From owner-chemistry@ccl.net Thu Sep 3 08:44:01 2009 From: "Peter Oledzki peter__biosolveit.de" To: CCL Subject: CCL: FREE Interactive BioSolveIT Workshop at FBLD 2009 Message-Id: <-40157-090903084312-28520-gaNt/bIrLhW/QgQiSOzzeQ[A]server.ccl.net> X-Original-From: "Peter Oledzki" Date: Thu, 3 Sep 2009 08:43:08 -0400 Sent to CCL by: "Peter Oledzki" [peter a biosolveit.de] Dear Scientist, BioSolveIT, a pioneer of computational fragment based drug design, would like to cordially invite you to attend our FREE interactive workshop on Fragment-Based Ligand Design which will be held on the 23rd September 2009. The workshop will be provided directly after FBLD 2009 in York, UK. All you need is a laptop and to register. For more details on the agenda of the workshop and how to sign up please take a look at the bottom of the draft timetable of FBLD 2009 - http://www.ysbl.york.ac.uk/fbld/2009/FBLD2009drafttimetable.pdf I look forward to seeing some of you there, Peter Oledzki BioSolveIT Application Scientist From owner-chemistry@ccl.net Thu Sep 3 09:19:00 2009 From: "Alex Henderson alex.henderson+*+manchester.ac.uk" To: CCL Subject: CCL: Graph traversal Message-Id: <-40158-090903084313-28536-GaIM8TwCsOSlI1D7R9orkw**server.ccl.net> X-Original-From: Alex Henderson Content-Type: multipart/alternative; boundary="------------070808070706000109060208" Date: Thu, 03 Sep 2009 13:42:47 +0100 MIME-Version: 1.0 Sent to CCL by: Alex Henderson [alex.henderson++manchester.ac.uk] This is a multi-part message in MIME format. --------------070808070706000109060208 Content-Type: text/plain; charset=ISO-8859-1; format=flowed Content-Transfer-Encoding: 7bit Thanks to all who replied for the suggestions. There's some great software out there! Alex Rajarshi Guha rajarshi.guha ~ gmail.com wrote: > > > On Sat, Aug 29, 2009 at 8:12 AM, Alex Henderson > alex.henderson{}manchester.ac.uk > > wrote: > > Hi, > > I'm looking for software (or a library) that will allow me to > visualise a directed graph. I need some zoom in/out functionality > since my graph contains thousands of nodes. > > Open source/cross-platform preferred. (Also free of course! :-) > > > Cytoscape LaNet-VI, Pajek (as applications) > igraph, Jung, Prefuse (as libraries) > > > -- > Rajarshi Guha > NIH Chemical Genomics Center -- ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Dr. Alex Henderson Surface Analysis Research Centre School of Chemical Engineering and Analytical Science The University of Manchester, PO Box 88, Manchester, M60 1QD, UK t. +44 (0)161 306 4462 | f. +44 (0)870 762 2743 e. Alex.Henderson_-_manchester.ac.uk w. http://www.manchester.ac.uk/sarc/ w. http://www.manchester.ac.uk/cias/ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ --------------070808070706000109060208 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Thanks to all who replied for the suggestions.
There's some great software out there!

Alex

Rajarshi Guha rajarshi.guha ~ gmail.com wrote:


On Sat, Aug 29, 2009 at 8:12 AM, Alex Henderson alex.henderson{}manchester.ac.uk <owner-chemistry!=!ccl.net> wrote:
Hi,

I'm looking for software (or a library) that will allow me to visualise a directed graph. I need some zoom in/out functionality since my graph contains thousands of nodes.

Open source/cross-platform preferred. (Also free of course! :-)

Cytoscape LaNet-VI, Pajek (as applications)
igraph, Jung, Prefuse (as libraries)


--
Rajarshi Guha
NIH Chemical Genomics Center

--

~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Dr. Alex Henderson
Surface Analysis Research Centre
School of Chemical Engineering and Analytical Science
The University of Manchester, PO Box 88, Manchester, M60 1QD, UK
t. +44 (0)161 306 4462 | f. +44 (0)870 762 2743
e. Alex.Henderson_-_manchester.ac.uk
w. http://www.manchester.ac.uk/sarc/
w. http://www.manchester.ac.uk/cias/
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 

