are these the correct formats? I have tried but I get the same message for both formats (limit atom # exceeded, though I use 100 atoms, and the limit is documented on the website to be 150 atoms. Best Regards Sergio Sergio Manzetti Research Scholar Centre of Molecular Biotechnology/ Supercomputer Facility Queensland University of Technology 2 George St. BRISBANE 4000 QLD AUSTRALIA email: s.manzetti@student.qut.edu.au Tlf: +61 7 3864 1434 Tlf2:+61 7 3864 1185 www: http://www.life.sci.qut.edu.au/html/research/cmgenetics.html www2: http://www.its.qut.edu.au/hpc/ From chemistry-request@server.ccl.net Wed May 30 06:49:39 2001 Received: from oc30.uni-paderborn.de ([131.234.240.90]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f4UAncS22241 for ; Wed, 30 May 2001 06:49:38 -0400 Received: from localhost (cpilger@localhost) by oc30.uni-paderborn.de (SGI-8.9.3/8.9.3) with ESMTP id OAA71896; Wed, 30 May 2001 14:23:30 +0200 (CEST) Date: Wed, 30 May 2001 14:23:30 +0200 From: Christian Pilger To: amber@heimdal.compchem.ucsf.edu cc: chemistry@ccl.net Subject: summary: titratable amino acids and counter ions Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi all, earlier this week I asked some questions about the preparation of protein structures prior to MD simulations with respect to the treatment of titrable residues and the placement of counter ions. I would like to thank Michal Otyepka, Malcolm Gillies, Deepak Singh, Rick Venable, Mike Ford, and Kenward Vaughan for their kind responses. As I received some requests for a summary, I send it to the lists. Cheers, Christian == response #1 == > From otyepka@aix.upol.cz Wed May 30 14:11:20 2001 Date: Mon, 28 May 2001 13:52:43 +0200 (DFT) From: Michal Otyepka To: Christian Pilger Subject: Re: titratable amino acids and counter ions Dear Mr. Pilger: > while preparing a protein structure as input for MD simulations, I > encountered the following points, which I would like to ask your advice: > > - How do you usually deal with titratable residues (GLU, ASP, LYS, ARG) ? > Are all of them simply taken in their ionized forms ? Would it be good > to try to rationalize the ionization states of these residues by > manually inspecting their environment ? Which methods/rules of thumb are > available for the estimation of these ionization states ? program GRID written by Peter Goodford (Molecular Discovery Limited) can help you > - In case the net charge is neutralized by counter ions: how and where > should these be positioned ? Should one counter ion be placed directly > at each titratable residue (i.e. number of counter ions = number of > ioniziable residues) or should counter ions be placed (arbitrarily ?) > around the protein structure (i.e. number counter ions = net charge of > the whole system) ? You can use GRID or Grasp. The counter ions are placed to the their positions to compensate electric field of a protein. Whole systen has to be neutralised by counter ions. The surface titratable residues behave obviously as free aminoacids (it is not rule!). I think that some people around Mr. McCammon and Mr. Cieplak develop methods to compute pKa of titrable aminoacids but I am not sure. With best regards, Michal Otyepka == response #2 == > From malcolm@kemi.dtu.dk Wed May 30 14:11:28 2001 Date: Mon, 28 May 2001 14:03:38 +0200 From: Malcolm Gillies To: Christian Pilger Subject: Re: CCL:titratable amino acids and counter ions Dear Christian, > - How do you usually deal with titratable residues (GLU, ASP, LYS, ARG) ? > Are all of them simply taken in their ionized forms ? Would it be good > to try to rationalize the ionization states of these residues by > manually inspecting their environment ? Which methods/rules of thumb are > available for the estimation of these ionization states ? I prepared a couple of slides on this topic for a talk a few years ago. You might like to look at them: http://wwwcmc.pharm.uu.nl/gillies/aio/ The bottom line is that there are no perfect solutions, but that a bit of common sense, and in some cases the application of continuum electrostatics calculations, can result in a much more reasonable model. cheers, Malcolm -- == response #3 == > From mndoci@yahoo.com Wed May 30 14:11:42 2001 Date: Mon, 28 May 2001 08:52:41 -0700 (PDT) From: Deepak To: Christian Pilger Subject: Re: CCL:titratable amino acids and