From owner-chemistry@ccl.net Sun Jan 6 06:11:01 2008 From: "Inbal Tuvi-Arad inbaltu+*+openu.ac.il" To: CCL Subject: CCL: AW: Continuous Symmetry Measures Message-Id: <-35991-080106060912-1885-yRXYU5JebpNCIX28qZrMBw]*[server.ccl.net> X-Original-From: "Inbal Tuvi-Arad" Content-class: urn:content-classes:message Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset="iso-8859-1" Date: Sun, 6 Jan 2008 13:09:46 +0200 MIME-Version: 1.0 Sent to CCL by: "Inbal Tuvi-Arad" [inbaltu**openu.ac.il] Hello, References to the literature are embedded within the Website - see the = references section under "theoretical background". =20 You may also want to check out David Avnir's list of publication on this = topic: http://chem.ch.huji.ac.il/employee/avnir/p_symmetry.html. =20 Calculations can be done online, for free.=20 I'm familiar with the "Brute force symmetry analyzer", though I never = tested it. =20 To the best of my understanding, our website contains more=20 calculation options (e.g., the distance of a structure from a particular = polyhedron). Sincerely, Inbal -----Original Message----- > From: owner-chemistry*ccl.net [mailto:owner-chemistry*ccl.net]=20 Sent: Saturday, January 05, 2008 1:00 AM To: Inbal Tuvi-Arad Subject: CCL: AW: Continuous Symmetry Measures Sent to CCL by: "joerg.wegner" [joerg.wegner]=3Deb.de] Inbal, can you please elaborate/point to 1. literature references or algorithm details? 2. algorithm availability? And do you know the "Brute force symmetry analyzer" algorithm C++: http://www.cobalt.chem.ucalgary.ca/ps/symmetry Java: http://www.koders.com/java/fid3CBF6CC1049E6930598D271C7F210404C36BB507.as= px Kind regards, Joerg Kurt Wegner > -----Urspr=FCngliche Nachricht----- > Von: owner-chemistry+joerg.wegner=3D=3Dweb.de:+:ccl.net [mailto:owner- > chemistry+joerg.wegner=3D=3Dweb.de:+:ccl.net] Im Auftrag von Inbal = Tuvi-Arad > inbaltu * openu.ac.il > Gesendet: Donnerstag, 3. Januar 2008 20:38 > An: Wegner, Joerg Kurt=20 > Betreff: CCL: Continuous Symmetry Measures >=20 >=20 > Sent to CCL by: "Inbal Tuvi-Arad" [inbaltu()openu.ac.il] > Dear Michel, > Thank you for your comments. Your paper looks interesting and I'll = be > happy to read it. > Best wishes, > Inbal >=20 > -----Original Message----- > > From: owner-chemistry|*|ccl.net [mailto:owner-chemistry|*|ccl.net] > Sent: Thursday, January 03, 2008 5:33 PM > To: Inbal Tuvi-Arad > Subject: CCL: Continuous Symmetry Measures >=20 >=20 >=20 > Sent to CCL by: Michel Petitjean [ptitjean _ itodys.jussieu.fr] > To: chemistry~!