From owner-chemistry@ccl.net Fri Apr 7 01:45:01 2006 From: "Senthil Kumar Natesan senthilkumar_natesan()bi.iiita.ac.in" To: CCL Subject: CCL: conversion of sdf to mol files(multiple) Message-Id: <-31447-060407014240-813-UGvWDV9SJ1P31XXZFt9JjA-x-server.ccl.net> X-Original-From: "Senthil Kumar Natesan" Date: Fri, 7 Apr 2006 01:42:35 -0400 Sent to CCL by: "Senthil Kumar Natesan" [senthilkumar_natesan*bi.iiita.ac.in] Dear Pals, I tried with the following command in open babel to convert multiple sdf file into individual new files, but end up with only single mol file. babel ligand.sdf new.mol -m Any help in this regard would be appreciated. sincerely, senthil kumar Natesan From owner-chemistry@ccl.net Fri Apr 7 02:52:00 2006 From: "Tamas Gunda tgunda2005{:}puma.unideb.hu" To: CCL Subject: CCL: conversion of sdf to mol files(multiple) Message-Id: <-31448-060407024801-28926-JPYcouHcfoDsO0iPV6jDKg++server.ccl.net> X-Original-From: "Tamas Gunda" Content-Transfer-Encoding: 7bit Content-Type: text/plain; format=flowed; charset="iso-8859-1"; reply-type=original Date: Fri, 7 Apr 2006 08:47:50 +0200 MIME-Version: 1.0 Sent to CCL by: "Tamas Gunda" [tgunda2005() puma.unideb.hu] Mol2Mol is capable to slice multiple molfiles (the reverse is also possible) Try http://web.interware.hu/frenzy/mol2mol/index.html Tamas E. Gunda ----- Original Message ----- > From: "Senthil Kumar Natesan senthilkumar_natesan()bi.iiita.ac.in" To: "Gunda, Tamas E " Sent: Friday, April 07, 2006 08:23 AM Subject: CCL: conversion of sdf to mol files(multiple) > Sent to CCL by: "Senthil Kumar Natesan" > [senthilkumar_natesan*bi.iiita.ac.in] > Dear Pals, > > I tried with the following command in open babel to convert multiple sdf > file into individual new files, but end up with only single mol file. > > babel ligand.sdf new.mol -m > > Any help in this regard would be appreciated. > > sincerely, > > senthil kumar Natesan> > > > From owner-chemistry@ccl.net Fri Apr 7 03:36:00 2006 From: "Jerome Pansanel j.pansanel=pansanel.net" To: CCL Subject: CCL: conversion of sdf to mol files(multiple) Message-Id: <-31449-060407033240-21104-2JdGlvhphhFByyZDIPJH4g^^^server.ccl.net> X-Original-From: Jerome Pansanel Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=ISO-8859-1 Date: Fri, 7 Apr 2006 09:32:33 +0200 MIME-Version: 1.0 Sent to CCL by: Jerome Pansanel [j.pansanel[#]pansanel.net] Hello, The command: babel -isdf input_file.sdf -omol -m works fine with OpenBabel 2.0 Regards, Jerome Pansanel Le Vendredi 07 Avril 2006 07:45, Senthil Kumar Natesan senthilkumar_natesan()bi.iiita.ac.in a écrit : > Sent to CCL by: "Senthil Kumar Natesan" > [senthilkumar_natesan*bi.iiita.ac.in] Dear Pals, > > I tried with the following command in open babel to convert multiple sdf > file into individual new files, but end up with only single mol file. > > babel ligand.sdf new.mol -m > > Any help in this regard would be appreciated. > > sincerely, > > senthil kumar Natesan > -------------------------------------------- Mail sent through IMP: http://horde.org/imp/ From owner-chemistry@ccl.net Fri Apr 7 04:58:00 2006 From: "makowskm/./chemia.uj.edu.pl" To: CCL Subject: CCL: TDDFT for Large Unsaturated pi-Systems Message-Id: <-31450-060407044720-19741-lky+hEg5/08k3IUVy/1BDw---server.ccl.net> X-Original-From: makowskm-*-chemia.uj.edu.pl Content-Transfer-Encoding: 8bit Content-Type: text/plain;charset=iso-8859-2 Date: Fri, 7 Apr 2006 10:47:06 +0200 (CEST) MIME-Version: 1.0 Sent to CCL by: makowskm::chemia.uj.edu.pl > Sent to CCL by: "Luca Bertini" [luca.bertini*o*istm.cnr.it] > > I'm refering to the paper by Maitra et al, JCP, 5932, 120, (2004). > > I'm not understant what you mean with implementation of TDDFT. I'm > thinking to > the standard RPA-TDDFT theory. > Very nice and insightful paper. Maybe a little bit of misunderstanding from my side referring to what you really claim. If you mean standard RPA-TDDFT I just agree with you. Regards, Marcin -- Dr Marcin Makowski Jagiellonian University Department of Theoretical Chemistry email:makowskm]![chemia.uj.edu.pl or Kyushu University email:marcin]![cube.kyushu-u.ac.jp From owner-chemistry@ccl.net Fri Apr 7 06:11:00 2006 From: "Luca Bertini luca.bertini(-)istm.cnr.it" To: CCL Subject: CCL: TDDFT for Large Unsaturated pi-Systems Message-Id: <-31451-060407060859-27366-jHFFl46tukYrVxRyYwj10w!^!server.ccl.net> X-Original-From: "Luca Bertini" Content-Type: text/plain; charset=iso-8859-1 Date: Fri, 7 Apr 2006 12:08:53 +0200 MIME-Version: 1.0 Sent to CCL by: "Luca Bertini" [luca.bertini[]istm.cnr.it] You can find papers about the xc kernel more physically-oriented which are sometime a bit obscure for me, while the paper by Maitra is clear. Regards, Luca ---------- Original Message ----------- > From: "makowskm/./chemia.uj.edu.pl" To: "Bertini, Luca " Sent: Fri, 7 Apr 2006 05:47:03 -0400 Subject: CCL: TDDFT for Large Unsaturated pi-Systems > Sent to CCL by: makowskm::chemia.uj.edu.pl > > Sent to CCL by: "Luca Bertini" [luca.bertini*o*istm.cnr.it] > > > > I'm refering to the paper by Maitra et al, JCP, 5932, 120, (2004). > > > > I'm not understant what you mean with implementation of TDDFT. I'm > > thinking to > > the standard RPA-TDDFT theory. > > > > Very nice and insightful paper. > Maybe a little bit of misunderstanding from my side referring to > what you really claim. If you mean standard RPA-TDDFT I just agree > with you. > > Regards, > Marcin > > -- > Dr Marcin Makowski > Jagiellonian University > Department of Theoretical Chemistry > email:makowskm*chemia.uj.edu.pl > or > Kyushu University > email:marcin*cube.kyushu-u.ac.jp > > -= This is automatically added to each message by the mailing script > =- To recover the email address of the author of the message, please > change the strange characters on the top line to the * sign. You can > also> > Search Messages: http://www.ccl.net/htdig (login: ccl, Password: > search)> > -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+- > +-+ ------- End of Original Message ------- From owner-chemistry@ccl.net Fri Apr 7 09:05:00 2006 From: "Shireen Al Falah shireenfalah_-_hotmail.com" To: CCL Subject: CCL: conversion of sdf to mol files(multiple) Message-Id: <-31452-060407030821-12868-D5Xbr2dKxWzVT9JZE8IaRg ~ server.ccl.net> X-Original-From: "Shireen Al Falah" Content-Type: text/html; format=flowed Date: Fri, 07 Apr 2006 09:08:15 +0200 Mime-Version: 1.0 Sent to CCL by: "Shireen Al Falah" [shireenfalah::hotmail.com]