counter ions Dear Dr. Pilger Those are very valid questions and I suspect different people will have different answers. The best solution is some experimental evidence pointing to the protonation states of such residues. In the absence of experimental evidence, I personally like to examine the local environment of each residue. Counterions are best used to neutralize a on-neutral protein. Althouth the isoelectric point gives you a decent handle on gross protein properties, it is the local pKa that governs the protonation state of titratable groups. In doubt, I have actually performed calculations using both both protonation states and examining the differences and trying to reconcile them with any known observations. There are of cousre, methods to try and calculate the protonation states but I do not trust them yet. Hope this helps Regards Deepak == response #4 == > From rvenable@gandalf.cber.nih.gov Wed May 30 14:11:50 2001 Date: Mon, 28 May 2001 13:45:12 -0400 From: Rick Venable To: Christian Pilger Subject: Re: CCL:titratable amino acids and counter ions On Mon, 28 May 2001, Christian Pilger wrote: > while preparing a protein structure as input for MD simulations, I > encountered the following points, which I would like to ask your advice: > > - How do you usually deal with titratable residues (GLU, ASP, LYS, ARG) ? > Are all of them simply taken in their ionized forms ? Would it be good > to try to rationalize the ionization states of these residues by > manually inspecting their environment ? Which methods/rules of thumb are > available for the estimation of these ionization states ? It might be worth considering (or calculating) burial, e.g. accessible surface area, for GLU, ASP, LYS, ARG; the rule of thumb for these 4 is that they are typically charged. HIS residues can be a bigger problem, esp. for enzymes, because of the tautomerism in addition to the charge state. People have used computational methods to try to estimate the protonation state, esp. Poisson-Boltzman methods. I know there are some freely available progs for this, but I don't have refs handy. > - In my case the protein has an experimentally determined isoelectric > point of roughly pH=4.7. Does this mean, that the protein will have a > negative net charge at pH=7 ? Then, is there a method to correlate the > isoelectric point with this net charge ? And, are MD calculations > reasonable, when the net charge of the system differs from zero ? Yes, the net charge will be negative. There can be problems with a non-zero net charge for particle-mesh Ewald methods. > - In case the net charge is neutralized by counter ions: how and where > should these be positioned ? Should one counter ion be placed directly > at each titratable residue (i.e. number of counter ions = number of > ioniziable residues) or should counter ions be placed (arbitrarily ?) > around the protein structure (i.e. number counter ions = net charge of > the whole system) ? I don't think there's complete agreement about the best wat to get a net zero charged system, or how to place the ions. I use a method for randomly replacing water molecules more than 5 or 6 A away from any non-water molecule. Two common neutralizing approaches are: (1) just enough counterions for net zero charge, or (2) e.g. 0.1 M salt added to (1) to better model ionic strength. =+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+= Rick Venable 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 =+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+= == response #5 == > From mford@ccrc.uga.edu Wed May 30 14:11:57 2001 Date: Mon, 28 May 2001 13:57:53 -0400 From: Michael Ford To: Christian Pilger Subject: Placing counter ions We have found that it may be best to simply place the ions near their corresponding charged group then run 500-100ps and take the avg coordinates for the ion. The CION program, part of AMBER, is really designed for DNA and my give you a "salty" system with a bunch of Na and Cl ions. Mike Ford == response #6 == > From kaynjay@igalaxy.net Wed May 30 14:12:03 2001 Date: Mon, 28 May 2001 14:28:19 -0700 From: Kenward Vaughan To: Christian Pilger Subject: Re: titratable amino acids and counter ions On Mon, May 28, 2001 at 01:49:36PM +0200, Christian Pilger wrote: > Dear protein modelers, > > while preparing a protein structure as input for MD