--------------070808070706000109060208-- From owner-chemistry@ccl.net Thu Sep 3 10:12:01 2009 From: "Chen Wang pleasant1789*gmail.com" To: CCL Subject: CCL: m06 single-point energy calculation failed to converge in nwchem Message-Id: <-40159-090903100959-18044-MVFOKb8Oy3pReD8PnUyFOA##server.ccl.net> X-Original-From: "Chen Wang" Date: Thu, 3 Sep 2009 10:09:55 -0400 Sent to CCL by: "Chen Wang" [pleasant1789() gmail.com] Dear CCLers, Recently, I have used the m06 method developed by Truhlar Group in 2008 with the NWCHEM programs to calculate the single-point energy. But some calculations failed to converge. The error information in the output was showed in the following ------------------------------------------------------------------------ dft energy failed 0 ------------------------------------------------------------------------ ------------------------------------------------------------------------ current input line : 48: task dft ------------------------------------------------------------------------ ------------------------------------------------------------------------ This type of error is most commonly associatated with calculations not reaching convergence criteria ------------------------------------------------------------------------ For more information see the NWChem manual at http://www.emsl.pnl.gov/docs/nwchem/nwchem.html For further details see manual section: 0:0:dft energy failed:: 0 (rank:0 hostname:a347 pid:2893):ARMCI DASSERT fail. armci.c:ARMCI_Error():260 cond:0 2:SigIntHandler: interrupt signal was caught: 2 3:SigIntHandler: interrupt signal was caught: 2 5:SigIntHandler: interrupt signal was caught: 2 6:SigIntHandler: interrupt signal was caught: 2 1:SigIntHandler: interrupt signal was caught: 2 7:SigIntHandler: interrupt signal was caught: 2 2:SigIntHandler: abort signal was caught: cleaning up: 2 3:SigIntHandler: abort signal was caught: cleaning up: 2 5:SigIntHandler: abort signal was caught: cleaning up: 2 1:SigIntHandler: abort signal was caught: cleaning up: 2 6:SigIntHandler: abort signal was caught: cleaning up: 2 7:SigIntHandler: abort signal was caught: cleaning up: 2 4:SigIntHandler: interrupt signal was caught: 2 4:SigIntHandler: abort signal was caught: cleaning up: 2 Signal 15 received. ********************************************************** What keyword should I add to the input file to solve the problem? And where should I put these keyword in the input file? Thank you for your help. Best regards From owner-chemistry@ccl.net Thu Sep 3 12:42:00 2009 From: "CCL CCL computationalchemist%x%gmail.com" To: CCL Subject: CCL: Transition States Message-Id: <-40160-090903120634-27511-C8g0CzEvj1la+nnHCuT/uQ(-)server.ccl.net> X-Original-From: CCL CCL Content-Type: multipart/alternative; boundary=0015175cf772a237c30472ade121 Date: Thu, 3 Sep 2009 11:17:21 -0400 MIME-Version: 1.0 Sent to CCL by: CCL CCL [computationalchemist###gmail.com] --0015175cf772a237c30472ade121 Content-Type: text/plain; charset=ISO-8859-1 Dear Friends, I am modelling a reaction pathway, using different level of theory, say AM1, HF/3-21G, HF/6-31G, B3LYP/6-31G etc., When, i use the semi-empirical approach, i could trace all the transition state species in the pathway. But, when i use the geometry in higher level, say HF and in DFT (B3LYP), i am not getting the same TSs, as I got in semi-empirical methods, but to the intermediates. Does that mean there is a change in the mechanism in the reaction, or it is just the inability of the DFT to trace the species. I was suggested to do the single point calculationes for those species using higher level denoted as (AM1//B3LYP/6-31G) for such a situation. Could anyone please help me to point out some references, where such situation has been used reported in the literature, where the single point calculationes at DFT and HF level are carried out for the TSs obtained over the semi-empirical approaches. Best regards, Dr. Sanjay -- Regards, Dr. Sanjay Bharathwaj Kumar Dharmendra Institute of Technology, Nagapattinam. --0015175cf772a237c30472ade121 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable
Dear Friends,

I am modelling a reaction pathw= ay, using different level of theory,=A0
say AM1, HF/3-21G, HF/6-3= 1G, B3LYP/6-31G etc.,

When, i use the semi-empiric= al approach, i could trace all the transition state species in the pathway.=
But, when i use the geometry in higher level, say HF and in DFT (B3LYP= ), i am not getting the
same TSs, as I got in semi-empirical meth= ods,=A0but to the intermediates.

Does that mean th= ere is a change in the mechanism in the reaction, or it is just=A0
the inability of the DFT to trace the species.

I was suggested to do the single point calculationes for those species us= ing higher level
denoted as (AM1//B3LYP/6-31G)=A0for such a situa= tion.

