From owner-chemistry@ccl.net Sat Jul 19 03:40:00 2008 From: "Utpal Sarkar utpalchemiitkgp. ~ .gmail.com" To: CCL Subject: CCL: Herman-Skillman Program Message-Id: <-37364-080718161208-2540-60meXA8KrFtopv+3HWiCbw ~ server.ccl.net> X-Original-From: "Utpal Sarkar" Content-Disposition: inline Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1 Date: Fri, 18 Jul 2008 21:09:10 +0200 MIME-Version: 1.0 Sent to CCL by: "Utpal Sarkar" [utpalchemiitkgp::gmail.com] Dear CCL Users, I am trying to use Herman-Skillman program for some atoms and ions. Is it possible to use Herman-Skillman code for ANIONs where the IONICITY is negative. I found in the net http://hermes.phys.uwm.edu/projects/elecstruct/hermsk/HS.InputInstruct.html that for Herman-Skilman code IONICITY must be positive or zero. Can anybody tell me whether Herman-Skilman code can usable for ANIONS? Thanking you With best regards Utpal Sarkar From owner-chemistry@ccl.net Sat Jul 19 11:16:01 2008 From: "Oellien, F (Frank) frank.oellien,+,sp.intervet.com" To: CCL Subject: CCL: 4. German Conference on Chemoinformatics - 2. Call for Papers Message-Id: <-37365-080718111105-16630-oB4mxsLHohZUVKDDCjYRGw^^^server.ccl.net> X-Original-From: "Oellien, F (Frank)" Content-class: urn:content-classes:message Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset="iso-8859-1" Date: Fri, 18 Jul 2008 16:31:12 +0200 MIME-Version: 1.0 Sent to CCL by: "Oellien, F (Frank)" [frank.oellien]*[sp.intervet.com] Second CALL FOR PAPERS 4th German Conference on Chemoinformatics Hotel 'Der Achtermann', Goslar, Germany 9 - 11 November 2008 Dear Colleagues, The CIC division of the German Chemical Society announces the 4. German = Conference on Chemoinformatics (http://www.gdch.de/gcc2008) to be held = in Goslar, Germany, November 9 - 11, 2008. We are inviting the submission of abstracts for talks and posters in the = following plenary sessions: * Chemoinformatics and Drug Development * Chemical Information * Molecular Modelling * Computational Material Science and Nanotechnology=20 and other highlights in the field of Computational Chemistry. We encourage the submission of papers on both applications and case = studies as well as on method development and algorithmic work.=20 Visit the conference website at www.gdch.de/gcc2008 for more = information, including a link to the online abstract submission = interface, a more detailed, downloadable PDF version of the 1. circular = as well as additional information. The deadline for the submission of abstracts is 29 July 2008. Invited Speakers are: J=FCrgen Bajorath, University of Bonn, D Michael Berthold, University of Konstanz , D=20 Marcus Elstner, University of Braunschweig, D=20 Robert Glen, Cambridge University, UK=20 Kurt Varmuza, Technical University of Vienna, A=20 Brian Vickery, Chemistry Central, London, UK Because of the strong increase of the number of attendees during the = last two conferences, we have to impose a limit for the number of = conference participants this year (200 max). So please register early. = The online registration is now open = (http://www.gdch.de/vas/tagungen/tg/5327/anmeld__e.htm). http://www.gdch.de/vas/tagungen/tg/circular1.pdf I hope to see you in Goslar. Frank Oellien, Conference Chairman ------------------=20 Dr. Frank Oellien BioChemInformatics Scientist Intervet Innovation GmbH Zur Propstei 55270 Schwabenheim, Germany =20 E-Mail: frank.oellien!