From owner-chemistry@ccl.net Thu Aug 19 08:14:01 2010 From: "Wendy Warr wendy . warr.com" To: CCL Subject: CCL: Report Message-Id: <-42564-100819080507-21142-rlFVhj5HFNWX/QapXKUYuA-,-server.ccl.net> X-Original-From: "Wendy Warr" Date: Thu, 19 Aug 2010 08:05:04 -0400 Sent to CCL by: "Wendy Warr" [wendy(!)warr.com] The 35th issue of our ACS report series is going to press. It has 40 transcripts of papers on: visual analysis of chemical data the future of chemical communication chemical entity extraction biochemical pathways and retrobiosynthesis, and finding synthetic methods plus six months' worth of news from about 70 companies. Contents list and order form at http://www.warr.com. Half price to academia and government. Dr. Wendy A. Warr Wendy Warr & Associates 6 Berwick Court, Holmes Chapel Cheshire, CW4 7HZ, England Tel./Fax +44 (0)1477 533837 wendy:-:warr.com http://www.warr.com From owner-chemistry@ccl.net Thu Aug 19 08:50:01 2010 From: "wangzc]-[iccas.ac.cn" To: CCL Subject: CCL: Spin density Message-Id: <-42565-100819031707-4893-aoybm8YKoraG/1IlD8zxMA||server.ccl.net> X-Original-From: wangzc^^^iccas.ac.cn Content-Type: multipart/alternative; boundary="----=_Part_191189_126736.1282202204302" Date: Thu, 19 Aug 2010 15:16:44 +0800 (CST) MIME-Version: 1.0 Sent to CCL by: wangzc,,iccas.ac.cn ------=_Part_191189_126736.1282202204302 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: base64 RGVhciBNb3VtaXRhLAoKIAoKICAgICAgUGxlYXNlIHVzZSBHViwgcmVhZCB0aGUgY2hrIG9yIGZj aGsgZmlsZSwgYW5kIHRoZW4gcmVzdWx0cy1zdXJmYWNlcwoKCgoKLS0tLS3ljp/lp4vpgq7ku7Yt LS0tLQrlj5Hku7bkuro6ICJNZXRoYWkgREMgbWRjY29tcGNoZW1eX15nbWFpbC5jb20iIDxvd25l ci1jaGVtaXN0cnlAY2NsLm5ldD4K5Y+R6YCB5pe26Ze0OiAyMDEw5bm0OOaciDE55pelIOaYn+ac n+WbmwrmlLbku7bkuro6ICJXYW5nLCBaaGUgQ2hlbiAtaWQjM3B5LSIgPHdhbmd6Y0BpY2Nhcy5h Yy5jbj4K5oqE6YCBOgrkuLvpopg6IENDTDogU3BpbiBkZW5zaXR5CgpEZWFyIEFsbCwKICAgSSBh bSBuZXcgaW4gdGhlIGZpZWxkIG9mIGNvbXB1dGF0aW9uYWwgY2hlbWlzdHJ5LiBTbyBwbGVhc2Ug aGVscCBtZSBpbiBmb2xsb3dpbmcgcmVnYXJkOiBIb3cgdG8gZ2VuZXJhdGUgU1BJTiBERU5TSVRZ IFBMT1Q/IElzIGl0IHBvc3NpYmxlIHRvIGdlbmVyYXRlIHVzaW5nIENoZW1jcmFmdD8gT3IgYW55 IGRpZmZlcmVudCBzb2Z0d2FyZSBpcyBuZWVkZWQ/IFdoYXQgaXMgdGhlIHByb2NlZHVyZT8KCk1h bnkgdGhhbmtzIGluIGFkdmFuY2UuCgpTaW5jZXJlbHksCk1vdW1pdGEKCg0KDQoKCg== ------=_Part_191189_126736.1282202204302 Content-Type: text/html; charset=UTF-8 Content-Transfer-Encoding: base64 PFA+RGVhciBNb3VtaXRhLDwvUD4KPFA+Jm5ic3A7PC9QPgo8UD4mbmJzcDsmbmJzcDsmbmJzcDsm bmJzcDsmbmJzcDsgUGxlYXNlIHVzZSBHViwgcmVhZCB0aGUgY2hrIG9yIGZjaGsgZmlsZSwgYW5k IHRoZW4gcmVzdWx0cy1zdXJmYWNlczxCUj48QlI+PEJSPjwvUD4KPEJMT0NLUVVPVEUgc3R5bGU9 IkJPUkRFUi1MRUZUOiAjYTBjNmU1IDJweCBzb2xpZDsgUEFERElORy1MRUZUOiA1cHg7IE1BUkdJ Ti1MRUZUOiA1cHg7IE1BUkdJTi1SSUdIVDogMHB4Ij4tLS0tLeWOn+Wni+mCruS7ti0tLS0tPEJS PjxCPuWPkeS7tuS6ujo8L0I+ICJNZXRoYWkgREMgbWRjY29tcGNoZW1eX15nbWFpbC5jb20iICZs dDtvd25lci1jaGVtaXN0cnlAY2NsLm5ldCZndDs8QlI+PEI+5Y+R6YCB5pe26Ze0OjwvQj4gMjAx