From owner-chemistry@ccl.net Fri Feb 12 08:57:00 2010 From: "anupam banerjee a.bandyopadhyay[]iiserpune.ac.in" To: CCL Subject: CCL: Xplor-NIH 2.16 Message-Id: <-41245-100209072436-3892-h/CxNDci0v+XlZe2X8CVug_._server.ccl.net> X-Original-From: "anupam banerjee" Date: Tue, 9 Feb 2010 07:24:31 -0500 Sent to CCL by: "anupam banerjee" [a.bandyopadhyay+*+iiserpune.ac.in] Dear sir, I am a beginner of xplor-NIH. I have installed in linux system this software. But how to use I dont know. I have gone through lot of tutorials, but i unable to understand.Kindly help me if you know any person from India,knows about this software(XPLOR-NIH). I will be grateful to you. From owner-chemistry@ccl.net Fri Feb 12 15:22:01 2010 From: "Robson Silva Oliboni rooliboni-*-gmail.com" To: CCL Subject: CCL:G: Orbital dipole using gaussian03 Message-Id: <-41246-100212133713-12929-qnFGuHQYivgPpzzCA9hPVQ ~ server.ccl.net> X-Original-From: "Robson Silva Oliboni" Date: Fri, 12 Feb 2010 13:37:10 -0500 Sent to CCL by: "Robson Silva Oliboni" [rooliboni%a%gmail.com] Hi, I'm trying to calculate the dipole moment of the individual molecular orbitals using gaussian. For this, I use cubegen to generate a cube with the appropriate molecular orbital, like $ cubegen 0 MO=11 orbital.fchk orbital.cube 0 h After this, I use cubman to calculate the proprieties of the cube (i. e., the MO=11). After this, the results are Alpha MO coefficients SumAP= 7.3110397131 SumAN= -7.2921897843 SumA= 0.0188499288 CAMax= 0.3893020000 XYZ= -2.6240520000 0.3278460000 0.1474330000 CAMin= -0.3932980000 XYZ= -2.6240520000 -0.3922340000 -0.2126070000 DipAE= 0.0690202616 -7.8794546051 -4.7197939658 DipAN= -0.0000020000 0.0000000000 0.0000030000 DipA= 0.0690182616 -7.8794546051 -4.7197909658 But looking for the dipole moments of the individual occupied orbitals, they don't make sense! I mean, don't agree at all with the dipole moment of the molecule. How this calculate (the dipole, using cubman) is made? Thanks. Robson mail: rooliboni a gmail.com Universidade Federal de Santa Catarina - UFSC From owner-chemistry@ccl.net Fri Feb 12 17:30:01 2010 From: "Barry Hardy barry.hardy ~~ vtxmail.ch" To: CCL Subject: CCL: Collaboration Pool Formation, Virtual Organisations, ICT Support Message-Id: <-41247-100212154754-3011-52gVL7VscTzArpZ7vH4KCw_-_server.ccl.net> X-Original-From: Barry Hardy Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-15; format=flowed Date: Fri, 12 Feb 2010 21:48:10 +0100 MIME-Version: 1.0 Sent to CCL by: Barry Hardy [barry.hardy-*-vtxmail.ch] We are establishing Collaboration Pools of individuals and organisations who have an interest in collaborating together in areas of drug discovery or life science innovation. For example, a selection of Pool members could participate in a collaborative research project, develop a funding proposal or response to a call opportunity together, or develop an innovation or best practice. To join the eCheminfo Collaboration Pool in drug design and discovery, please complete the short form located at https://www.surveymonkey.com/s/V6T2YSD To join the InnovationWell Collaboration Pool in life science innovation please complete the short form located at https://www.surveymonkey.com/s/782L9DZ During April - October 2010 we will be running two pilots which will create two virtual organisations (VOs) of research partners who will collaborate on projects in drug design and predictive toxicology: a) Drug Design project will examine the application of a variety of leading modelling and design approaches to novel target kinases, to experimentally test predictions, and to initiate a best practices virtual screening resource. b) Predictive Toxicology project will apply a combination of in silico and in vitro approaches to predict in vivo toxicity including exposure. Both VOs will be supported by a variety of leading modelling and design software, informatics infrastructure, and collaborative content management and electronic lab notebook