Could anyone please help me to point out some reference= s, where such situation has been used
reported in the literature,= where the single point calculationes at DFT and HF level are carried out
for the TSs obtained over the semi-empirical approaches.
Best regards,
Dr. Sanjay

-- <= br> Regards,
Dr. Sanjay Bharathwaj Kumar
Dharmendra Institute of Technology,
Nagapattinam.
--0015175cf772a237c30472ade121-- From owner-chemistry@ccl.net Thu Sep 3 13:25:00 2009 From: "Wayne Steinmetz WES04747]=[pomona.edu" To: CCL Subject: CCL: unsubscribe Message-Id: <-40161-090903131351-14411-sBYwAxDEwX7vZ+RThR02gA[a]server.ccl.net> X-Original-From: Wayne Steinmetz Content-Language: en-US Content-Type: multipart/alternative; boundary="_000_C17A158BE957E340BF09F4E302DB8CC701AF44443F8DPOSTOFFICEc_" Date: Thu, 3 Sep 2009 10:13:17 -0700 MIME-Version: 1.0 Sent to CCL by: Wayne Steinmetz [WES04747[A]pomona.edu] --_000_C17A158BE957E340BF09F4E302DB8CC701AF44443F8DPOSTOFFICEc_ Content-Type: text/plain; charset="us-ascii" Content-Transfer-Encoding: quoted-printable Please unsubscribe. Wayne E. Steinmetz Professor Emeritus of Chemistry USFS Volunteer Chemistry Department Pomona College 645 North College Avenue Claremont, California 91711-6338 USA phone: 1-909-621-8447 FAX: 1-909-607-7726 Email: wsteinmetz*|*pomona.edu WWW: pages.pomona.edu/~wsteinmetz ________________________________ > From: owner-chemistry+wsteinmetz=3D=3Dpomona.claremont.edu*|*ccl.net [mailto:= owner-chemistry+wsteinmetz=3D=3Dpomona.claremont.edu*|*ccl.net] On Behalf Of = CCL CCL computationalchemist%x%gmail.com Sent: Thursday, September 03, 2009 8:17 AM To: Wayne Steinmetz Subject: CCL: Transition States Dear Friends, I am modelling a reaction pathway, using different level of theory, say AM1, HF/3-21G, HF/6-31G, B3LYP/6-31G etc., When, i use the semi-empirical approach, i could trace all the transition s= tate species in the pathway. But, when i use the geometry in higher level, say HF and in DFT (B3LYP), i = am not getting the same TSs, as I got in semi-empirical methods, but to the intermediates. Does that mean there is a change in the mechanism in the reaction, or it is= just the inability of the DFT to trace the species. I was suggested to do the single point calculationes for those species usin= g higher level denoted as (AM1//B3LYP/6-31G) for such a situation. Could anyone please help me to point out some references, where such situat= ion has been used reported in the literature, where the single point calculationes at DFT and= HF level are carried out for the TSs obtained over the semi-empirical approaches. Best regards, Dr. Sanjay -- Regards, Dr. Sanjay Bharathwaj Kumar Dharmendra Institute of Technology, Nagapattinam. ------------------------------------------------------------- This message has been scanned by Postini anti-virus software. =0D --_000_C17A158BE957E340BF09F4E302DB8CC701AF44443F8DPOSTOFFICEc_ Content-Type: text/html; charset="us-ascii" Content-Transfer-Encoding: quoted-printable

Please unsubscribe.<= /font>

 

Wayne E. Steinmetz
Professor Emeritus of Chemistry
USFS Volunteer
Chemistry Department
Pomona College
645 North College Avenue
Claremont, California 91711-6338
USA=
phone: 1-909-621-8447
FAX: 1-909-607-7726
Email: wsteinmetz*|*pomona.edu
WWW: pages.pomona.edu/~wsteinmetz
 


From: owner-chemistry+wsteinmetz=3D=3Dpomona.claremont.edu*|*ccl.net [mailto:owner-chemistry+wsteinmetz=3D=3Dpomona.claremont.edu*|*ccl.net] On Behalf Of CCL CCL computationalchemist%x%gmail.com
Sent: Thursday, September 03= , 2009 8:17 AM
To: Wayne Steinmetz
Subject: CCL: Transition Sta= tes

 

Dear Friends,

 

I am modelling a reaction pathway, using different level of theory, 

say AM1, HF/3-21G, HF/6-31G, B3LYP/6-31G etc.,

 

When, i use the semi-empirical approach, i could trace all the transition state species in the pathway.

But, when i use the geometry in higher level, say HF and in DFT (B3LYP), i am not getting the

same TSs, as I got in semi-empirical methods, but to the intermediates.

 

Does that mean there is a change in the mechanism in the reaction, = or it is just 

the inability of the DFT to trace the species.

 

I was suggested to do the single point calculationes for those spec= ies using higher level

denoted as (AM1//B3LYP/6-31G) for such a situation.=

 

Could anyone please help me to point out some references, where suc= h situation has been used

reported in the literature, where the single point calculationes at= DFT and HF level are carried out

for the TSs obtained over the semi-empirical approaches.=

 

Best regards,

Dr. Sanjay=

 

--
Regards,
Dr. Sanjay Bharathwaj Kumar

Dharmendra Institute of Technology,

Nagapattinam.

