From owner-chemistry@ccl.net Tue Apr 19 00:46:01 2011 From: "psavita|crlindia.com" To: CCL Subject: CCL: Transition state calculation Message-Id: <-44417-110419004002-10675-gkCD8xIVKvdJSKsjwoJJqQ- -server.ccl.net> X-Original-From: psavita#crlindia.com Content-Transfer-Encoding: quoted-printable Content-Type: text/html; charset=ISO-8859-1 Date: Tue, 19 Apr 2011 10:15:14 +0530 MIME-Version: 1.0 MIME-Version: 1.0 Sent to CCL by: psavita+/-crlindia.com
Hello Upendra,

As per what I understand, a transition st= ate is a minimum along all dimensions except along the reaction coordinate = path
hence there is one negati= ve frequency. It there are several, then I believe it is still not the tran= sition state, the geometry
needs to be optimized further.

<= div>
Savita Pundlik
Computational Materials A= pplied Research Group
Computational Research Laboratorie= s Ltd.,
Taco House, Damle Path, Off Law C= ollege Road
Pune - 41= 1004, India.



-----owner-chemistry+psavita=3D=3Dcrlindia.com * ccl.ne= t wrote: -----

To: "Pundlik, Savita Sunil " <psavita * crlindia.com>=
From: "upendra adhikari upendra.adhikari%x%aggiemail.usu.edu" <owne= r-chemistry * ccl.net>
Sent by: owner-= chemistry+psavita=3D=3Dcrlindia.com * ccl.net
Date: 04/19/2011 04:37AM=
Subject: CCL: Transition state calculation


Sent to CCL by: "upendra  adhik= ari" [upendra.adhikari:aggiemail.usu.edu]
Hello all!
I am doing some = calculations on transition state, I got some negative frequencies ranging f= rom -100 to -600, Is their any relation of this with geometry or barrier he= ight or anything else?. I will appreciate if you can post some papers relat= ed to that.
Thank You

