From owner-chemistry@ccl.net Sun Apr 11 02:16:00 2010 From: "SUBHADEEP SAHA saha.subhadeep,,gmail.com" To: CCL Subject: CCL:G: how to generate .mol file with partial charge from gaussview Message-Id: <-41642-100411021420-15473-UGDCcJVilowrepIFmAWPkQ{=}server.ccl.net> X-Original-From: SUBHADEEP SAHA Content-Type: text/plain; charset=ISO-8859-1 Date: Sun, 11 Apr 2010 11:44:14 +0530 MIME-Version: 1.0 Sent to CCL by: SUBHADEEP SAHA [saha.subhadeep+/-gmail.com] Dear all, I have generated partial charge of each atom of a molecule using gaussian. Now I want to generate a .mol or any other file which will contain the co-ordinates of each atom and the respective partial charges.I tried to write a code,but due to variety of partial charge on the atoms I failed.Can any one of you please help me out? -- Regards, Subhadeep Saha C/O Dr.Rahul Banerjee Materials and Physical Chemistry Division National Chemical Laboratory Dr. Homi Bhabha Road Pune:411008 Maharasthra India Ph:+91-20-2590-2387 +91-20-2590-2535 +91-20-2590-2598 From owner-chemistry@ccl.net Sun Apr 11 20:06:01 2010 From: "Mario Saavedra mario.saavedra.torres-.-gmail.com" To: CCL Subject: CCL:G: how to generate .mol file with partial charge from gaussview Message-Id: <-41643-100411161655-978-3w/gm8/3dQVg8DExYkmDgA*server.ccl.net> X-Original-From: Mario Saavedra Content-Type: multipart/alternative; boundary=000e0cd6d0144cabaf0483fac380 Date: Sun, 11 Apr 2010 15:09:08 -0400 MIME-Version: 1.0 Sent to CCL by: Mario Saavedra [mario.saavedra.torres%gmail.com] --000e0cd6d0144cabaf0483fac380 Content-Type: text/plain; charset=ISO-8859-1 You can use openbabel to convert gaussian output to mol2 format. MDL MOL format, work only with connectivities. 2010/4/11 SUBHADEEP SAHA saha.subhadeep,,gmail.com > > Sent to CCL by: SUBHADEEP SAHA [saha.subhadeep+/-gmail.com] > Dear all, > > I have generated partial charge of each atom of a molecule using > gaussian. Now I want to generate a .mol or any other file which will > contain the co-ordinates of each atom and the respective partial > charges.I tried to write a code,but due to variety of partial charge > on the atoms I failed.Can any one of you please help me out? > > -- > Regards, > Subhadeep Saha > C/O Dr.Rahul Banerjee > Materials and Physical Chemistry Division > National Chemical Laboratory > Dr. Homi Bhabha Road > Pune:411008 > Maharasthra > India > Ph:+91-20-2590-2387 > +91-20-2590-2535 > +91-20-2590-2598> > > -- Mario Saavedra Physical Chemistry, PhD Program Universidad Andres Bello Santiago, Chile --000e0cd6d0144cabaf0483fac380 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable You can use openbabel to convert gaussian output to mol2 format.
MDL MOL= format, work only with connectivities.

2= 010/4/11 SUBHADEEP SAHA saha.subhadeep,,gmail.com <owner-chemistry-,-ccl.net>

Sent to CCL by: SUBHADEEP SAHA [saha.subhadeep+/-gmail.com]
Dear all,

=A0I have generated partial charge of each atom of a molecule using
gaussian. Now I want to generate a .mol or any other file which will
contain the =A0co-ordinates of each atom and the respective partial
charges.I tried to write a code,but due to variety of partial charge
on the atoms I failed.Can any one of you please help me out?

--
Regards,
Subhadeep Saha
C/O Dr.Rahul Banerjee
Materials and Physical Chemistry Division
National Chemical Laboratory
Dr. Homi Bhabha Road
Pune:411008
Maharasthra
India
Ph:+91-20-2590-2387
=A0 =A0 +91-20-2590-2535
=A0 =A0 +91-20-2590-2598



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--
Mario Saavedra
Physical Chemistry, PhD Pro= gram
Universidad Andres Bello
Santiago, Chile
--000e0cd6d0144cabaf0483fac380-- From owner-chemistry@ccl.net Sun Apr 11 20:40:00 2010 From: "Joseph M Leonard jleonard42*gmail.com" To: CCL Subject: CCL: KNIME question Message-Id: <-41644-100411105551-1326-wNGWW76mOpvkzWNGaAVLbA_-_server.ccl.net> X-Original-From: Joseph M Leonard Content-Type: multipart/alternative; boundary=0016e6d7e3451ea51e0483f65f11 Date: Sun, 11 Apr 2010 09:54:47 -0400 MIME-Version: 1.0 Sent to CCL by: Joseph M Leonard [jleonard42]_[gmail.com] --0016e6d7e3451ea51e0483f65f11 Content-Type: text/plain; charset=ISO-8859-1 Question for the KNIME users: How is chemical data passed from node to node? Is there a (or several) standard formats used? Is the data supposed to be self-describing? Can it handle structural and quantum data, or merely structural data? I know that other dataflow systems had chemical datatypes long ago, which was an effort to improve interoperability. Is this the case with KNIME, or is it up to each author to define the format used? Thanks in advance! Joe Leonard jleonard42]~[gmail.com -- Disclaimer: I do not speak for my employer. If it's too early in the morning, I am not sure I speak for myself... --0016e6d7e3451ea51e0483f65f11 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Question for the KNIME users:

How is chemical data passe= d from node to node? =A0Is there a (or several) standard formats used? =A0I= s the data supposed to be self-describing? =A0Can it handle structural and = quantum data, or merely structural data?

I know that other dataflow systems had chemical datatyp= es long ago, which was an effort to improve interoperability. =A0Is this th= e case with KNIME, or is it up to each author to define the format used?

Thanks in advance!

Joe Leonard=
jleonard42]~[gmail.com=

--
Disclaimer: I do not speak for my employer. = =A0If it's too early in the morning, I am not sure I speak for myself..= .

--0016e6d7e3451ea51e0483f65f11-- From owner-chemistry@ccl.net Sun Apr 11 23:28:00 2010 From: "Carlos F Lagos cflagos===uc.cl" To: CCL Subject: CCL: CUDA enabled docking codes Message-Id: <-41645-100411232633-4574-5ZVM6tUpweGubr5Svxneqw^^^server.ccl.net> X-Original-From: "Carlos F Lagos" Date: Sun, 11 Apr 2010 23:26:32 -0400 Sent to CCL by: "Carlos F Lagos" [cflagos[]uc.cl] Hello everyone, please I would like to have information about small molecule-protein docking codes available for CUDA Regards QF Carlos F. Lagos Medicinal Chemistry Laboratory MCL, Faculty of Chemistry P. Universidad Catolica de Chile Portugal 49, Zocalo I 8330025 Santiago-Chile Phone: +56 2 3541911 I http://www.quimica.uc.cl