systems. The VOs will be created from partners from the Collaboration Pools, who will bring contributing knowledge, computational or experimental capabilities to the partnership for the duration of the projects. We are also currently seeking Expressions of Interest in the ICT support role for the pilots which should be submitted by 17.00 CET, 19 February 2010 through the following form: https://www.surveymonkey.com/s/QSHKDCH The ICT support role will support the informatics requirements of the researchers in organising, processing and sharing data, and in collaborative analysis and decision making. The VOs will also be supported by knowledge-oriented collaboration services developed under the FP7 Synergy research project, including a reactive complex event driven engine, collaboration moderator, collaboration pattern services and partner knowledge base. Summary on Synergy project: http://barryhardy.blogs.com/theferryman/2008/02/knowledge-orien.html The Predictive Toxicology VO will be supported by distributed REST-driven web services for data management, model building, validation and reporting, developed under the OpenTox Framework (http://www.opentox.org/). best regards Barry Hardy PhD Director, Community of Practice & Research Activities and OpenTox Project Coordinator (www.opentox.org) Douglas Connect Switzerland Tel: +41 61 851 0170 Email: barry.hardy -(at)- douglasconnect.com From owner-chemistry@ccl.net Fri Feb 12 18:04:01 2010 From: "Jiabo Li jiaboli**yahoo.com" To: CCL Subject: CCL:G: Orbital dipole using gaussian03 Message-Id: <-41248-100212163548-23814-BZWyLOHRPeRRpDR5s1aEIQ,server.ccl.net> X-Original-From: Jiabo Li Content-Type: multipart/alternative; boundary="0-1305536892-1266010532=:37443" Date: Fri, 12 Feb 2010 13:35:32 -0800 (PST) MIME-Version: 1.0 Sent to CCL by: Jiabo Li [jiaboli%x%yahoo.com] --0-1305536892-1266010532=:37443 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable Robson, =A0 What you get is the centroid of the electrons on the orbital. The dipole mo= ment of a molecule =A0is the summation of the contributions from all electr= ons AND nuclear charges. =A0 Jiabo --- On Fri, 2/12/10, Robson Silva Oliboni rooliboni-*-gmail.com wrote: > From: Robson Silva Oliboni rooliboni-*-gmail.com Subject: CCL:G: Orbital dipole using gaussian03 To: "Li, Jiabo " Date: Friday, February 12, 2010, 10:37 AM Sent to CCL by: "Robson Silva Oliboni" [rooliboni%a%gmail.com] Hi, I'm trying to calculate the dipole moment of the individual molecular=20 orbitals using gaussian. For this, I use cubegen to generate a cube with th= e=20 appropriate molecular orbital, like $ cubegen 0 MO=3D11 orbital.fchk orbital.cube 0 h After this, I use cubman to calculate the proprieties of the cube (i. e., t= he=20 MO=3D11). After this, the results are Alpha MO coefficients=20 SumAP=3D=A0 =A0 7.3110397131 SumAN=3D=A0=A0=A0-7.2921897843 SumA=3D=A0 =A0 = 0.0188499288=20 CAMax=3D=A0 =A0 0.3893020000 XYZ=3D=A0=A0=A0-2.6240520000=A0 =A0 0.32784600= 00=A0 =A0 0.1474330000=20 CAMin=3D=A0=A0=A0-0.3932980000 XYZ=3D=A0=A0=A0-2.6240520000=A0=A0=A0-0.3922= 340000=A0=A0=A0-0.2126070000=20 DipAE=3D=A0 =A0 0.0690202616=A0=A0=A0-7.8794546051=A0=A0=A0-4.7197939658=20 DipAN=3D=A0=A0=A0-0.0000020000=A0 =A0 0.0000000000=A0 =A0 0.0000030000=20 DipA=3D=A0 =A0=A0=A00.0690182616=A0=A0=A0-7.8794546051=A0=A0=A0-4.719790965= 8=20 But looking for the dipole moments of the individual occupied orbitals, the= y=20 don't make sense! I mean, don't agree at all with the dipole moment of the= =20 molecule. How this calculate (the dipole, using cubman) is made? Thanks. Robson mail: rooliboni+/-gmail.com Universidade Federal de Santa Catarina - UFSC -=3D This is automatically added to each message by the mailing script =3D-=A0 =A0 =A0=A0 =A0 =A0Subscribe/Unsubscribe:=20 =A0 =A0 =A0Job: http://www.ccl.net/jobs=20=A0 =A0 =A0--0-1305536892-1266010532=:37443 Content-Type: text/html; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable
Robson,
 