MOW5tDjmnIgxOeaXpSDmmJ/mnJ/lm5s8QlI+PEI+5pS25Lu25Lq6OjwvQj4gIldhbmcsIFpoZSBD aGVuIC1pZCMzcHktIiAmbHQ7d2FuZ3pjQGljY2FzLmFjLmNuJmd0OzxCUj48Qj7mioTpgIE6PC9C PiA8QlI+PEI+5Li76aKYOjwvQj4gQ0NMOiBTcGluIGRlbnNpdHk8QlI+PEJSPkRlYXIgQWxsLDxC Uj4mbmJzcDsmbmJzcDsgSSBhbSBuZXcgaW4gdGhlIGZpZWxkIG9mIGNvbXB1dGF0aW9uYWwgY2hl bWlzdHJ5LiBTbyBwbGVhc2UgaGVscCBtZSBpbiBmb2xsb3dpbmcgcmVnYXJkOiBIb3cgdG8gZ2Vu ZXJhdGUgU1BJTiBERU5TSVRZIFBMT1Q/IElzIGl0IHBvc3NpYmxlIHRvIGdlbmVyYXRlIHVzaW5n IENoZW1jcmFmdD8gT3IgYW55IGRpZmZlcmVudCBzb2Z0d2FyZSBpcyBuZWVkZWQ/IFdoYXQgaXMg dGhlIHByb2NlZHVyZT88QlI+PEJSPk1hbnkgdGhhbmtzIGluIGFkdmFuY2UuPEJSPjxCUj5TaW5j ZXJlbHksPEJSPk1vdW1pdGE8QlI+PC9CTE9DS1FVT1RFPjxCUj48U1BBTj48L1NQQU4+PGJyPjxi cj4KCg== ------=_Part_191189_126736.1282202204302-- From owner-chemistry@ccl.net Thu Aug 19 09:27:01 2010 From: "Yi (Yves) Wang yves.wang*_*duke.edu" To: CCL Subject: CCL:G: NEDA Analysis with NBO keyword in Gaussian03 Message-Id: <-42566-100818152146-3559-0RTv1Dgtf/qJeL5CIAe0hA*server.ccl.net> X-Original-From: "Yi (Yves) Wang" Content-Type: multipart/alternative; boundary=Apple-Mail-6-1056896629 Date: Wed, 18 Aug 2010 15:21:30 -0400 Mime-Version: 1.0 (Apple Message framework v1081) Sent to CCL by: "Yi (Yves) Wang" [yves.wang*_*duke.edu] --Apple-Mail-6-1056896629 Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset=GB2312 Hi Nuno, NEDA is only possible with GAMESS. The Gaussian version of NBO 5.G will = simply ignore the NEDA keyword in your input file. Best, = __________________________________________________________________________= ___ Yi (Yves) Wang Department of Biochemistry Structural Biology & Biophysics Program Duke University BS: University of Science and Technology of China School of Life Sciences, National Laboratory for Physical Sciences at = Microscale Tel: +1-919-236-3307 (Cell) +1-919-684-0235 (Lab 1) +1-919-660-1634 (Lab 2) Office: A20 LSRC / 5301 FFSC E-Mail: yves.wang _ duke.edu Mail: Box 90317, Chemistry Department =D4=DA 2010-8-18=A3=AC=C9=CF=CE=E710:36=A3=AC Nuno A. G. Bandeira = nuno.bandeira]-[ist.utl.pt =D0=B4=B5=C0=A3=BA >=20 > Sent to CCL by: "Nuno A. G. Bandeira" [nuno.bandeira\a/ist.utl.pt] > Dear Sagarika, >=20 > The NBO manual states that NEDA is only available with the GAMESS = program after recompiling from the NBO source. >=20 > Best wishes, > Nuno >=20 > --=20 > Nuno A. G. Bandeira, AMRSC > Laboratoire de Chimie LR6 > Ecole Normale Superieure de Lyon > 46, Allee d'Italie > 69364 Lyon Cedex 07 - France > http://cqb.fc.ul.pt/intheochem/nuno/ > -- >=20 >=20 >=20 > -=3D This is automatically added to each message by the mailing script = =3D- > To recover the email address of the author of the message, please = change>=20>=20>=20=>=20>=20Conferences: = http://server.ccl.net/chemistry/announcements/conferences/ >=20>=20>=20>=20 >=20 --Apple-Mail-6-1056896629 Content-Transfer-Encoding: quoted-printable Content-Type: text/html; charset=GB2312 Hi = Nuno,

