From owner-chemistry@ccl.net Fri Jan 4 03:24:00 2008 From: "Michel Petitjean ptitjean(a)itodys.jussieu.fr" To: CCL Subject: CCL: how to calculate electronic interaction energy Message-Id: <-35978-080104031407-20507-XoD/hx10ws1Pgm8iiiAYnw!^!server.ccl.net> X-Original-From: Michel Petitjean Date: Fri, 4 Jan 2008 09:13:52 +0100 (MET) Sent to CCL by: Michel Petitjean [ptitjean**itodys.jussieu.fr] To: chemistry-,-ccl.net Subject: CCL: Re: how to calculate electronic interaction energy Dear Thomas, Assuming that you produce atomic coordinates in a mol2 or pdb or hyperchem file, the freeware RADI2 can help you for 1 and 3: it computes the smallest size and the diameter (largest size), and the area of the convex hull of the atomic centers. You can download RADI2 from: http://petitjeanmichel.free.fr/itoweb.petitjean.freeware.html#RADI Best wishes, Michel Petitjean, DSV/iBiTec-S/SB2SM (CNRS URA 2096) CEA Saclay, bat. 528 91191 Gif-sur-Yvette Cedex Phone: +33(0)1 6908 9681 / Fax: +33(0)1 6908 4007 E-mail: petitjean-,-itodys.jussieu.fr, michel.petitjean-,-cea.fr http://petitjeanmichel.free.fr/itoweb.petitjean.html Formerly: ITODYS (CNRS, UMR 7086), 1 rue Guy de la Brosse, 75005 Paris, France. > Sent to CCL by: "Thomas Joe" [alabarae*_*yahoo.com] > I would like to calculate these following parameters > 1. Molecular Planarity (area/depth2 ratio) > 2. Electronic Interaction Energy (difference between E homo and E Lomo) > 3. length/ Width ratio. > > how to do this. > I have referred some papers from CMC. But I don,t have the tools to calcualte those parameters. > Your kind help is deeply appreciated. >Thomas From owner-chemistry@ccl.net Fri Jan 4 08:59:00 2008 From: "Naser Eltaher Eltayeb nasertaha90|-|yahoo.co.uk" To: CCL Subject: CCL:G: Error on ZINDO on G03 "Missing ZINDO/S parameters " Message-Id: <-35979-080104084735-14350-Lxe+Zo4vUtScjk8dhjAMZg.:.server.ccl.net> X-Original-From: "Naser Eltaher Eltayeb" Date: Fri, 4 Jan 2008 08:47:32 -0500 Sent to CCL by: "Naser Eltaher Eltayeb" [nasertaha90-x-yahoo.co.uk] Dear All I am trying to calculate energy using ZINDO in Gaussian 03 for manganese complex with schiff base , this complex contain chloride ion attched to Mn atom, I get the message below, could anyone help me. Thank you " Warning! Cl atom 2 may be hypervalent but has no d functions. Do NDO integrals. One-electron integrals computed using PRISM. Generate ZINDO/S integrals. Missing ZINDO/S parameters for atomic number 17. Error termination via Lnk1e in C:\G03W\l302.exe at Fri Jan 04 21:39:44 2008. Job cpu time: 0 days 0 hours 0 minutes 3.0 seconds. File lengths (MBytes): RWF= 11 Int= 0 D2E= 0 Chk= 1 Scr= 1" From owner-chemistry@ccl.net Fri Jan 4 14:13:01 2008 From: "Sean O Brien sobrien{=}cylenepharma.com" To: CCL Subject: CCL: Contactos: a program for analysis of docking results Message-Id: <-35980-080103210357-28031-GaIM8TwCsOSlI1D7R9orkw::server.ccl.net> X-Original-From: "Sean O'Brien" Content-class: urn:content-classes:message Content-Type: multipart/mixed; boundary="----_=_NextPart_001_01C84E71.9E4B42A4" Date: Thu, 3 Jan 2008 17:32:07 -0800 MIME-Version: 1.0 Sent to CCL by: "Sean O'Brien" [sobrien||cylenepharma.com] This is a multi-part message in MIME format. ------_=_NextPart_001_01C84E71.9E4B42A4 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Analysis of ligand binding modes using complementary fingerprint = approaches is outlined in this paper: =20 J Mol Graph Model: 2005 Dec 24(3):186-94 "Computational Tools for the analysis and visualization of multiple = protein-ligand complexes", O'Brien SE, Brown DG, Mills JE, Phillips C, = Morris G =20 http://www.sciencedirect.com/science?