^!sp.intervet.com Phone: +49 (6130) 948 365 Fax: +49 (6130) 948 517 Home http://www.intervet.com =20 Sitz der Gesellschaft: Schwabenheim Amtsgericht Mainz, HRB 23 166 = Gesch=E4ftsf=FChrer: Dr. Peter Schmid -------------------------------------- This message and any attachments are solely for the intended recipient. If you are not the intended recipient, disclosure, copying, use or distribution of the information included in this message is prohibited -- please immediately and permanently delete. -------------------------------------- From owner-chemistry@ccl.net Sat Jul 19 11:51:01 2008 From: "Subhash M Agarwal smagarwal-.-yahoo.com" To: CCL Subject: CCL: Corina or Open Babel Message-Id: <-37366-080719005625-4863-/ZnvYLLabE3Am2J1OfKvaA]~[server.ccl.net> X-Original-From: "Subhash M Agarwal" Date: Sat, 19 Jul 2008 00:56:21 -0400 Sent to CCL by: "Subhash M Agarwal" [smagarwal#,#yahoo.com] Hi Can anybody let me know firstly is there any difference between Open babel and Corina? Secondly, for docking studies large small molecule databases are used. Should one use CORINA or Open babel for converting 2D molecules to 3D molecules and why? Thanks Subhash M Agarwal From owner-chemistry@ccl.net Sat Jul 19 13:44:01 2008 From: "John McKelvey jmmckel],[gmail.com" To: CCL Subject: CCL: Corina or Open Babel Message-Id: <-37367-080719133308-3555-srxlf36j4ks5FWNxgT1EGA-x-server.ccl.net> X-Original-From: "John McKelvey" Content-Type: multipart/alternative; boundary="----=_Part_84464_25941243.1216488384811" Date: Sat, 19 Jul 2008 13:26:24 -0400 MIME-Version: 1.0 Sent to CCL by: "John McKelvey" [jmmckel|,|gmail.com] ------=_Part_84464_25941243.1216488384811 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Content-Disposition: inline It is not clear to me whether or not that O-B has been calibrated to the extent that CORINA has in creating 3D geometries. My $0.02 bet is that it has not, but I would be delighted to learn otherwise! John McKelvey On Sat, Jul 19, 2008 at 12:56 AM, Subhash M Agarwal smagarwal-.-yahoo.com < owner-chemistry..ccl.net> wrote: > > Sent to CCL by: "Subhash M Agarwal" [smagarwal#,#yahoo.com] > Hi > > Can anybody let me know firstly is there any difference between Open babel > and Corina? Secondly, for docking studies large small molecule databases are > used. Should one use CORINA or Open babel for converting 2D molecules to 3D > molecules and why? > > Thanks > Subhash M Agarwal> > > ------=_Part_84464_25941243.1216488384811 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Content-Disposition: inline
It is not clear to me whether or not that O-B has been calibrated to the extent that CORINA has in creating 3D geometries. My $0.02 bet is that it has not, but I would be delighted to learn otherwise!