NEDA is only possible with GAMESS. The Gaussian = version of NBO 5.G will simply ignore the NEDA keyword in your input = file.

Best,


Yi (Yves) Wang
Department of Biochemistry
Structural Biology & Biophysics = Program
Duke = University
BS: University = of Science and Technology of China
   +1-919-660-1634 (Lab 2)
Office: A20 LSRC / 5301 = FFSC
Mail: Box 90317, Chemistry = Department

=D4=DA 2010-8-18=A3=AC=C9=CF=CE=E710:36=A3=AC Nuno A. G. = Bandeira nuno.bandeira]-[ist.utl.pt =D0=B4=B5=C0=A3=BA


Sent to CCL by: "Nuno A. G. Bandeira" = [nuno.bandeira\a/ist.utl.pt]
Dear Sagarika,

The NBO manual = states that NEDA is only available with the GAMESS program after = recompiling from the NBO source.

Best wishes,
Nuno

-- =
Nuno A. G. Bandeira, AMRSC
Laboratoire de Chimie LR6
Ecole = Normale Superieure de Lyon
46, Allee d'Italie
69364 Lyon Cedex 07 = - France
http://cqb.fc.ul.pt/intheoch= em/nuno/
--



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= --Apple-Mail-6-1056896629-- From owner-chemistry@ccl.net Thu Aug 19 16:20:00 2010 From: "Carlos Alberto Ortega Zu iga caoz96 a yahoo.es" To: CCL Subject: CCL: Usage of script prepare_ligand4.py in Red Hat Linux 5.3 Message-Id: <-42567-100819161658-12954-Mzko45kY7zYPeskfe0v3vw]![server.ccl.net> X-Original-From: "Carlos Alberto Ortega Zu iga" Date: Thu, 19 Aug 2010 16:16:55 -0400 Sent to CCL by: "Carlos Alberto Ortega Zu iga" [caoz96-$-yahoo.es] Dear CCL users, Is known advances in Virtual Screening strategies, I think that i only know a few of them, The reason of my message is: I would like use AutoDock Vina Program to Virtual Screening, with large number of molecules, but when i try use the script "prepare_ligand4.py" from MGL Tools to convert the molecules (mol2 to pdbqt) dont work, In windows this script works well, with the line: prepare_ligand4.py -l filename But in linux (i have Red Hat 5.3) this line dont work. Can help me with this? Maybe i dont know how is the usage of this script in linux. I am learning but is difficult to me. Thanks for your help and info! Carlos Alberto Ortega Zuiga