Upendra



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= From owner-chemistry@ccl.net Tue Apr 19 05:14:00 2011 From: "Wojciech Kolodziejczyk dziecial::icnanotox.org" To: CCL Subject: CCL:G: Converting 3D to 2D Message-Id: <-44418-110419051150-3679-anyacX30wX9BVcu1ODuwWA]-[server.ccl.net> X-Original-From: Wojciech Kolodziejczyk Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=ISO-8859-1 Date: Tue, 19 Apr 2011 11:11:43 +0200 MIME-Version: 1.0 Sent to CCL by: Wojciech Kolodziejczyk [dziecial]*[icnanotox.org] Hi, I am not sure if I understood what you ment. Do you want to visualize it? If your answer is --> yes use specialized software to do it. There are a lot of programs that are able to do it: -VMD http://www.ks.uiuc.edu/Research/vmd/ -molden http://www.cmbi.ru.nl/molden/ -GaussView http://www.gaussian.com/g_prod/gv5.htm and more. Just google it Best regards W. 2011/4/18 Laleh Rezaei lalerezaei ~ gmail.com : > > Sent to CCL by: "Laleh  Rezaei" [lalerezaei]-[gmail.com] > > To whom it may concern, > > I am a graduate student in organic chemistry. As part of my project I need to work with Gaussian software. I faced a problem in converting 3D gaussian output to 2D. I am wondering if there any way that I can do it. I would be grateful if you could help me. > > Regards, > Laleh>      http://www.ccl.net/cgi-bin/ccl/send_ccl_message>      http://www.ccl.net/cgi-bin/ccl/send_ccl_message>      http://www.ccl.net/chemistry/sub_unsub.shtml>      http://www.ccl.net/spammers.txt> > > From owner-chemistry@ccl.net Tue Apr 19 09:36:00 2011 From: "Jun Zhang coolrainbow:yahoo.cn" To: CCL Subject: CCL: Problems with Reproducing MEX geometry by GAMESS Message-Id: <-44419-110419093437-5717-nc+F6JSxqm54tP2/2VMurg-.-server.ccl.net> X-Original-From: Jun Zhang Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=utf-8 Date: Tue, 19 Apr 2011 21:34:24 +0800 (CST) MIME-Version: 1.0 Sent to CCL by: Jun Zhang [coolrainbow{:}yahoo.cn] Hello Everyone: I am trying to reproduce the result of J Chem Phys,104:7988, especially the MEX geometry of PbH2 between 1A1 and 3B1 state. I use the same method and basis set in the literature and compute it by GAMESS. For 1A1 and 3B1 state, I can reproduce the result well, but for MEX, the geomoetry differs greatly with that of the literature: r(Pb-H): (unit: Ang) literature my result 1A1 1.885 1.886 3B1 1.812 1.808 MEX 1.75 2.597 Does anyont have any suggestions? Thanks in advance. Below is my input file of the MEX: $CONTRL RUNTYP=MEX PP=SBKJC ICHARG=0 $END $SYSTEM MWORDS=10 MEMDDI=21 TIMLIM=1000000.0 $END $BASIS GBASIS=SBKJC NDFUNC=1 NPFUNC=1 $END $GUESS GUESS=MOREAD NORB=24 $END $MEX SCF1=MCSCF MULT1=3 NMOS1=24 SCF2=MCSCF MULT2=1 NMOS2=24 NRDMOS=3 TDE=1.0D-05 $END $MCSCF FULLNR=.T. CISTEP=ALDET $END $DET1 ISTSYM=3 NCORE=1 NACT=6 NELS=4 NSTATE=1 $END $DET2 ISTSYM=1 NCORE=1 NACT=6 NELS=4 NSTATE=1 $END $DATA PbH2 MEX STATE Cnv 2 LEAD 82.0 0.0000000000 0.0000000000 -1.2855596707 HYDROGEN 1.0 0.0000000000 -0.9943919522 1.3506798347 $END $VEC1 ...omit... $END $VEC2 ...omit... $END --- Jun Zhang Nankai University coolrainbow-#-yahoo.cn From owner-chemistry@ccl.net Tue Apr 19 10:11:00 2011 From: "Anup thomas anupvthomas|-|gmail.com" To: CCL Subject: CCL: Embedded Cluster Approach Message-Id: <-44420-110419072710-23365-/ZbNOpqCyYI5P2UCF4uNiA]_[server.ccl.net> X-Original-From: "Anup thomas" Date: Tue, 19 Apr 2011 07:27:08 -0400 Sent to CCL by: "Anup thomas" [anupvthomas:_:gmail.com] Dear CCl Subscribers I have read some papers calculating reorganization energies by Embedded Cluster aproach (to mimic the surrounding). Is it possible with any quantum chemistry/ab-initio softwares where we can specify the