~ccl.net > Subject: CCL: Re: Continuous Symmetry Measures >=20 > Dear Inbal, >=20 > There are very few programs able to compute symmetry/chirality = measures: > thank you very much for having put yours runnable via your web page. > The history of symmetry and chirality measures is summarized in my = open > access paper > in Entropy 2003, 5(3), 271-312 > (http://www.mdpi.org/entropy/papers/e5030271.pdf) > and my freeware QCM may be downloaded from: > http://petitjeanmichel.free.fr/itoweb.petitjean.freeware.html#QCM > (computes both the degree of chirality and the degree of direct > symmetry). >=20 > Best regards, >=20 > 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: "Inbal Tuvi-Arad" [inbaltu]^[openu.ac.il] >=20 > Dear CCL Subscribers, >=20 > 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: >=20 > "CoSyM - Continuous symmetry measures": > http://telem.openu.ac.il/symmetry/csm. >=20 >=20 > 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:=3D20 > * 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.=3D20 >=20 > 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 >=20 > 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. >=20 > I would be very grateful for any feedback, suggestions or comments > regarding the Website. >=20 > Sincerely, > Inbal >=20 > __________________________________________ > Dr. Inbal Tuvi-Arad > Department of Natural Sciences > The Open University of Israel > 108 Ravutski St., POB 808,=3D20 > Raanana, 43107, Israel > Tel: 972-9-778-1773=3D20 > Fax: 972-9-778-0661 > Email: inbaltu+/-openu.ac.il > __________________________________________ >=20 >=20 >=20 > -=3D This is automatically added to each message by the mailing script = =3D-Job: > http://www.ccl.net/jobs>=20 >=20 > -=3Dhis is automatically added to each message by the mailing script = =3D > To recover the email address of the author of the message, please = change> > > > > > Conferences: = http://server.ccl.net/chemistry/announcements/conferences/ >=20 > Search Messages: http://www.ccl.net/htdig (login: ccl, Password: = search) > >=20 -=3Dhis is automatically added to each message by the mailing script =3Dhttp://www.ccl.net/cgi-bin/ccl/send_ccl_messageSubscribe/Unsubscribe:=20Job: http://www.ccl.net/jobs=20Search Messages: http://www.ccl.net/htdig (login: ccl, Password: = search)http://www.ccl.net/spammers.txt From owner-chemistry@ccl.net Sun Jan 6 09:03:00 2008 From: "izwan zainurul zainurulizwan80 .. yahoo.com" To: CCL Subject: CCL: Binding energy Message-Id: <-35992-080106060238-1446-qlnzTn4N7Ks43B6psRskfw[#]server.ccl.net> X-Original-From: izwan zainurul Content-Transfer-Encoding: 8bit Content-Type: multipart/alternative; boundary="0-987041444-1199613749=:21973" Date: Sun, 6 Jan 2008 02:02:29 -0800 (PST) MIME-Version: 1.0 Sent to CCL by: izwan zainurul [zainurulizwan80-$-yahoo.com] --0-987041444-1199613749=:21973 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit Hai All, I want to calculate binding energy for complex using Hyperchem. In order to calculate binding energy we should know energy of guest and host in complex? How to get energy of guest and host? for MM+ methods. Thanks in advanced. Besh Wishes, -izwan --------------------------------- Be a better friend, newshound, and know-it-all with Yahoo! Mobile. Try it now. --0-987041444-1199613749=:21973 Content-Type: text/html; charset=iso-8859-1 Content-Transfer-Encoding: 8bit