What you get is the centroid of the electrons on the orbital. The dipo= le moment of a molecule  is the summation of the contributions from al= l electrons AND nuclear charges.
 
Jiabo

--- On Fri, 2/12/10, Robson Silva Oliboni rooliboni-*-= gmail.com <owner-chemistry/./ccl.net> wrote:

From: Robson Silva Oliboni rooliboni-*-gmail.com = <owner-chemistry/./ccl.net>
Subject: CCL:G: Orbital dipole using gau= ssian03
To: "Li, Jiabo " <jiaboli/./yahoo.com>
Date: Frid= ay, February 12, 2010, 10:37 AM


Sent to CCL by: "Robson Silva Oliboni" [roolibon= i%a%gmail.com]
Hi,
I'm trying to calculate the dipole moment of the i= ndividual molecular
orbitals using gaussian. For this, I use cubegen to= generate a cube with the
appropriate molecular orbital, like
$ cube= gen 0 MO=3D11 orbital.fchk orbital.cube 0 h

After this, I use cubman= to calculate the proprieties of the cube (i. e., the
MO=3D11). After t= his, the results are

Alpha MO coefficients

SumAP=3D  &n= bsp; 7.3110397131 SumAN=3D   -7.2921897843 SumA=3D  &nb= sp; 0.0188499288
CAMax=3D    0.3893020000 XYZ=3D  &= nbsp;-2.6240520000    0.3278460000    0.1474330000
= CAMin=3D   -0.3932980000 XYZ=3D   -2.62405200= 00   -0.3922340000   -0.2126070000

Di= pAE=3D    0.0690202616   -7.8794546051   -4.7197939658=
DipAN=3D   -0.0000020000    0.0000000000 = ;   0.0000030000
DipA=3D     0.0690182616 = ;  -7.8794546051   -4.7197909658

But looki= ng for the dipole moments of the individual occupied orbitals, they
don= 't make sense! I mean, don't agree at all with the dipole moment of the molecule.
How this calculate (the dipole, using cubman) is made?
Thanks.

Robson
mail: rooliboni+/-gmail.com
Universidade Feder= al de Santa Catarina - UFSC



-=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
the strange characters on t= he top line to the /./ sign. You can also
look up the X-Original-From: lin= e in the mail header.

E-mail to subscribers: CHEMISTRY/./ccl.net or use:
 = ;     http://www.ccl.net/cgi-bin/ccl/send_ccl_message
E-mail to administrators: CHEMISTRY-REQUEST/./ccl.net or use
      http:/= /www.ccl.net/cgi-bin/ccl/send_ccl_message

Subscribe/Unsubscribe:=
      http://www.ccl.net/chemistry/sub_unsub.shtml
Before posting, check wait time at: http://www.ccl.net

Job: http://www.ccl.net/jobs
Conferences: h= ttp://server.ccl.net/chemistry/announcements/conferences/

Search= Messages: http://www.ccl.net/chemistry/searchccl/index.shtml
    &= nbsp; http://ww= w.ccl.net/spammers.txt

RTFI: http://www.ccl.net/chemistry/a= boutccl/instructions/


--0-1305536892-1266010532=:37443--