simulations, I > encountered the following points, which I would like to ask your advice: > > - How do you usually deal with titratable residues (GLU, ASP, LYS, ARG) ? > Are all of them simply taken in their ionized forms ? Would it be good > to try to rationalize the ionization states of these residues by > manually inspecting their environment ? Which methods/rules of thumb are > available for the estimation of these ionization states ? I have no experience with this in the field of MD,etc, but from a chemical perspective the side chains of residues (not the amino acids themselves) will behave like any other carboxylic acid or amine. With the vast bulk of those having pKa's and pKb's in the range of 4-5 (the amines being related to pOH), it is totally reasonable to assume they are >99% ionized at neutral pH (pOH). If surrounded by others of similar behavior (bases-bases and acids-acids) the expected effect of multiple ionizations becoming less and less likely makes sense, but as the strength of electrostatic attractions follow the inverse-square law I cannot guess how important this effect is. Unless there are several within say.. 5 or 6 angstroms, it may not make a lot of difference on the % ionization. But this is speculation on my part. > - In my case the protein has an experimentally determined isoelectric > point of roughly pH=4.7. Does this mean, that the protein will have a > negative net charge at pH=7 ? Then, is there a method to correlate the > isoelectric point with this net charge ? And, are MD calculations > reasonable, when the net charge of the system differs from zero ? Yes to the negative at pH 7 question. Don't know about the 2nd one. And an "I would certainly hope so!" to the 3rd. :-) > - In case the net charge is neutralized by counter ions: how and where > should these be positioned ? Should one counter ion be placed directly > at each titratable residue (i.e. number of counter ions = number of > ioniziable residues) or should counter ions be placed (arbitrarily ?) > around the protein structure (i.e. number counter ions = net charge of > the whole system) ? Beyond my experience, sorry. I would guess place them arbitrarily and let them settle into place. > Any comments are highly appreciated. ... Hope this helps! Kenward Vaughan From chemistry-request@server.ccl.net Wed May 30 06:09:20 2001 Received: from melia.qut.edu.au ([131.181.127.2]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f4UA9GS20319 for ; Wed, 30 May 2001 06:09:17 -0400 Received: from tu02m2.qut.edu.au ([131.181.127.148]) by melia.qut.edu.au (PMDF V5.2-33 #40788) with ESMTP id <0GE50766Z80ODP@melia.qut.edu.au> for chemistry@ccl.net; Wed, 30 May 2001 20:05:13 +1000 (EST) Received: by tu02m2.qut.edu.au id UAA1416798; Wed, 30 May 2001 20:05:02 +1000 (EST) Date: Wed, 30 May 2001 20:05:01 +1000 (EST) From: Sergio Manzetti Subject: SWISS PDB Viewr and it's PDB file format To: chemistry@ccl.net Message-id: <991217101.3b14c5cdce2a8@email.qut.edu.au> MIME-version: 1.0 Content-type: text/plain; charset=ISO-8859-1 Content-transfer-encoding: 8bit User-Agent: IMP/PHP IMAP webmail program 2.2.3 X-IMP-User: n2618117 X-Originating-IP: 131.181.24.49 Dear colleagues, I have noticed that the PDB files saved in SWISS PDB Viewer are not recognized by MOLSCRIPT nor MOLMOL, CN3d, or AUTODOCK. I am attempting to dock in AUTODOCK but since the conventional INSIGHT/SYBYL packages are too expensive for us, I am trying to find an alternative way of writing these molecules.. Do any of you have knowledge of a Protein Viewer that can open a PDB file from SWISS PDB Viewer and write it properly? Best Regards Sergio Sergio Manzetti Research Scholar Centre of Molecular Biotechnology/ Supercomputer Facility Queensland University of Technology 2 George St. BRISBANE 4000 QLD AUSTRALIA email: s.manzetti@student.qut.edu.au Tlf: +61 7 3864 1434 Tlf2:+61 7 3864 1185 www: http://www.life.sci.qut.edu.au/html/research/cmgenetics.html www2: http://www.its.qut.edu.au/hpc/ From chemistry-request@server.ccl.net Wed May 30 08:08:52 2001 Received: from mailserver.unimi.it ([159.149.10.1]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f4UC8qS24619 for ; Wed, 30 May 2001 08:08:52 -0400 Received: from vega (vega.farma.unimi.it [159.149.79.32]) by mailserver.unimi.it (8.9.3/8.9.3) with SMTP id OAA27927; Wed, 30 May 2001 14:08:43 +0200 (MET DST) Message-ID: <010101c0e901$3732f760$204f959f@farma.unimi.it.farma.unimi.it> From: "Giulio Vistoli" To: "Sergio Manzetti" , References: <991210374.3b14ab86b410b@email.qut.edu.au> Subject: Re: CCL:MOPAC for WIndows Date: Wed, 30 May 2001 14:08:19 +0200 Organization: Ist. Chimica Farmaceutica 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 Dear Sergio Manzetti, Our program VEGA is able to translate files *.pdb and *.mol (and several other file formats) in *.dat files for MOPAC. Moreover VEGA can insert in dat file the correct keyword, calculating the total charge. Not only but VEGA is also able to reconvert the *.arc files(output from MOPAC) in several formats, including pdb and mol. To download VEGA, please point our browser to http://users.unimi.it/~ddl/ Best regards Giulio Vistoli -- Dr. Giulio Vistoli Ist. di Chimica Farmaceutica e Tossicologica Viale Abruzzi, 42 I-20131 Milano (Italy) Tel. +39-02-29502230 Fax +39-02-29514197 E-Mail: giulio.vistoli@unimi.it WWW: http://users.unimi.it/~ddl From chemistry-request@server.ccl.net Wed May 30 09:58:22 2001 Received: from vytautas.vdu.lt ([193.219.38.33]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f4UDwH500925 for ; Wed, 30 May 2001 09:58:19 -0400 Received: from vaidila.vdu.lt ([193.219.38.52] ident=root) by vytautas.vdu.lt with esmtp id 1557Hz-0006pf-00; Wed, 30 May 2001 16:49:35 +0200 Received: from vejas.vdu.lt (vejas.vdu.lt [193.219.38.82]) by vaidila.vdu.lt (8.9.3/8.9.3) with ESMTP id QAA16158; Wed, 30 May 2001 16:50:04 +0200 (GMT) Date: Wed, 30 May 2001 04:46:33 +0200 From: a3arzi X-Mailer: The Bat! (v1.44) UNREG / CD5BF9353B3B7091 Reply-To: "Art'" X-Priority: 3 (Normal) Message-ID: <43203709316.20010530044633@vaidila.vdu.lt> To: Sergio Manzetti CC: chemistry@ccl.net Subject: Re: CCL:SWISS PDB Viewr and it's PDB file format In-reply-To: <991217101.3b14c5cdce2a8@email.qut.edu.au> References: <991217101.3b14c5cdce2a8@email.qut.edu.au> Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Hi, Try WebLab Viewer from MSI... ----------------------------> SM> Dear colleagues, I have noticed that the PDB files saved in SWISS PDB Viewer are SM> not recognized by MOLSCRIPT nor MOLMOL, CN3d, or AUTODOCK. SM> I am attempting to dock in AUTODOCK but since the conventional INSIGHT/SYBYL SM> packages are too expensive for us, I am trying to find an alternative way of SM> writing these molecules.. Do any of you have knowledge of a Protein Viewer that SM> can open a PDB file from SWISS PDB Viewer and write it properly? <--------------------------- good day Arturas From chemistry-request@server.ccl.net Wed May 30 11:16:24 2001 Received: from yendor.qf.uab.es (root@[158.109.14.59]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f4UFGN504486 for ; Wed, 30 May 2001 11:16:23 -0400 Received: from klingon.uab.es (escr@localhost [127.0.0.1]) by yendor.qf.uab.es (8.9.3/8.9.3) with ESMTP id RAA00873 for ; Wed, 30 May 2001 17:08:26 +0200 Sender: escr@yendor.qf.uab.es Message-ID: <3B150CEA.2FBA5774@klingon.uab.es> Date: Wed, 30 May 2001 17:08:26 +0200 From: congresill bertran X-Mailer: Mozilla 4.73 [en] (X11; I; Linux 2.2.7 i686) X-Accept-Language: en MIME-Version: 1.0 To: chemistry@ccl.net Subject: 01.09.30 ESCR conference in Barcelona Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit The International Symposium Electronic Structure and Chemical Reactivity (ESCR) in honor to Prof. Juan Bertran, will be held at the campus of the Universitat Autonoma of Barcelona from September 19 to 22, 2001. The scientific program will consist of 20 plenary talks and two poster sessions. The list of invited speakers that have confirmed their participation is: - Juan Andres (Castello, Spain) - Evert J. Baerends (Amsterdam, Netherlands) - Joseph J. Dannenberg (New York, USA) - Odile Eisenstein (Montpellier, France) - Gernot Frenking (Marburg, Germany) - James T. Hynes (Paris, France) - Yves Jean (Orsay, France) - William H. Miller (Berkeley, USA) - Otilia Mo (Madrid, Spain) - Keiji Morokuma (Emory, USA) - Santiago Olivella (Barcelona, Spain) - Jean-Louis Rivail (Nancy, France) - Michael Robb (London, UK) - Enrique Sanchez-Marcos (Sevilla, Spain) - Tomas Sordo (Oviedo, Spain) - Jiri Sponer (Prague, Czech Republic) - Jacopo Tomasi (Pisa, Italy) - Donald G. Truhlar (Minneapolis, USA) - Arieh Warshel (Los Angeles, USA) - Tomas