John McKelvey 

On Sat, Jul 19, 2008 at 12:56 AM, Subhash M Agarwal smagarwal-.-yahoo.com <owner-chemistry..ccl.net> wrote:

Sent to CCL by: "Subhash M  Agarwal" [smagarwal#,#yahoo.com]
Hi

Can anybody let me know firstly is there any difference between Open babel and Corina? Secondly, for docking studies large small molecule databases are used. Should one use CORINA or Open babel for converting 2D molecules to 3D molecules and why?

Thanks
Subhash M Agarwal



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------=_Part_84464_25941243.1216488384811-- From owner-chemistry@ccl.net Sat Jul 19 22:09:00 2008 From: "nahren manuel meetnahren~!~yahoo.com" To: CCL Subject: CCL: Corina or Open Babel Message-Id: <-37368-080719215451-13835-V8IESCM5nmz4IKvw9Qi3Bw#server.ccl.net> X-Original-From: nahren manuel Content-Type: multipart/alternative; boundary="0-1717356037-1216515599=:72897" Date: Sat, 19 Jul 2008 17:59:59 -0700 (PDT) MIME-Version: 1.0 Sent to CCL by: nahren manuel [meetnahren*o*yahoo.com] --0-1717356037-1216515599=:72897 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable Dear Subhash, =A0 It does not matter. The thing is your starting structure should not be very= distorted. Your docking method will do the conformational exploration of t= he ligand on its own. So it does not matter what initial conformation you g= ive. all you got to worry is your benzene does not look like cyclohexane. =A0 But CORINA worked best for me, it may not for you. But try also Minimising = using MMFF /or other small molecules FF . TEST YOURSELF =A0 nahren --- On Sat, 7/19/08, Subhash M Agarwal smagarwal-.-yahoo.com wrote: > From: Subhash M Agarwal smagarwal-.-yahoo.com Subject: CCL: Corina or Open Babel To: "Mascarenhas, Nahren Manuel " Date: Saturday, July 19, 2008, 10:26 AM Sent to CCL by: "Subhash M Agarwal" [smagarwal#,#yahoo.com] Hi Can anybody let me know firstly is there any difference between Open babel = and Corina? Secondly, for docking studies large small molecule databases are us= ed. Should one use CORINA or Open babel for converting 2D molecules to 3D molec= ules and why? Thanks Subhash M Agarwal -=3D This is automatically added to each message by the mailing script =3D-http://www.ccl.net/cgi-bin/ccl/send_ccl_messageSubscribe/Unsubscribe:=20Job: http://www.ccl.net/jobs=20http://www.ccl.net/spammers.txt=0A=0A=0A --0-1717356037-1216515599=:72897 Content-Type: text/html; charset=us-ascii

Dear Subhash,

 

It does not matter. The thing is your starting structure should not be very distorted. Your docking method will do the conformational exploration of the ligand on its own. So it does not matter what initial conformation you give. all you got to worry is your benzene does not look like cyclohexane.

 

But CORINA worked best for me, it may not for you. But try also Minimising using MMFF /or other small molecules FF . TEST YOURSELF

 

nahren



--- On Sat, 7/19/08, Subhash M Agarwal smagarwal-.-yahoo.com <owner-chemistry]_[ccl.net> wrote:

From: Subhash M Agarwal smagarwal-.-yahoo.com <owner-chemistry]_[ccl.net>
Subject: CCL: Corina or Open Babel
To: "Mascarenhas, Nahren Manuel " <meetnahren]_[yahoo.com>
Date: Saturday, July 19, 2008, 10:26 AM

Sent to CCL by: "Subhash M  Agarwal" [smagarwal#,#yahoo.com]
Hi

Can anybody let me know firstly is there any difference between Open babel and
Corina? Secondly, for docking studies large small molecule databases are used.
Should one use CORINA or Open babel for converting 2D molecules to 3D molecules
and why?

Thanks
Subhash M Agarwalhttp://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt

--0-1717356037-1216515599=:72897-- From owner-chemistry@ccl.net Sat Jul 19 23:16:01 2008 From: "Geoffrey Hutchison geoffh+ .. pitt.edu" To: CCL Subject: CCL: Corina or Open Babel Message-Id: <-37369-080719231003-8704-FJWZI1aTdbEjVGPzaO0pJQ],[server.ccl.net> X-Original-From: Geoffrey Hutchison Content-transfer-encoding: 8bit Content-type: text/plain; charset=iso-8859-1 Date: Sat, 19 Jul 2008 23:09:50 -0400 (EDT) MIME-version: 1.0 Sent to CCL by: Geoffrey Hutchison [geoffh+_+_pitt.edu] > It is not clear to me whether or not that O-B has been calibrated to the > extent that CORINA has in creating 3D geometries. My $0.02 bet is that it > has not, but I would be delighted to learn otherwise! I don't know of anyone who's done a rigorous comparison of the 3D coordinates generated from Open Babel 2.2. Yet. Certainly it's easy to run MMFF94 minimization and conformer searching with Open Babel, so the resulting structures are probably fine. However, it also states pretty clearly in the version 2.2 release notes that 3D coordinate generation does not yet guarantee stereochemistry. To be honest, I wouldn't use it for docking from a SMILES string for this exact issue. Besides CORINA, I believe Open Eye's OMEGA has also received significant testing. (Last time I checked, there were a number of programs which could generate 3D coordinates. Since I don't do docking research, I'm not the best person to ask.) Cheers, -Geoff --- Prof. Geoffrey Hutchison Department of Chemistry University of Pittsburgh tel: (412) 648-0492 email: geoffh:pitt.edu web: http://hutchison.chem.pitt.edu/