From owner-chemistry@ccl.net Mon Jul 10 01:51:01 2006 From: "andras.borosy/a\givaudan.com" To: CCL Subject: CCL: simulate lipid bilayers Message-Id: <-32094-060706131022-26096-+ZNCp63P/cMHP7ayn6iiqw|*|server.ccl.net> X-Original-From: andras.borosy%x%givaudan.com Content-Type: multipart/alternative; boundary="=_alternative 005963F5C12571A3_=" Date: Thu, 6 Jul 2006 18:16:22 +0200 MIME-Version: 1.0 Sent to CCL by: andras.borosy(_)givaudan.com This is a multipart message in MIME format. --=_alternative 005963F5C12571A3_= Content-Type: text/plain; charset="ISO-8859-2" Content-Transfer-Encoding: quoted-printable Dear Colleagues, I wish to simulate lipid bilayers containing small organic molecules.=20 Which software do I need for that? Regards, Andr=E1s --=_alternative 005963F5C12571A3_= Content-Type: text/html; charset="ISO-8859-2" Content-Transfer-Encoding: quoted-printable
Dear Colleagues,

I wish to simulate lipid bilayers co= ntaining small organic molecules. Which software do I need for that?

Regards,

Andr=E1s
--=_alternative 005963F5C12571A3_=-- From owner-chemistry@ccl.net Mon Jul 10 04:56:00 2006 From: "jitrayut jitonnom jitrayut.018]*[gmail.com" To: CCL Subject: CCL: ADL: peptide simulation before docking Message-Id: <-32095-060709053315-13096-0mjyulirf3Zh8W4yEwMbzA * server.ccl.net> X-Original-From: "jitrayut jitonnom" Content-Type: multipart/alternative; boundary="----=_Part_3197_23356421.1152437219388" Date: Sun, 9 Jul 2006 16:26:59 +0700 MIME-Version: 1.0 Sent to CCL by: "jitrayut jitonnom" [jitrayut.018#gmail.com] ------=_Part_3197_23356421.1152437219388 Content-Type: text/plain; charset=TIS-620; format=flowed Content-Transfer-Encoding: base64 Content-Disposition: inline SGkgZXZlcnlvbmUsCgpJIHRoaW5rIHRoYXQgYXV0b2RvY2sgdXN1YWxseSBkbyB3aGVuIHRoZSBs aWdhbmQgYW5kIGVuenltZSBmcm9tIHgtcmF5LCBidXQKc29tZXRpbWVzIGxpZ2FuZHMgYW5kIGVu enltZSBjYW4gYmUgY3JlYXRlZCBhbmQgb3B0aW1pemVkIHByaW9yIHRvCmRvY2tpbmcuIE1vc3Qg bGlnYW5kIHdpbGwgYmUgb3B0aW1pemVkIGJ5IGdhdXNzaWFuIG9yIG90aGVyIHByb2dyYW0KdG8g b2J0YWluIHRoZSBzdHJ1Y3R1cmUgYW5kIGNoYXJnZS4gQnV0IEkgd2FzIHdvbmRlcmluZyBpbiBj YXNlIG9mCmhlcHRhcGVwdGlkZSBzaG91bGQgSSBkbyBvcHRpbWl6ZSBieSBnYXVzc2lhbiBvciBv dGhlciBxdWFudHVtIHByb2dyYW0sIG9yCnNob3VsZCBJIGRvIHRoZSBtZCBzaW11bGF0aW9uIGJ5 IHByb3RlaW4gZm9yY2UgZmllbGQgcHJvZ3JhbSBsaWtlIGFtYmVyCixldGMuCgpDYW4gYW55b25l IGV4cGxhaW4gdGhpcyBwcm9ibGVtID8gc28gSSB3aWxsIHRoYW5rcyBhIGxvdC4KCkppdHJheXV0 CgoKLS0tLS0tLS0tLSBGb3J3YXJkZWQgbWVzc2FnZSAtLS0tLS0tLS0tCkZyb206IFBhdWwgV2ls aGVsbSBFbHNpbmdob3JzdCA8cGF1bEB1bmktYm9ubi5kZT4KRGF0ZTogOSChLqQuIDIwMDYsIDE1 OjE4ILkuClN1YmplY3Q6IFJlOiBBREw6IHBlcHRpZGUgc2ltdWxhdGlvbiBiZWZvcmUgZG9ja2lu ZwpUbzogaml0cmF5dXQgaml0b25ub20gPGppdHJheXV0LjAxOEBnbWFpbC5jb20+CgpIaSBndXlz LAoKCkkgcGljayB1cCB0aGlzIHF1ZXN0aW9uIGZvciBJIGhhZCBzaW1pbGFyIHRob3VnaHRzLiBV c2luZyBHQSBkb2NraW5nIEkKd2FzIHdvbmRlcmluZyBpZiBJIHdvdWxkIG5lZWQgZW5lcmd5IG1p