_ob=3DArticleURL&_udi=3DB6TGP-4H4T13= Y-3&_user=3D10&_rdoc=3D1&_fmt=3D&_orig=3Dsearch&_sort=3Dd&view=3Dc&_acct=3D= C000050221&_version=3D1&_urlVersion=3D0&_userid=3D10&md5=3Df9060b7c6f7584= e1036aec8bc5618c52 ________________________________ > From: Mikko Huhtala mhuhtala . abo.fi [mailto:owner-chemistry]_[ccl.net] Sent: Thu 1/3/2008 2:31 PM To: Sean O'Brien Subject: CCL: Contactos: a program for analysis of docking results Sent to CCL by: "Mikko Huhtala" [mhuhtala[-]abo.fi] We needed a tool to cluster a set of small-molecule docking results for = which RMSD did not work very well as a measure of similarity. I ended up = writing a small, 530-line Python program named Contactos. It calculates = similarity values based on ligand -- protein contacts, which are = independent of the superposition and conformation of the docked = solutions. The program can also calculate similarities between different = molecules docked to one receptor. Contactos produces a matrix of = similarity values, which can be used to cluster the docking results = using an external clustering tool, such as MCL by Stijn van Dongen. = Contactos itself does not include clustering. Both Contactos and MCL are = distributed under the GPL license. Read more and download at http://web.abo.fi/~mhuhtala/contactos.html Mikko Huhtala -=3D This is automatically added to each message by the mailing script = =3D-http://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtml= =20Search Messages: http://www.ccl.net/htdig (login: ccl, Password: = search)http://www.ccl.net/spammers.txt------_=_NextPart_001_01C84E71.9E4B42A4-- From owner-chemistry@ccl.net Fri Jan 4 14:47:00 2008 From: "John Stone johns*ks.uiuc.edu" To: CCL Subject: CCL: Grid file formats Message-Id: <-35981-080104142510-30197-5ntI5CsinuADGjqzj/Ti/Q-$-server.ccl.net> X-Original-From: John Stone Content-Disposition: inline Content-Type: text/plain; charset=us-ascii Date: Fri, 4 Jan 2008 12:55:47 -0600 Mime-Version: 1.0 Sent to CCL by: John Stone [johns(~)ks.uiuc.edu] Hi, This may or may not be useful to you, but there are various visualization-oriented formats such as the one used by OpenDX. VMD will read the subset of the OpenDX format used by tools like APBS and others, and can display isosurfaces, field lines, slice planes, and so on. The VMD dxplugin documentation page has some more notes on this: http://www.ks.uiuc.edu/Research/vmd/plugins/molfile/dxplugin.html The VMD plugin source is licensed under the UIUC Open Source license, so you can grab the code for the DX plugin if you like. Hope that helps. Cheers, John Stone vmd ~~ ks.uiuc.edu On Fri, Dec 21, 2007 at 07:08:19PM -0500, Joe Leonard jleonard42^-^gmail.com wrote: > Folks, are there simple, standard file formats for storing/ > transmitting rectilinear gridded data (i.e. something that can be > isosurfaced)? I'm familiar with a few Xray formats, but I'd rather > use something simpler. I'd also like to use things other programs > can read rather than thinking up yet another format - one for binary > data and one for ascii. Something to hold the tic marks and data... > > Pointers welcome! Thanks in advance! > > Joe Leonard > jleonard42!A!gmail.com > > -- > I remember one Christmas morning > A winters light and a distant choir > And the peal of a bell and that Christmas Tree smell > And their eyes full of tinsel and fire > > -- Greg Lake > > > -- NIH Resource for Macromolecular Modeling and Bioinformatics Beckman Institute for Advanced Science and Technology University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801 Email: johns ~~ ks.uiuc.edu Phone: 217-244-3349 WWW: http://www.ks.uiuc.edu/~johns/ Fax: 217-244-6078 From owner-chemistry@ccl.net Fri Jan 4 16:01:01 2008 From: "Praveen Kumar Shrivastava praveenshrivastav[]gmail.com" To: CCL Subject: CCL: Software to Create Schematic Diagram Message-Id: <-35982-080103005120-6361-eJX8e3k/uaMacvxBZLCB/g*o*server.ccl.net> X-Original-From: "Praveen