Hai All,
I want to calculate binding energy for complex using Hyperchem. In order to calculate binding energy we should know energy of guest and host in complex? How to get energy of guest and host? for MM+ methods. Thanks in advanced.
 
Besh Wishes,
-izwan
 

Be a better friend, newshound, and know-it-all with Yahoo! Mobile. Try it now. --0-987041444-1199613749=:21973-- From owner-chemistry@ccl.net Sun Jan 6 09:38:01 2008 From: "Subramani Kullagounder dr.subramanik(a)gmail.com" To: CCL Subject: CCL: gOpenMol: Average structure Message-Id: <-35993-080106092114-14834-Lde0Ek0IJ9YKJN6fhRcipw+*+server.ccl.net> X-Original-From: "Subramani Kullagounder" Date: Sun, 6 Jan 2008 09:21:10 -0500 Sent to CCL by: "Subramani Kullagounder" [dr.subramanik{:}gmail.com] Hi all Could any body please point me out to a tutorial or help me with brief steps to calculate "average structure" for a set of 20 protein derivatives (Varying R, for a constant Residue), all optimised at the ab initio level using gOpenMol or MOLDEN. I am able to read the outputs, but unable to calculate average structure of the Residue. Many Thanks and best regards Subramani From owner-chemistry@ccl.net Sun Jan 6 10:26:01 2008 From: "Alimet Sema Ozen semaozen^^sabanciuniv.edu" To: CCL Subject: CCL:G: Question on the definition of the solvent in PCM Message-Id: <-35994-080106092412-16138-xWYC+K4Jj3yW7JW3WRfmHQ*o*server.ccl.net> X-Original-From: Alimet Sema Ozen Content-Disposition: inline Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-9; DelSp="Yes"; format="flowed" Date: Sun, 6 Jan 2008 15:16:06 +0200 MIME-Version: 1.0 Sent to CCL by: Alimet Sema Ozen [semaozen*sabanciuniv.edu] Dear members of CCL, I would like to examine the properties of some molecules in o-dichlorobenzene using Gaussian 03. Since o-dichlorobenzene is not one of the standard solvents of the PCM method, I picked chlorobenzene as the closest relative and modified the properties of that solvent by introducing the EPS and RSOLV parameters of o-dichlorobenzene. Are there any further modifications or parameter changes that you can suggest? What is the best way of defining o-dichlorobenzene as solvent in Gaussian? Thanks in advance... Best Regards and Happy 2008! Alimet From owner-chemistry@ccl.net Sun Jan 6 22:18:00 2008 From: "=?gb2312?B?Y2Ns?= ccl:_:mail.sioc.ac.cn" To: CCL Subject: CCL: =?gb2312?B?UmVsZWFzZSBub3RlIG9mIFhMT0dQMw==?= Message-Id: <-35995-080106220558-9011-lAYADWMKX57yRq13EUle9A]_[server.ccl.net> X-Original-From: "=?gb2312?B?Y2Ns?=" Content-Type: Multipart/Alternative; boundary="Boundary-=_WgBAuTZvkiikwYwGkWupCipXVHdV" Date: Mon, 7 Jan 2008 10:33:35 +0800 (CST) MIME-Version: 1.0 Sent to CCL by: "=?gb2312?B?Y2Ns?