charge to particular fragment rather than to whole cluster. look forward to hear from you. Regards Anup thms CC Lab IICT Hyderbad India From owner-chemistry@ccl.net Tue Apr 19 10:46:00 2011 From: "Djamila Benrezkallah benrezkallah : gmail.com" To: CCL Subject: CCL:G: Gaussian 09 with keword "External" Message-Id: <-44421-110419065441-4681-P4RThcxMw2gmP3S6rwjwkA(-)server.ccl.net> X-Original-From: "Djamila Benrezkallah" Date: Tue, 19 Apr 2011 06:54:39 -0400 Sent to CCL by: "Djamila Benrezkallah" [benrezkallah(0)gmail.com] Dear users, I am new in gaussian09, i would like to perform QM/MM calculations with the programm gaussian09 (for the QM part), and I like to call for the CHARMM programm (for the MM part).i will submit my jobs to a calculation center where the two programms Gaussian09 and Charmm are installed. I have searched the gaussian help, I found that the "external" keyword can do that, but I don't know how? I think that it needs a script, but i am very limited in this. so, please i would be very thankful, if someone send me an input exemple to execute with gaussian, and a script if needed. thank you in advance; djamila From owner-chemistry@ccl.net Tue Apr 19 11:21:00 2011 From: "baljinder baljinder7(~)gmail.com" To: CCL Subject: CCL:G: Converting 3D to 2D Message-Id: <-44422-110418233950-28289-sNJ1RYg7iYXabE68OhbORg]*[server.ccl.net> X-Original-From: baljinder Content-Type: multipart/alternative; boundary=00032555b22224324204a13d423e Date: Tue, 19 Apr 2011 09:09:41 +0530 MIME-Version: 1.0 Sent to CCL by: baljinder [baljinder7(~)gmail.com] --00032555b22224324204a13d423e Content-Type: text/plain; charset=ISO-8859-1 Dear Vlad, Could you kindly inform me that whether Jamberoo is free for academics . Thanks in advance. On Tue, Apr 19, 2011 at 5:08 AM, Vlad vvv900,+,anusf.anu.edu.au < owner-chemistry(a)ccl.net> wrote: > Sent to CCL by: Vlad [vvv900],[anusf.anu.edu.au] > Hi Laleh, > > > > I am a graduate student in organic chemistry. As part of my project I > > need to work with Gaussian software. I faced a problem in converting > > 3D gaussian output to 2D. I am wondering if there any way that I can > > do it. I would be grateful if you could help me. > > I suggest you to try Jamberoo > . > > Jamberoo can parse both the inputand output Gaussian files. In the case of the output files Jamberoo can > extract the optimization information and frequencies data and plot them > using the interactive charting. > It can also animate vibrations. > Jamberoo can also parse Gaussian cube files and visualize the volumetric > data(MOs, electrostatic potential). > > As for the data presentation you have several options in Jamberoo: > > 1) You can create the jpeg or png image of your molecular scene. > > 2) For the high quality graphics you can create input file for the PovRay. > > 3) Finally, you can create a file in the VRML format and use it for > creation of the 3D PDF documents > . > > Regards, > VladTo > recover the email address of the author of the message, please change the > strange characters on the top line to the (a) sign. You can also look up the > X-Original-From: line in the mail header. E-mail to subscribers: > CHEMISTRY(a)ccl.net or use:E-mail to administrators: > CHEMISTRY-REQUEST(a)ccl.net or useBefore posting, check wait > time at: http://www.ccl.netConferences: > http://server.ccl.net/chemistry/announcements/conferences/ Search > Messages: http://www.ccl.net/chemistry/searchccl/index.shtml If your mail > bounces from CCL with 5.7.1 error, check:RTFI: > http://www.ccl.net/chemistry/aboutccl/instructions/ > --00032555b22224324204a13d423e Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable
Dear Vlad,