Hi,

Have you tried the command

babel -isdf  ligand.sdf  -omol  new.mol 

actually, I am not sure if the "-isdf" or "-omol" is the right thing but you can check with the list in babel by typing "babel -m". It should be the abbreviation fir this formate in babel.

regards,

shireen

From:  "Senthil Kumar Natesan senthilkumar_natesan()bi.iiita.ac.in" <owner-chemistry _ ccl.net>
Reply-To:  "CCL Subscribers" <chemistry _ ccl.net>
To:  "Alfalah, Sherin " <shireenfalah _ hotmail.com>
Subject:  CCL: conversion of sdf to mol files(multiple)
Date:  Fri, 7 Apr 2006 02:07:11 -0400
>Sent to CCL by: "Senthil Kumar  Natesan" [senthilkumar_natesan*bi.iiita.ac.in]
>Dear Pals,
>
>I tried with the following command in open babel to convert multiple sdf file into individual new files, but end up with only single mol file.
>
>babel ligand.sdf new.mol -m
>
>Any help in this regard would be appreciated.
>
>sincerely,
>
>senthil kumar Natesan
>
>
>
>
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From owner-chemistry@ccl.net Fri Apr 7 10:24:00 2006 From: "Geoffrey Hutchison grh25**cornell.edu" To: CCL Subject: CCL: conversion of sdf to mol files(multiple) Message-Id: <-31453-060407102119-3299-GaoskOICQCQ+LGkfGEtsQw[*]server.ccl.net> X-Original-From: Geoffrey Hutchison Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=ISO-8859-1; delsp=yes; format=flowed Date: Fri, 7 Apr 2006 10:21:05 -0400 Mime-Version: 1.0 (Apple Message framework v749.3) Sent to CCL by: Geoffrey Hutchison [grh25~~cornell.edu] > actually, I am not sure if the "-isdf" or "-omol" is the right > thing but you can check with the list in babel by typing "babel - > m". It should be the abbreviation fir this formate in babel. Open Babel does not have the "-m" menu feature that was in Babel-1.6. Since there are several GUI interfaces to Open Babel, not to mention the -H help flag which lists formats, the "-m" menu feature is superfluous. Remember, there are differences in usage between the old Babel and Open Babel -- these are two different programs. (And yes, in Open Babel, both -isdf and -omol are acceptable formats. Many formats have multiple acceptable file extensions.) Again, there's quite a bit of information about using Open Babel on the website: http://openbabel.sourceforge.net/ And there's a separate e-mail list for questions, concerns, complaints, compliments... https://lists.sourceforge.net/lists/listinfo/openbabel-discuss Cheers, -Geoff -- -Dr. Geoffrey Hutchison Cornell University, Department of Chemistry and Chemical Biology Abruña Group http://abruna.chem.cornell.edu/ From owner-chemistry@ccl.net Fri Apr 7 14:00:00 2006 From: "Shaohui Zheng szheng3 .. gmail.com" To: CCL Subject: CCL: nbo 5.0 analysis for J-coupling Message-Id: <-31454-060407134602-9190-9npsmt30WZS6VIpp5HwFtA{}server.ccl.net> X-Original-From: "Shaohui Zheng" Content-Type: multipart/alternative; boundary="----=_Part_47948_4305536.1144431954421" Date: Fri, 7 Apr 2006 13:45:54 -0400 MIME-Version: 1.0 Sent to CCL by: "Shaohui Zheng" [szheng3+*+gmail.com] ------=_Part_47948_4305536.1144431954421 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Content-Disposition: inline Dear All, I tried to do natural bond orbital analysis for J-coupling. But = I got very bad result and unresonable J-coupling comparing with expreimental data. Here is my input file. %chk=3Dfile #ubp86/6-311g* Pop=3Dnboread field=3Df(1)200 This is for spin-spin 0,1 atoms coordination $NBO file=3Dfile_1 NJC $end --link1-- %chk=3Dfile #ubp86/6-311g* Pop=3Dnboread field=3Df(1)200 guess=3Dread geom=3Dallcheckp= oint $nbo file=3Dfile_2 NJC print=3D0 $end --link1-- %chk=3Dfile #ubp86/6-311g* Pop=3Dnboread field=3Df(1)200 guess=3Dread geom=3Dallcheckp= oint $nbo file=3Dfile_3 NJC print=3D0 $end --link1-- %chk=3Dfile #ubp86/6-311g* Pop=3Dnboread field=3Df(1)200 guess=3Dread geom=3Dallcheckp= oint $nbo file=3Dfile_4 NJC print=3D0 $end Any help will be highly appreciated. Best regards, Shaohui -- shaohui zheng Ph.D. Candidate: Computational chemistry Department of Chemistry 345 Natural Sciences Complex University at Buffalo State University of New York Buffalo, NY 14260-3000 ------=_Part_47948_4305536.1144431954421 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Content-Disposition: inline
Dear All,
           I tried t= o do natural bond orbital analysis for J-coupling. But I got
very bad result and unresonable J-coupling comparing with expreimental= data. 
 