Kumar Shrivastava" Content-Type: multipart/alternative; boundary="----=_Part_13890_23596177.1199335949175" Date: Wed, 2 Jan 2008 20:52:29 -0800 MIME-Version: 1.0 Sent to CCL by: "Praveen Kumar Shrivastava" [praveenshrivastav .. gmail.com] ------=_Part_13890_23596177.1199335949175 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Content-Disposition: inline Dear Deepangi could you pleas send me reference or copy or nature article by email thanks praveen On Dec 31, 2007 2:17 PM, Deepangi Pandit deepangi.pandit .. gmail.com < owner-chemistry_._ccl.net> wrote: > Hi: > I find schematic diagrams/figures published in Nature Reviews of Drug > Discovery(and similar publications) informative and useful. However, I do > not know how could I create my own schematic diagrams to explain biological > interactions like protein-ligand interactions, neurotransmitter interaction > etc. I would like to know which commercial or free software could be used > for these purposes. > > Thank you. > Deepangi > ------=_Part_13890_23596177.1199335949175 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Content-Disposition: inline
Dear Deepangi
could you pleas send me reference or copy or nature article by email
thanks
praveen

On Dec 31, 2007 2:17 PM, Deepangi Pandit deepangi.pandit .. gmail.com <owner-chemistry_._ccl.net> wrote:
Hi:
I find schematic diagrams/figures published in Nature Reviews of Drug Discovery(and similar publications) informative and useful. However, I do not know how could I create my own  schematic diagrams to explain biological interactions like protein-ligand interactions, neurotransmitter interaction etc. I would like to know which commercial or free software could be used for these purposes.
 
Thank you.
Deepangi

------=_Part_13890_23596177.1199335949175-- From owner-chemistry@ccl.net Fri Jan 4 16:37:01 2008 From: "Michael K. Gilson gilson::umbi.umd.edu" To: CCL Subject: CCL: Continuous Symmetry Measures Message-Id: <-35983-080104163514-415-FZMx+Dlyw4Wie/JMqjjZWw~!~server.ccl.net> X-Original-From: "Michael K. Gilson" Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Fri, 04 Jan 2008 16:05:51 -0500 MIME-Version: 1.0 Sent to CCL by: "Michael K. Gilson" [gilson_._umbi.umd.edu] Dear Inbal, Although I can envision practical applications of continuous symmetry measures, I would caution against using such measures in place of symmetry numbers in statistical thermodynamics and thermochemistry. The symmetry number is used to correct for overcounting of configurations (classically) or states (quantum mechanically), and hence is necessarily integer. Regards, Mike Inbal Tuvi-Arad inbaltu*openu.ac.il wrote: > Sent to CCL by: "Inbal Tuvi-Arad" [inbaltu]^[openu.ac.il] > > Dear CCL Subscribers, > > I would like to inform you about a new website I have recently developed > in collaboration with Prof. David Avnir, the Institute of Chemistry, at > the Hebrew University: > > "CoSyM - Continuous symmetry measures": > http://telem.openu.ac.il/symmetry/csm. > > > The Website provides tools for calculating continuous symmetry measures > online for any molecule given in pdb format, and uses Jmol for > three-dimensional visualization. Answers to questions like: > * How far is a given molecule from having rotational symmetry? > * By how much is one molecule more chiral than the other? > * How much of perfect tetrahedricity is there in a distorted > tetrahedron? > as well as many other related questions can be answered by these tools. > > A number, on a scale from zero to 100, describes the distance of a given > structure from perfect symmetry; or how much chirality it contains; or > to what extent it resembles a polyhedron. The approach to all of these > questions is based on the same general principle. That general principle > is translated into