Ziegler (Calgary, Canada) Further information can be collected from the website: http://klingon.uab.es/escr From chemistry-request@server.ccl.net Wed May 30 11:17:45 2001 Received: from femail13.sdc1.sfba.home.com ([24.0.95.140]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f4UFHi504525 for ; Wed, 30 May 2001 11:17:44 -0400 Received: from C1353359A ([65.4.172.51]) by femail13.sdc1.sfba.home.com (InterMail vM.4.01.03.20 201-229-121-120-20010223) with SMTP id <20010530160907.REWK1515.femail13.sdc1.sfba.home.com@C1353359A>; Wed, 30 May 2001 09:09:07 -0700 Message-ID: <002b01c0e921$8209d950$33ac0441@sttln1.wa.home.com> From: "Mark A. Thompson" To: "Novak Igor" , References: Subject: Re: CCL:UVCD software Date: Wed, 30 May 2001 08:59:28 -0700 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 5.00.3018.1300 X-MimeOLE: Produced By Microsoft MimeOLE V5.00.3018.1300 Dear Dr. Novak, ArgusLab will calculate UV/vis spectra and rotary strength using the ZINDO method. http://www.planaria-software.com/ Sincerely, Mark Thompson ------------------------------------------------------------------------- home page: http://members.home.net/markt158/ ----- Original Message ----- From: "Novak Igor" To: Sent: Wednesday, May 23, 2001 5:10 PM Subject: CCL:UVCD software > Dear netters, > I would be grateful if someone can suggest to me the software (freeware or > commercial) > which predict the UVCD spectra of a given molecule. > Many thanks!! > > Yours sincerely > > I.Novak > Dept.of Chemistry > National University of Singapore > Singapore 117543 > > chmigorn@nus.edu.sg > > > > -= This is automatically added to each message by mailing script =- > CHEMISTRY@ccl.net -- To Everybody | CHEMISTRY-REQUEST@ccl.net -- To Admins > MAILSERV@ccl.net -- HELP CHEMISTRY or HELP SEARCH > CHEMISTRY-SEARCH@ccl.net -- archive search | Gopher: gopher.ccl.net 70 > Ftp: ftp.ccl.net | WWW: http://www.ccl.net/chemistry/ | Jan: jkl@ccl.net > > > > > From chemistry-request@server.ccl.net Wed May 30 13:36:42 2001 Received: from tibre.ujf-grenoble.fr ([193.54.238.31]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f4UHaf507798 for ; Wed, 30 May 2001 13:36:42 -0400 Received: from volga.ujf-grenoble.fr (volga.ujf-grenoble.fr [152.77.6.1]) by tibre.ujf-grenoble.fr (Pro-8.9.3/8.9.3/Configured by AD & JE 25/10/1999) with ESMTP id TAA11571 for ; Wed, 30 May 2001 19:36:36 +0200 (MET DST) Received: from ujf-grenoble.fr (cahn.ujf-grenoble.fr [152.77.209.147]) by volga.ujf-grenoble.fr (8.9.3/8.8.5) with ESMTP id TAA14314 for ; Wed, 30 May 2001 19:35:23 +0200 (MET DST) Sender: Pierre.Antoine@ujf-grenoble.fr Message-ID: <3B153017.F0AA203B@ujf-grenoble.fr> Date: Wed, 30 May 2001 19:38:31 +0200 From: Antoine FORTUNE X-Mailer: Mozilla 4.77 [fr] (X11; U; Linux 2.2.19-4.1mdk i686) X-Accept-Language: fr-FR, en MIME-Version: 1.0 To: CCL Subject: Autodock3 / mol2topdbq : error Content-Type: multipart/alternative; boundary="------------EF0BA1A6DF350BCD23E6784E" --------------EF0BA1A6DF350BCD23E6784E Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Hi All, Trying to convert a macro.mol2 file to macro.pdbqs file with mol2topdbqs script, i always get that error message : awk: cmd. line:77: fatal: expression for `<' redirection has null string value It comes from mol2fftopdbq script. I used sybyl to prepare the macro.mol2 file, deleting all unknown atoms, water and ions (Cl-) and adding "Essential_only" hydrogens and assigning "KOLL UNI" partial charges. Thank's for any help, Antoine -- o----------------------------------------o Antoine FORTUNE Ingenieur Modelisation Moleculaire Dept. Pharmacologie Moleculaire - UMR 5063 Universite Joseph Fourier Faculte de Pharmacie 38706 LA TRONCHE - FRANCE Tel: 04 76 63 71 40 Fax: 04 76 51 86 67 e-mail: Antoine.Fortune@ujf-grenoble.fr o---------------------------------------o --------------EF0BA1A6DF350BCD23E6784E Content-Type: text/html; charset=us-ascii Content-Transfer-Encoding: 7bit Hi All,

Trying to convert a macro.mol2 file to macro.pdbqs file with mol2topdbqs script, i always get that error message :

awk: cmd. line:77: fatal: expression for `<' redirection has null string value

It comes from mol2fftopdbq script.  I used sybyl to prepare the macro.mol2 file, deleting all unknown atoms, water and ions (Cl-) and adding "Essential_only" hydrogens and assigning "KOLL UNI" partial charges.