bmltaXphdGlvbiBhdCBhbGwgcHJpb3IgdG8KZG9ja2luZy4gV2h5IG5vdCBqdXN0IHRha2UgYSB0 aGUgc3RyZXRjaGVkIG1vbGVjdWxlIChzbWFsbCBsaWdhbmQsCmhlcHRhcGVwdGlkZSwgZXRjLikg YW5kIGRvY2sgaXQuIEdhcyBwaGFzZSBlbmVyZ3kgbWluaW1pemF0aW9uIHNob3VsZApub3QgZ2l2 ZSByZXN1bHRzIGNsb3NlIHRvIHRoZSBlbnp5bWUgYmluZGluZyBtb2RlIGFuZCB0aHVzIHdvbid0 IHNwZWVkCnVwIHRoZSBkb2NraW5nIHByb2Nlc3MuCgoKV2hhdCBkbyBZb3UgdGhpbms/CgoKUGF1 bAo= ------=_Part_3197_23356421.1152437219388 Content-Type: text/html; charset=TIS-620 Content-Transfer-Encoding: base64 Content-Disposition: inline PGRpdj5IaSBldmVyeW9uZSw8L2Rpdj4KPGRpdj4mbmJzcDs8L2Rpdj4KPGRpdj5JIHRoaW5rIHRo YXQgYXV0b2RvY2smbmJzcDt1c3VhbGx5IGRvIHdoZW4gdGhlIGxpZ2FuZCBhbmQgZW56eW1lIGZy b20geC1yYXksIGJ1dCBzb21ldGltZXMmbmJzcDtsaWdhbmRzIGFuZCBlbnp5bWUmbmJzcDtjYW4g YmUgY3JlYXRlZCBhbmQgb3B0aW1pemVkIHByaW9yIHRvIGRvY2tpbmcuJm5ic3A7TW9zdCBsaWdh bmQgd2lsbCBiZSBvcHRpbWl6ZWQgYnkmbmJzcDtnYXVzc2lhbiZuYnNwO29yIG90aGVyIHByb2dy YW0gdG8mbmJzcDtvYnRhaW4gdGhlIHN0cnVjdHVyZSBhbmQgY2hhcmdlLiBCdXQmbmJzcDtJIHdh cyB3b25kZXJpbmcgaW4gY2FzZSBvZiBoZXB0YXBlcHRpZGUgc2hvdWxkIEkgZG8mbmJzcDtvcHRp bWl6ZSZuYnNwO2J5IGdhdXNzaWFuIG9yIG90aGVyIHF1YW50dW0gcHJvZ3JhbSwgb3Igc2hvdWxk IEkgZG8gdGhlIG1kIHNpbXVsYXRpb24gYnkgcHJvdGVpbiBmb3JjZSBmaWVsZCBwcm9ncmFtJm5i c3A7bGlrZSBhbWJlciAsZXRjLgo8L2Rpdj4KPGRpdj4mbmJzcDs8L2Rpdj4KPGRpdj5DYW4gYW55 b25lJm5ic3A7ZXhwbGFpbiB0aGlzIHByb2JsZW0gPyBzbyBJIHdpbGwgdGhhbmtzIGEgbG90Ljwv ZGl2Pgo8ZGl2PiZuYnNwOzwvZGl2Pgo8ZGl2PkppdHJheXV0PC9kaXY+CjxkaXY+Jm5ic3A7PGJy Pjxicj4tLS0tLS0tLS0tIEZvcndhcmRlZCBtZXNzYWdlIC0tLS0tLS0tLS08YnI+PHNwYW4gY2xh c3M9ImdtYWlsX3F1b3RlIj5Gcm9tOiA8YiBjbGFzcz0iZ21haWxfc2VuZGVybmFtZSI+UGF1bCBX aWxoZWxtIEVsc2luZ2hvcnN0PC9iPiAmbHQ7PGEgaHJlZj0ibWFpbHRvOnBhdWxAdW5pLWJvbm4u ZGUiPnBhdWxAdW5pLWJvbm4uZGU8L2E+Jmd0Ozxicj5EYXRlOiA5IAqhLqQuIDIwMDYsIDE1OjE4 ILkuPGJyPlN1YmplY3Q6IFJlOiBBREw6IHBlcHRpZGUgc2ltdWxhdGlvbiBiZWZvcmUgZG9ja2lu Zzxicj5Ubzogaml0cmF5dXQgaml0b25ub20gJmx0OzxhIGhyZWY9Im1haWx0bzpqaXRyYXl1dC4w MThAZ21haWwuY29tIj5qaXRyYXl1dC4wMThAZ21haWwuY29tPC9hPiZndDs8YnI+PGJyPjwvc3Bh bj5IaSBndXlzLDxicj48YnI+PGJyPkkgcGljayB1cCB0aGlzIHF1ZXN0aW9uIGZvciBJIGhhZCBz aW1pbGFyIHRob3VnaHRzLiBVc2luZyBHQSBkb2NraW5nIEkKPGJyPndhcyB3b25kZXJpbmcgaWYg SSB3b3VsZCBuZWVkIGVuZXJneSBtaW5pbWl6YXRpb24gYXQgYWxsIHByaW9yIHRvPGJyPmRvY2tp bmcuIFdoeSBub3QganVzdCB0YWtlIGEgdGhlIHN0cmV0Y2hlZCBtb2xlY3VsZSAoc21hbGwgbGln YW5kLDxicj5oZXB0YXBlcHRpZGUsIGV0Yy4pIGFuZCBkb2NrIGl0LiBHYXMgcGhhc2UgZW5lcmd5 IG1pbmltaXphdGlvbiBzaG91bGQ8YnI+bm90IGdpdmUgcmVzdWx0cyBjbG9zZSB0byB0aGUgZW56 eW1lIGJpbmRpbmcgbW9kZSBhbmQgdGh1cyB3b24ndCBzcGVlZAo8YnI+dXAgdGhlIGRvY2tpbmcg cHJvY2Vzcy48YnI+PGJyPjxicj5XaGF0IGRvIFlvdSB0aGluaz88YnI+PGJyPjxicj5QYXVsPGJy Pjxicj4mbmJzcDs8L2Rpdj4K ------=_Part_3197_23356421.1152437219388-- From owner-chemistry@ccl.net Mon Jul 10 20:19:00 2006 From: "Zhe Li lizhe3#%#mail.ustc.edu.cn" To: CCL Subject: CCL:G: How to calculate reaction rates without transition states? Message-Id: <-32096-060710094356-27122-i9OKTMeMop7+Q38KC5/xaA---server.ccl.net> X-Original-From: "Zhe Li" Date: Mon, 10 Jul 2006 09:43:51 -0400 Sent to CCL by: "Zhe Li" [lizhe3(0)mail.ustc.edu.cn] For example, a coordination reaction: PH3+Pd(PH3)->Pd(PH3)2, I can not find the transition state of this reaction, at least with Gaussian. Then how can I calculate the reaction rate? From owner-chemistry@ccl.net Mon Jul 10 20:54:00 2006 From: "Didier Rognan didier.rognan*pharma.u-strasbg.fr" To: CCL Subject: CCL: generating SMIRKS files Message-Id: <-32097-060710101020-30581-MER7+ERLzZINH5Lwsbh+gA-,-server.ccl.net> X-Original-From: Didier Rognan Content-Type: text/plain; charset="us-ascii"; format=flowed Date: Mon, 10 Jul 2006 15:31:23 +0200 Mime-Version: 1.0 Sent to CCL by: Didier Rognan [didier.rognan:-:pharma.u-strasbg.fr] Dear colleagues, Has anyone a free routine able to convert a MDL rxn file into SMIRKS ? Many thanks for your answer Kind regards ----------------------------------------------------------------------------------------------- Dr. Didier ROGNAN Directeur de Recherche CNRS UMR 7175-LC1 Institut Gilbert-Laustriat 74, route du Rhin, B.P.24 F-67401 Illkirch direct line: +33 (0)3 90 24 42 35 secretary: +33(0)3 90 24 42 20 fax: +33 (0)3 90 24 43 10 email: didier.rognan- -pharma.u-strasbg.fr www:http://bioinfo-pharma.u-strasbg.fr From owner-chemistry@ccl.net Mon Jul 10 21:29:01 2006 From: "Didier ROGNAN didier.rognan{}pharma.u-strasbg.fr" To: CCL Subject: CCL: RXN to SMIRKS Message-Id: <-32098-060710103209-1469-bAryKcaXWvkPKcgDcn2Q5w]=[server.ccl.net> X-Original-From: "Didier ROGNAN" Date: Mon, 10 Jul 2006 10:32:07 -0400 Sent to CCL by: "Didier ROGNAN" [didier.rognan(-)pharma.u-strasbg.fr] Dear colleagues, Has anyone a free routine able to convert a MDL rxn file into SMIRKS ? Many thanks for your answer Kind regards ----------------------------------------------------------------------------------------------- Dr. Didier ROGNAN Directeur de Recherche CNRS UMR 7175-LC1 Institut Gilbert-Laustriat 74, route du Rhin, B.P.24 F-67401 Illkirch direct line: +33 (0)3 90 24 42 35 secretary: +33(0)3 90 24 42 20 fax: +33 (0)3 90 24 43 10 email: didier.rognan|pharma.u-strasbg.fr www:http://bioinfo-pharma.u-strasbg.fr From owner-chemistry@ccl.net Mon Jul 10 22:04:00 2006 From: "Tapta K Roy ch05ph03-#-uohyd.ernet.in" To: CCL Subject: CCL: how to find out hybridization ? Message-Id: <-32099-060710021247-5628-uUisTt9BVjBRr6nQmwBD1g_-_server.ccl.net> X-Original-From: "Tapta K Roy" Date: Mon, 10 Jul 2006 02:12:45 -0400 Sent to CCL by: "Tapta K Roy" [ch05ph03%%uohyd.ernet.in] Dear friend. How to find out hybridization of an atom in a molecule by G-03. I have tried with pop=nbo keyword in a optimised structure by B3lyp method, but couldn't able to find out or calculate it from log file. Thank you for your help. Best regards, Tapta K Roy Hydrabad School of Chemistry India