Could you kindly inform me that whether = Jamberoo is free for academics .

Thanks in advance.

On Tue, Apr 19, 2011 at 5:08 AM, Vlad vvv900,+,anusf.anu.edu.au <owner-chemistry(a)ccl.net>= wrote:
Sent to CCL by: Vlad [vvv900],[anusf.anu.edu.au] =20 =20 =20 =20
Hi Laleh,


> I am a graduate student in organic chemistry. As part of my project I
> need to work with Gaussian software. I faced a problem in converting
> 3D gaussian output to 2D. I am wondering if there any way that I can
> do it. I would be grateful if you could help me.

I suggest you to try Jamberoo.

Jamberoo can parse both the input and output Gaussian files. In the case of the output files Jamberoo can extract the optimization information and frequencies data and plot them using the interactive charting. It can also animate vibrations. Jamberoo can also parse Gaussian cube files and visualize the volumetric data (MOs, electrostatic potential).

As for the data presentation you have several options in Jamberoo:

1) You can create the jpeg or png image of your molecular scene.

2) For the high quality graphics you can create input file for the PovRay.

3) Finally, you can create a file in the VRML format and use it for creation of the 3D PDF documents.

Regards,
Vlad

--00032555b22224324204a13d423e-- From owner-chemistry@ccl.net Tue Apr 19 11:56:00 2011 From: "Andor Nadj nadj[-]chemie.uni-frankfurt.de" To: CCL Subject: CCL:G: radial distribution of basis set Message-Id: <-44423-110419095900-12482-PR+LoZnni2L0XKMas5obxg(_)server.ccl.net> X-Original-From: "Andor Nadj" Date: Tue, 19 Apr 2011 09:58:58 -0400 Sent to CCL by: "Andor Nadj" [nadj+/-chemie.uni-frankfurt.de] Hello CCL users, It would be helpful to have a program that provides a graphical representation of the radial distribution of the electron density/basis functions from a Gaussian type basis set. That could aid in identifying the specific effects of different basis sets on these characteristics and would be of huge help for some problems I am currently confronted with. Your help is appreciated. Andi From owner-chemistry@ccl.net Tue Apr 19 12:32:00 2011 From: "joseph.golab a ineos.com" To: CCL Subject: CCL: AIChE National Meeting -- Call for Paper (Industrial) Computational Chemistry Sessions Message-Id: <-44424-110419113613-15331-3nLX7QiRR61WocKSm1n0gw##server.ccl.net> X-Original-From: joseph.golab###ineos.com Content-Type: multipart/alternative; boundary="=_alternative 0055B1FF86257877_=" Date: Tue, 19 Apr 2011 10:36:01 -0500 MIME-Version: 1.0 Sent to CCL by: joseph.golab/./ineos.com This is a multipart message in MIME format. --=_alternative 0055B1FF86257877_= Content-Type: text/plain; charset="US-ASCII" Dear Colleagues, It is my pleasure to invite you to participate in the upcoming AIChE National Meeting that will take place October 16-21, 2011 at the Minneapolis Convention Center. Specifically, I call your attention to the Call For Papers for the Industrial Applications of Computational Chemistry and Molecular Simulation sessions hosted by the Computational Molecular Science and Engineering Forum (CoMSEF, http://comsef.org/). Papers are solicited that illustrate new applications of computational chemistry and molecular simulation to industrial problems. Papers exploring novel applications of well established software as well as more exploratory algorithmic development are welcomed. Simulations of chemical reactions, equilibria, and transport would be appropriate for this session, as would the molecular aspects of materials modeling. This session is expected to encompass a diverse range of application areas and will be interesting to anyone practicing computational chemistry. The call deadline is May 2. If you submit your material before APRIL 24 and are accepted, you will be entered in a drawing to receive 50% off the registration fee. The AIChE plans on awarding ten such reductions. You do not have to a member of AIChE to attend this meeting. The instructions for submitting are here: http://aiche.confex.com/aiche/2011/cfp.cgi I will be very pleased to see you in Minneapolis in October! Best regards, Joe ___________________________ Joseph T. Golab, PhD Senior Research Associate Molecular Modeling & Simulation Scientist INEOS Technologies, Nitriles R&D Phone: +1 (630) 420-5063 Cell: +1 (630) 336-0063 Email: Joseph.Golab_at_ineos.com --=_alternative 0055B1FF86257877_= Content-Type: text/html; charset="US-ASCII" Dear Colleagues,

It is my pleasure to invite you to participate in the upcoming AIChE National Meeting that will take place October 16-21, 2011 at the Minneapolis Convention Center.

Specifically, I call your attention to the Call For Papers for the Industrial Applications of Computational Chemistry and Molecular Simulation sessions hosted by the Computational Molecular Science and Engineering Forum (CoMSEF, http://comsef.org/).

Papers are solicited that illustrate new applications of computational chemistry and molecular simulation to industrial problems. Papers exploring novel applications of well established software as well as more exploratory algorithmic development are welcomed. Simulations of chemical reactions, equilibria, and transport would be appropriate for this session, as would the molecular aspects of materials modeling. This session is expected to encompass a diverse range of application areas and will be interesting to anyone practicing computational chemistry.

The call deadline is May 2. If you submit your material before APRIL 24 and are accepted, you will be entered in a drawing to receive 50% off the registration fee. The AIChE plans on awarding ten such reductions. You do not have to a member of AIChE to attend this meeting.

The instructions for submitting are here: http://aiche.confex.com/aiche/2011/cfp.cgi

I will be very pleased to see you in Minneapolis in October!

Best regards,
Joe
___________________________
Joseph T. Golab, PhD
Senior Research Associate
Molecular Modeling & Simulation Scientist
INEOS Technologies, Nitriles R&D
Phone: +1 (630) 420-5063
Cell:  +1 (630) 336-0063
Email: Joseph.Golab_at_ineos.com