Thank's for any help,
Antoine
  

-- 
o----------------------------------------o
Antoine FORTUNE

Ingenieur Modelisation Moleculaire
Dept. Pharmacologie Moleculaire - UMR 5063
Universite Joseph Fourier

Faculte de Pharmacie
38706 LA TRONCHE  - FRANCE

Tel: 04 76 63 71 40   Fax: 04 76 51 86 67
e-mail: Antoine.Fortune@ujf-grenoble.fr
o---------------------------------------o
  --------------EF0BA1A6DF350BCD23E6784E-- From chemistry-request@server.ccl.net Wed May 30 14:35:05 2001 Received: from pxq76.iq.ufrj.br (root@[146.164.6.76]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f4UIYw509415 for ; Wed, 30 May 2001 14:35:03 -0400 Received: from localhost (localhost [[UNIX: localhost]]) by pxq76.iq.ufrj.br (8.9.3/8.9.3/SuSE Linux 8.9.3-0.1) id CAA02012 for chemistry@ccl.net; Wed, 9 Aug 2000 02:02:42 -0300 From: Daniel Lopes Bhering Reply-To: bhering@iq.ufrj.br Organization: LARHCO-IQ-UFRJ To: chemistry@ccl.net Subject: Trasition Metals NMR shifts Date: Wed, 9 Aug 2000 01:57:59 -0300 X-Mailer: KMail [version 1.0.28] Content-Type: text/plain References: <4.3.0.20010102121419.00b70530@service2.area.fi.cnr.it> In-Reply-To: <4.3.0.20010102121419.00b70530@service2.area.fi.cnr.it> MIME-Version: 1.0 Message-Id: <00080902024200.01945@pxq76> Content-Transfer-Encoding: 8bit Dear CCLs: I would like to get some references of ab initio NMR calculations in organometals compounds. Does anyone can help me? Thanks in advance, Daniel Bhering From chemistry-request@server.ccl.net Wed May 30 15:20:52 2001 Received: from hope.edu ([198.110.98.17]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f4UJKq510498 for ; Wed, 30 May 2001 15:20:52 -0400 Received: from [198.110.101.2] (polik@hope.edu); Wed, 30 May 2001 15:20:39 -0400 X-WM-Posted-At: hope.edu; Wed, 30 May 01 15:20:39 -0400 Message-Id: <5.0.2.1.2.20010530151114.0456aec0@webmail.hope.edu> X-Sender: polik@webmail.hope.edu X-Mailer: QUALCOMM Windows Eudora Version 5.0.2 Date: Wed, 30 May 2001 15:19:49 -0400 To: chemistry@ccl.net From: "William F. Polik" Subject: WebMO 3.0: WWW-based interface to Gaussian, GAMESS, MOPAC Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii"; format=flowed WebMO and WebMO Pro version 3.0 have been officially released and are available for download at the WebMO website. A tour of screenshots, a working demo server, and download information can be found at http://www.webmo.net WebMO is a FREE web-based interface to popular computational chemistry programs including Gaussian, MOPAC, and GAMESS. WebMO permits users to build 3-D molecular structures, submit multiple jobs, monitor job progress, and view text and graphical results all from within a standard web-browser. WebMO has a very fast learning curve for novices, yet offers total control over every job for experts. Features new to WebMO version 3.0 include: * Updated WebMO Editor featuring - Better support for large molecules - Free translation/rotation of selected fragments - Duplication of selected fragments - Built-in fragment library - Enhanced toolbar * Updated daemon to support multiple simultaneous running jobs * Fragment manager to extend built-in fragment library * Folder-based job organization system * Support for MOPAC 2000 * Automatic bond creation during import of existing jobs * Various interface improvements and bug fixes WebMO Pro is a commercial add-on to the freeware WebMO computational chemistry package. WebMO Pro features a variety of powerful enhancements that are suitable for serious education, commercial, or research-level users. In addition to all of the