a computational method for measuring the degree of > symmetry point groups, from which several additional specific important > measures are derived: > * Measuring the degree of the basic symmetry elements > * Measuring the degree of polyhedral shape content > * Measuring the degree of chirality > > This website can be used by both researchers, teachers and students, and > is part of an undergraduate course for chemistry students at the Open > University of Israel. > > I would be very grateful for any feedback, suggestions or comments > regarding the Website. > > Sincerely, > Inbal > > __________________________________________ > Dr. Inbal Tuvi-Arad > Department of Natural Sciences > The Open University of Israel > 108 Ravutski St., POB 808, > Raanana, 43107, Israel > Tel: 972-9-778-1773 > Fax: 972-9-778-0661 > Email: inbaltu+/-openu.ac.il > __________________________________________ > > > > -=his is automatically added to each message by the mailing script =-> > > -- Michael K. Gilson, M.D., Ph.D. CARB Fellow and Professor Center for Advanced Research in Biotechnology University of Maryland Biotechnology Institute 9600 Gudelsky Drive Rockville, MD 20850 Voice: 240-314-6217 Fax: 240-314-6255 gilsonumbi.umd.edu Lab Page: gilsonlab.umbi.umd.edu BindingDB: www.bindingdb.org From owner-chemistry@ccl.net Fri Jan 4 18:11:01 2008 From: "Igor Filippov Contr igorf()helix.nih.gov" To: CCL Subject: CCL: Software to Create Schematic Diagram Message-Id: <-35984-080104173650-4434-ARmof1Uer7tYW3WEbq6v/g()server.ccl.net> X-Original-From: "Igor Filippov [Contr]" Content-Transfer-Encoding: 7bit Content-Type: text/plain Date: Fri, 04 Jan 2008 17:04:23 -0500 Mime-Version: 1.0 Sent to CCL by: "Igor Filippov [Contr]" [igorf{=}helix.nih.gov] Not sure if this is the kind of diagrams you are talking about here but I find Kivio to be useful for flowchart drawing. http://www.koffice.org/kivio/ Igor On Mon, 2007-12-31 at 17:17 -0500, Deepangi Pandit deepangi.pandit .. gmail.com wrote: > Hi: > I find schematic diagrams/figures published in Nature Reviews of Drug > Discovery(and similar publications) informative and useful. However, I > do not know how could I create my own schematic diagrams to explain > biological interactions like protein-ligand interactions, > neurotransmitter interaction etc. I would like to know which > commercial or free software could be used for these purposes. > > Thank you. > Deepangi From owner-chemistry@ccl.net Fri Jan 4 20:49:01 2008 From: "Deepangi Pandit deepangi.pandit ~~ gmail.com" To: CCL Subject: CCL: Software to Create Biochemical Schematic Diagram Message-Id: <-35985-080104204400-7493-I0K0chKeLNzqgwms3dArRQ*|*server.ccl.net> X-Original-From: "Deepangi Pandit" Content-Disposition: inline Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1 Date: Fri, 4 Jan 2008 20:43:26 -0500 MIME-Version: 1.0 Sent to CCL by: "Deepangi Pandit" [deepangi.pandit|-|gmail.com] Let me rephrase my question, I am looking for freely available software to draw cartoons of protein-ligand interactions and other cellular structures ... something like BioDraw Ultra 11.0. http://www.cambridgesoft.com/software/BioDraw/ Thank you. Deepangi On 1/2/08, Praveen Kumar Shrivastava praveenshrivastav[]gmail.com wrote: > > > On Dec 31, 2007 2:17 PM, Deepangi Pandit deepangi.pandit .. gmail.com > wrote: > > > > Hi: > > I find schematic diagrams/figures published in Nature Reviews of Drug > Discovery(and similar publications) informative and useful. However, I do > not know how could I create my own schematic diagrams to explain biological > interactions like protein-ligand interactions, neurotransmitter interaction > etc. I would like to know which commercial or free software could be used > for these purposes. > > > > Thank you. > > Deepangi > > -- - Deepangi