=" [ccl%x%mail.sioc.ac.cn] --Boundary-=_WgBAuTZvkiikwYwGkWupCipXVHdV Content-Type: text/plain; charset="gb2312" Content-Transfer-Encoding: base64 RGVhciBDQ0xlcnMsDQogDQpXZSBhbm5vdW5jZSB0aGUgcmVsZWFzZSBvZiB0aGUgbGF0ZXN0 IHZlcnNpb24gb2YgdGhlIFhMT0dQIHByb2dyYW0sIG5hbWVseSBYTE9HUDMuIFhMT0dQMyBj b21wdXRlcyBvY3Rhbm9sL3dhdGVyIHBhcnRpdGlvbiBjb2VmZmljaWVudHMgKGxvZ1ApIG9m IG9yZ2FuaWMgY29tcG91bmRzIGJ5IGNvbWJpbmluZyB0aGUgcG93ZXJzIG9mIGFuIGFkZGl0 aXZlIG1vZGVsIGFuZCBhIHNpbWlsYXJpdHktYmFzZWQgc3RyYXRlZ3kgKEouIENoZW0uIElu Zi4gTW9kZWwuIDIwMDcsIDQ3LCAyMTQwLTIxNDgpLiBJdCBkZW1vbnN0cmF0ZXMgbXVjaCBp bXByb3ZlZCBhY2N1cmFjeSBvdmVyIGl0cyBwcmV2aW91cyB2ZXJzaW9ucywgYW5kIGlzIGF0 IGxlYXN0IGNvbXBhcmFibGUgdG8gb3RoZXIgc3VjY2Vzc2Z1bCBsb2dQIG1ldGhvZHMgaW4g b3VyIHRlc3RzLg0KIA0KWExPR1AzIGlzIGF2YWlsYWJsZSBmb3IgZnJlZSB0byBkb3dubG9h ZCBmb3IgYWNhZGVtaWMgYW5kIGdvdmVybm1lbnRhbCB1c2Vycy4gV2UgcHJvdmlkZSBwcmUt Y29tcGlsZWQgZXhlY3V0YWJsZSBjb2RlcyBmb3IgVU5JWC9MSU5VWCBhbmQgV2luZG93cyBw bGF0Zm9ybXMuIE9uLWxpbmUgY29tcHV0aW5nIGJ5IFhMT0dQMyBpcyBwcm92aWRlZCB0byBh bGwgdXNlcnMgYXQgaHR0cDovL3d3dy5zaW9jLWNjYmcuYWMuY24vc29mdHdhcmUveGxvZ3Az Ly4gQSBkaXNjdXNzaW9uIGZvcnVtIGZvciBYTE9HUDMgaXMgcHJvdmlkZWQgYXQgaHR0cDov L3d3dy5zaW9jLWNjYmcuYWMuY24vZm9ydW0vLiBXZSB3ZWxjb21lIGFueSBmZWVkYmFjayBm cm9tIHlvdSEgDQoNCkJlc3QgcmVnYXJkcywNCiANClJlbnhpYW8gV2FuZywgUGguRC4NClBy b2Zlc3Nvcg0KU2hhbmdoYWkgSW5zdGl0dXRlIG9mIE9yZ2FuaWMgQ2hlbWlzdHJ5DQpDaGlu YSwgUC5SLg0KIA0KDQo= --Boundary-=_WgBAuTZvkiikwYwGkWupCipXVHdV Content-Type: text/html; charset="gb2312" Content-Transfer-Encoding: base64 PERJVj5EZWFyIENDTGVycyw8L0RJVj4NCjxESVY+Jm5ic3A7PC9ESVY+DQo8RElWPldlIGFu bm91bmNlIHRoZSByZWxlYXNlIG9mIHRoZSBsYXRlc3QgdmVyc2lvbiBvZiB0aGUgWExPR1Ag cHJvZ3JhbSwgbmFtZWx5IFhMT0dQMy4gWExPR1AzIGNvbXB1dGVzIG9jdGFub2wvd2F0ZXIg cGFydGl0aW9uIGNvZWZmaWNpZW50cyAobG9nUCkgb2Ygb3JnYW5pYyBjb21wb3VuZHMgYnkg Y29tYmluaW5nIHRoZSBwb3dlcnMgb2YgYW4gYWRkaXRpdmUgbW9kZWwgYW5kIGEgc2ltaWxh cml0eS1iYXNlZCBzdHJhdGVneSAoSi4gQ2hlbS4gSW5mLiBNb2RlbC4gMjAwNywgNDcsIDIx NDAtMjE0OCkuIEl0IGRlbW9uc3RyYXRlcyBtdWNoIGltcHJvdmVkIGFjY3VyYWN5IG92ZXIg aXRzIHByZXZpb3VzIHZlcnNpb25zLCBhbmQgaXMgYXQgbGVhc3QgY29tcGFyYWJsZSB0byBv dGhlciBzdWNjZXNzZnVsIGxvZ1AgbWV0aG9kcyBpbiBvdXIgdGVzdHMuPC9ESVY+DQo8RElW PiZuYnNwOzwvRElWPg0KPERJVj5YTE9HUDMgaXMgYXZhaWxhYmxlIGZvciBmcmVlIHRvIGRv d25sb2FkIGZvciBhY2FkZW1pYyBhbmQgZ292ZXJubWVudGFsIHVzZXJzLiBXZSBwcm92aWRl IHByZS1jb21waWxlZCBleGVjdXRhYmxlIGNvZGVzIGZvciBVTklYL0xJTlVYIGFuZCBXaW5k b3dzIHBsYXRmb3Jtcy4gT24tbGluZSBjb21wdXRpbmcgYnkgWExPR1AzIGlzIHByb3ZpZGVk IHRvIGFsbCB1c2VycyBhdCA8QSBocmVmPSJodHRwOi8vd3d3LnNpb2MtY2NiZy5hYy5jbi9z b2Z0d2FyZS94bG9ncDMvIj5odHRwOi8vd3d3LnNpb2MtY2NiZy5hYy5jbi9zb2Z0d2FyZS94 bG9ncDMvPC9BPi4gQSBkaXNjdXNzaW9uIGZvcnVtIGZvciBYTE9HUDMgaXMgcHJvdmlkZWQg YXQgPEEgaHJlZj0iaHR0cDovL3d3dy5zaW9jLWNjYmcuYWMuY24vZm9ydW0vIj5odHRwOi8v d3d3LnNpb2MtY2NiZy5hYy5jbi9mb3J1bS88L0E+LiBXZSB3ZWxjb21lIGFueSBmZWVkYmFj ayBmcm9tIHlvdSEgPC9ESVY+DQo8RElWPjxCUj5CZXN0IHJlZ2FyZHMsPC9ESVY+DQo8RElW PiZuYnNwOzwvRElWPg0KPERJVj5SZW54aWFvIFdhbmcsIFBoLkQuPEJSPlByb2Zlc3NvcjxC Uj5TaGFuZ2hhaSBJbnN0aXR1dGUgb2YgT3JnYW5pYyBDaGVtaXN0cnk8QlI+Q2hpbmEsIFAu Ui48QlI+PC9ESVY+IDxicj48IS0tIHVybGZpbGVzIC0tPjxicj48YnI+PCEtLSBmb290ZXIg LS0+PGJyPgoK --Boundary-=_WgBAuTZvkiikwYwGkWupCipXVHdV--