--=_alternative 0055B1FF86257877_=-- From owner-chemistry@ccl.net Tue Apr 19 16:54:00 2011 From: "James Gary Prudhomme jprudhomme*o*healthtech.com" To: CCL Subject: CCL: New Targets and Drug Modalities Message-Id: <-44425-110419142531-18363-JaeDcNazwnQopK4mHFx0Pw^^^server.ccl.net> X-Original-From: "James Gary Prudhomme" Date: Tue, 19 Apr 2011 14:25:29 -0400 Sent to CCL by: "James Gary Prudhomme" [jprudhomme[]healthtech.com] CHI and Bio-IT World's "Structure-Based Design" Conference to be held on June 8-10, 2011 in Cambridge, MA, will feature a new session: New Targets and Drug Modalities. The following presentations have just been added and are scheduled on Friday, June 10 from 1:30-3:50 p.m. Structure-Based Ligand Discovery for GPCRs Ruben Abagyan, Ph.D., Professor, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego The Role of Recent Crystal Structures of Membrane Bound Proteins in Drug Discovery for CNS Targets Sid Topiol, Ph.D., CSO, Computational and Structural Investigations, 3D-2Drug Hitting a Moving Target: Characterizing GPCR Signaling through Long-timescale Molecular Dynamics Simulations Ron Dror, Ph.D., Senior Research Scientist and Special Advisor to the Chairman, D. E. Shaw Research Beyond the Orthosteric Binding Site: A Structure-Based SAR Analysis of the D3R Selective Compounds Lei Shi, Ph.D., Assistant Professor, Department of Physiology and Biophysics, HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medical College Moving in New Circles Exploiting Macrocycles for Drug Discovery Nick Terrett, Ph.D., CSO, Ensemble Therapeutics Corp View full details and register at: http://www.healthtech.com/sbd or call 781-972-5400. Those that register by April 29 will receive the advanced registration discount. *** James Prudhomme Marketing Manager Cambridge Healthtech Institute 250 First Avenue, Suite 300 Needham, MA 02494 Tel: 781-972-5486 Fax: 781-972-5425 www.healthtech.com From owner-chemistry@ccl.net Tue Apr 19 19:07:00 2011 From: "upendra Adhikari upendra.adhikari.++.aggiemail.usu.edu" To: CCL Subject: CCL: Any relation between Imaginary frequency and barrier height? Message-Id: <-44426-110419190541-20881-/XpCIFhiSbd64I78zd8lHw++server.ccl.net> X-Original-From: "upendra Adhikari" Date: Tue, 19 Apr 2011 19:05:38 -0400 Sent to CCL by: "upendra Adhikari" [upendra.adhikari|a|aggiemail.usu.edu] Dear all, While calculating for the transition state I got different magnitude of imaginary frequencies for different methods, in some cases I got like -100 cm-1 and for some cases -300 cm-1, so I was wondering that is there any relationship between the magnitude of imaginary frequency with barrier height or geometry or something like that? Thank you!! Upendra From owner-chemistry@ccl.net Tue Apr 19 20:25:00 2011 From: "Maura Mooney mmooney05]![qub.ac.uk" To: CCL Subject: CCL:G: Gaussian error? Message-Id: <-44427-110419202255-12199-QHWnDoqpkxCJLwYXj4avsg+*+server.ccl.net> X-Original-From: "Maura Mooney" Date: Tue, 19 Apr 2011 20:22:53 -0400 Sent to CCL by: "Maura Mooney" [mmooney05|a|qub.ac.uk] Hi all, I've seen this error posted previously but have not seen any solutions, as yet. I am running a gaussian rhf GeoOpt, but it fails to complete. SDV returned info= 518 to GenInv. SVD failed for GenInv. Error termination via Lnkle in ... Can anyone help with the source of this error? Thanx From owner-chemistry@ccl.net Tue Apr 19 21:39:01 2011 From: "Jun Zhang coolrainbow .. yahoo.cn" To: CCL Subject: CCL: Any relation between Imaginary frequency and barrier height? Message-Id: <-44428-110419195538-18768-Sn+hYpE3sXTOKeEMHncZvg*o*server.ccl.net> X-Original-From: Jun Zhang Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=iso-8859-1 Date: Wed, 20 Apr 2011 07:55:25 +0800 (CST) MIME-Version: 1.0 Sent to CCL by: Jun Zhang [coolrainbow*yahoo.cn] Hello Upendra: Actually the frequency (whether real or imaginary) describes the curvature of the PES, i.e. a local property rather than a global one, so in my point of view I think it has little connection with barrier height. Good Luck! --- Jun Zhang Nankai University coolrainbow*|*yahoo.cn upendra.adhikari.*|*.aggiemail.usu.edu >upendra Adhikari upendra.adhikari.*|*.aggiemail.usu.edu >CCL: Any relation between Imaginary frequency and barrier height? > "Zhang, Jun " > > Sent to CCL by: "upendra  Adhikari" > [upendra.adhikari|a|aggiemail.usu.edu] > Dear all, > While calculating for the transition state I got different > magnitude of imaginary frequencies for different methods, in > some cases I got like -100 cm-1 and for some cases -300 > cm-1, so I was wondering that is there any relationship > between the magnitude of imaginary frequency with barrier > height or geometry or something like that? > > Thank you!! > > Upendra >