Here is my input file.
 
%chk=3Dfile
#ubp86/6-311g*  Pop=3Dnboread field=3Df(1)200

This is for spin-spin

0,1
atoms coordination

$NBO file=3Dfile_1 NJC  $end

--link1--
%chk=3Dfile
#ubp86/6-311g*  Pop=3Dnboread field=3Df= (1)200 guess=3Dread geom=3Dallcheckpoint

$nbo file=3Dfile_2 NJC print=3D0 $end

--link1--
%chk=3Dfile
#ubp86/6-311g*  Pop=3Dnboread field=3Df= (1)200 guess=3Dread geom=3Dallcheckpoint

$nbo file=3Dfile_3 NJC print=3D0 $end

--link1--
%chk=3Dfile
#ubp86/6-311g*  Pop=3Dnboread field=3Df= (1)200 guess=3Dread geom=3Dallcheckpoint

$nbo file=3Dfile_4 NJC print=3D0 $end


Any help will be highly appreciated.
Best regards,
Shaohui
--
shaohui zheng
Ph.D. Candidate: Computational chem= istry
Department of Chemistry
345 Natural Sciences Complex
Univers= ity at Buffalo
State University of New York
Buffalo, NY 14260-3000=20
------=_Part_47948_4305536.1144431954421-- From owner-chemistry@ccl.net Fri Apr 7 15:27:00 2006 From: "Juan E. Peralta juanp]~[rice.edu" To: CCL Subject: CCL: nbo 5.0 analysis for J-coupling Message-Id: <-31455-060407152009-8686-OuRVGla+UnjWOzBfzWcJqQ]_[server.ccl.net> X-Original-From: "Juan E. Peralta" Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=us-ascii; format=flowed Date: Fri, 07 Apr 2006 13:20:25 -0500 MIME-Version: 1.0 Sent to CCL by: "Juan E. Peralta" [juanp%a%rice.edu] Dear Shaohui The 6-311G* is a very poor basis set for SSCC calculations. Also, depending on the system, calculating the Fermi contact term only could be a bad approximation. Check these references: Chem. Phys. Lett. 375, 542-458 (2003). J. Chem. Theory Comput. 4, 541 (2005). Chem. Rev. 99 (1999), p. 293. Theor. Chem. Acc. 105, 165 (2000). Theor. Chem. Acc. 99 (1998), p. 175. J. Chem. Phys. 115 (2001), p. 1324. For the original reference to the NJC method: Chem. Commun., 2000, 2025 (2000). I hope this helps. Juan > > Dear All, > I tried to do natural bond orbital analysis for J-coupling. But = > I > got > very bad result and unresonable J-coupling comparing with expreimental > data. > > Here is my input file. > > %chk=3Dfile > #ubp86/6-311g* Pop=3Dnboread field=3Df(1)200 > > This is for spin-spin > > 0,1 > atoms coordination > > $NBO file=3Dfile_1 NJC $end > -- Juan E. Peralta Rice University Department of Chemistry 6100 Main St. Houston TX 77005 (USA) http://www.ruf.rice.edu/~juanp/ 713-348-2826