-------------------------------------------------------------
This message has been scanned by Postini anti-virus software.
=0D
--_000_C17A158BE957E340BF09F4E302DB8CC701AF44443F8DPOSTOFFICEc_--


From owner-chemistry@ccl.net Thu Sep  3 14:35:00 2009
From: "Johannes Johansson johjo76 * gmail.com" 
To: CCL
Subject: CCL: Transition States
Message-Id: <-40162-090903143308-28968-YdLAKeclsz81pc6UEe4i3A{}server.ccl.net>
X-Original-From: Johannes Johansson 
Content-Type: multipart/alternative; boundary=000e0cd240bcc01e170472b02906
Date: Thu, 3 Sep 2009 20:00:47 +0200
MIME-Version: 1.0


Sent to CCL by: Johannes Johansson [johjo76{:}gmail.com]
--000e0cd240bcc01e170472b02906
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: quoted-printable

Dear Dr. Sanjay,
it would be much easier to help you if you explained which reaction and
mechanism you are trying to model ;-)

Kind regards/Johannes

2009/9/3 CCL CCL computationalchemist%x%gmail.com 

> Dear Friends,
>
> I am modelling a reaction pathway, using different level of theory,
> say AM1, HF/3-21G, HF/6-31G, B3LYP/6-31G etc.,
>
> When, i use the semi-empirical approach, i could trace all the transition
> state species in the pathway.
> But, when i use the geometry in higher level, say HF and in DFT (B3LYP), =
i
> am not getting the
> same TSs, as I got in semi-empirical methods, but to the intermediates.
>
> Does that mean there is a change in the mechanism in the reaction, or it =
is
> just
> the inability of the DFT to trace the species.
>
> I was suggested to do the single point calculationes for those species
> using higher level
> denoted as (AM1//B3LYP/6-31G) for such a situation.
>
> Could anyone please help me to point out some references, where such
> situation has been used
> reported in the literature, where the single point calculationes at DFT a=
nd
> HF level are carried out
> for the TSs obtained over the semi-empirical approaches.
>
> Best regards,
> Dr. Sanjay
>
> --
> Regards,
> Dr. Sanjay Bharathwaj Kumar
> Dharmendra Institute of Technology,
> Nagapattinam.
>



--=20
Adam Johannes Johansson
Ph.D., M.Sc.
Institut f=C3=BCr Organische Chemie
RWTH Aachen University
Landoltweg 1
52056 Aachen
Germany
Cell phone:0708178487
E-mail:johjo76 . gmail.com 
Research web page:www.physto.se/~johjo

--000e0cd240bcc01e170472b02906
Content-Type: text/html; charset=UTF-8
Content-Transfer-Encoding: quoted-printable

Dear Dr. Sanjay,

it would be much easier to help you if = you explained which reaction and mechanism you are trying to model ;-)

Kind regards/Johannes

2009/9/3 CCL CCL computationalchemist%x%gmail.= com <ow= ner-chemistry . ccl.net>
Dear Friends,

I am modelling a reaction pathw= ay, using different level of theory,=C2=A0
say AM1, HF/3-21G, HF/= 6-31G, B3LYP/6-31G etc.,

When, i use the semi-empi= rical approach, i could trace all the transition state species in the pathw= ay.
But, when i use the geometry in higher level, say HF and in DFT (B3LYP= ), i am not getting the
same TSs, as I got in semi-empirical meth= ods,=C2=A0but to the intermediates.

Does that mean= there is a change in the mechanism in the reaction, or it is just=C2=A0
the inability of the DFT to trace the species.

I was suggested to do the single point calculationes for those species us= ing higher level
denoted as (AM1//B3LYP/6-31G)=C2=A0for such a si= tuation.

Could anyone please help me to point out some reference= s, where such situation has been used
reported in the literature,= where the single point calculationes at DFT and HF level are carried out
for the TSs obtained over the semi-empirical approaches.
Best regards,
Dr. Sanjay

--
Regards,
Dr. Sanjay Bharathwaj Kumar
Dharmendra Institute of Technology,
Nagapattinam.



--
Adam Johannes Jo= hansson
Ph.D., M.Sc.
Institut f=C3=BCr Organische Chemie
RWTH Aach= en University
Landoltweg 1
52056 Aachen
Germany
Cell phone:0708= 178487
E-mail:johjo76 . gmail.com<= br>Research web page:www.physto.se/= ~johjo

--000e0cd240bcc01e170472b02906--