WebMO features, WebMO Pro adds the following: * Support for multiple remote computational servers * Visualization of molecular orbitals (Windows/PC clients only) * Improved job organization with unlimited user-customizable folders * Creation of spreadsheet summaries to compare results from multiple jobs * Individual user job calculation templates Information on features, purchasing, and pricing of WebMO Pro can be found at http://www.webmo.net/pro For a complete list of features, system requirements, screenshots, a working demo, download information, installation and upgrade instructions, general support information, and curriculum usage examples, visit the WebMO homepage at http://www.webmo.net Enjoy! The WebMO Team From chemistry-request@server.ccl.net Wed May 30 21:50:19 2001 Received: from melia.qut.edu.au ([131.181.127.2]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f4V1oH520196 for ; Wed, 30 May 2001 21:50:17 -0400 Received: from tu02m2.qut.edu.au ([131.181.127.148]) by melia.qut.edu.au (PMDF V5.2-33 #40788) with ESMTP id <0GE6083JKF6MIJ@melia.qut.edu.au> for chemistry@ccl.net; Thu, 31 May 2001 11:37:34 +1000 (EST) Received: by tu02m2.qut.edu.au id LAA1439292; Thu, 31 May 2001 11:37:23 +1000 (EST) Date: Thu, 31 May 2001 11:37:23 +1000 (EST) From: Sergio Manzetti Subject: PDB file structure To: chemistry@ccl.net Message-id: <991273043.3b15a0533ec3b@email.qut.edu.au> MIME-version: 1.0 Content-type: text/plain; charset=ISO-8859-1 Content-transfer-encoding: 8bit User-Agent: IMP/PHP IMAP webmail program 2.2.3 X-IMP-User: n2618117 X-Originating-IP: 131.181.120.220 Hi everyone. I have recently understood that many Protein programs don't understand a PDB file with only the ATOM and CONECT records. I am attempting to dock ligands to a modelled molecule that unfurtunately is not accepted by the software (AUTODOCK). Do you have knowledge to which other records are relevant for such procedures? Best Regards Sergio Sergio Manzetti Research Scholar Centre of Molecular Biotechnology/ Supercomputer Facility Queensland University of Technology 2 George St. BRISBANE 4000 QLD AUSTRALIA email: s.manzetti@student.qut.edu.au Tlf: +61 7 3864 1434 Tlf2:+61 7 3864 1185 www: http://www.life.sci.qut.edu.au/html/research/cmgenetics.html www2: http://www.its.qut.edu.au/hpc/ From chemistry-request@server.ccl.net Wed May 30 22:52:55 2001 Received: from ivory.trentu.ca ([192.75.12.103]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f4V2qt521985 for ; Wed, 30 May 2001 22:52:55 -0400 Received: from trentu.ca ([204.225.13.50]) by trentu.ca (PMDF V5.2-32 #37862) with ESMTP id <01K46WWLDE0Q0009N3@trentu.ca> for chemistry@ccl.net; Wed, 30 May 2001 22:52:31 EDT Date: Wed, 30 May 2001 22:58:29 -0400 From: elewars Subject: GAUSSIAN QUESTION-BONDORDER To: chemistry@ccl.net Message-id: <3B15B355.A3FED3A4@trentu.ca> MIME-version: 1.0 X-Mailer: Mozilla 4.7 [en] (WinNT; I) Content-type: text/plain; charset=us-ascii Content-transfer-encoding: 7bit X-Accept-Language: en 2001 May 30 Hello, Gaussian 98 has several options for atomic charges, but appears to offer very little for bond orders. Preferred over Mulliken bond orders nowadays are some based on less arbitrary schemes, like Meyer bond orders and Lowdin bond orders (AIM is too slow for routine use). A quick calculation of such bond orders at e.g. the HF/3-21G level can be useful. ?Has anyone being able to get G98 to print out a Meyer or Lowdin *bond order matrix*, i.e. C 1 C 2 H3 ...... C 1 3.9421 C 2 1.0378 3.9421 H 3 0.0025 0.9953 0.4322 ..... Thanks E. Lewars =====