From owner-chemistry@ccl.net Fri Mar 20 05:42:00 2009
From: "taner atalar taneratalar%%gmail.com" <owner-chemistry{:}server.ccl.net>
To: CCL
Subject: CCL:G: TD-DFT
Message-Id: <-38880-090320045844-15017-LT+Jd5m5kGSRrjTm0A0feg{:}server.ccl.net>
X-Original-From: taner atalar <taneratalar###gmail.com>
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Date: Fri, 20 Mar 2009 10:02:11 +0200
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Sent to CCL by: taner atalar [taneratalar- -gmail.com]
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Hi,

I am the beginner for the TD-DFT learning by using the Gaussian 03 w, so are
there any good sources and/or references for learning TD-DFT (freely
available) ?

Also any useful materials about the Gaussian usage and about output
interpretation for this method (TD-DFT) ?

I tried to do some calculations by using TD-DFT with Gaussian 03 W,
unfortunately all the my calculations terminated with errors.

Any suggestions? or Any help ?


Thank you very much in advance,

Taner Atalar

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<div>Hi,</div>
<div>=A0</div>
<div>I am the beginner for the TD-DFT learning by using the Gaussian 03 w, =
so are there any good sources and/or references for learning TD-DFT (freely=
 available) ?</div>
<div>=A0</div>
<div>Also any=A0useful=A0materials=A0about the Gaussian usage and about=A0o=
utput interpretation=A0for this method (TD-DFT) ?</div>
<div>=A0</div>
<div>I tried to do some calculations by using TD-DFT with Gaussian 03 W, un=
fortunately all the my calculations terminated with errors.</div>
<div>=A0</div>
<div>Any suggestions? or Any help ?</div>
<div>=A0</div>
<div>=A0</div>
<div>Thank you very much in advance,</div>
<div>=A0</div>
<div>Taner Atalar</div>

--0015174c3c668071b704658855d9--


From owner-chemistry@ccl.net Fri Mar 20 06:05:01 2009
From: "Siamkhanthang Neihsial sktn06!A!gmail.com" <owner-chemistry%%server.ccl.net>
To: CCL
Subject: CCL: Difficulty of DFT calculation on dianions species
Message-Id: <-38881-090320060147-31008-Yp7mPP8U8IlyEYCMy/ithQ%%server.ccl.net>
X-Original-From: "Siamkhanthang  Neihsial" <sktn06:-:gmail.com>
Date: Fri, 20 Mar 2009 06:01:43 -0400


Sent to CCL by: "Siamkhanthang  Neihsial" [sktn06*o*gmail.com]
Dear,
 CClers

I have read lots of literatures regarding the difficulties of DFT calculations on dianions species, but i have to admit that i donot understand it properly. Can any one explain it to me. Thanks in advance

Siamkhanthang Neihsial
PhD Research Scholar
Deptt. of Chemistry
NEHU , Shillong ,India
sktn06(!)gmail.com


From owner-chemistry@ccl.net Fri Mar 20 06:44:01 2009
From: "Harald Lanig harald.lanig|a|chemie.uni-erlangen.de" <owner-chemistry(_)server.ccl.net>
To: CCL
Subject: CCL: Announcement of Model(l)ing 09 - The annual 2009 MGMS Meeting in Erlangen, Germany
Message-Id: <-38882-090320051941-17141-JI6DCzwwkaYGHQtbv9P1ag(_)server.ccl.net>
X-Original-From: Harald Lanig <harald.lanig%chemie.uni-erlangen.de>
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Date: Fri, 20 Mar 2009 09:41:25 +0100
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Sent to CCL by: Harald Lanig [harald.lanig ~ chemie.uni-erlangen.de]
Dear CCL subscribers,

The Annual International Meeting of the Molecular Graphics and Modelling=20
Society (MGMS) will take place in Erlangen, Germany  from September 7th=20
(registration and mixer) - 11th 2009. The meeting will be preceded by=20
the annual Molecular Modelling Workshop organised by the Molecular=20
Graphics and Modelling Society - Deutschsprachige Sektion (MGMS-DS) from=20
Sunday 6th to Monday, September 7th.

Model(l)ing 09 is also a celebration of Tim Clark's 60th birthday.

The following speakers already agreed to give invited lectures:

     * Frank Blaney (GlaxoSmithKline)
     * Gabriele Cruciani (University of Perugia)
     * Jon Essex (University of Southhampton)
     * Robert Glen (University of Cambridge)
     * Holger Gohlke (University of D=FCsseldorf)
     * Andreas Goerling (University of Erlangen-N=FCrnberg)
     * Trevor Howe (Johnson & Johnson)
     * Christof Jaeger (University of Erlangen-N=FCrnberg)
     * Christian Kramer (Boehringer Ingelheim)
     * Harald Lanig (University of Erlangen-N=FCrnberg)
     * Adrian Mulholland (University of Bristol)
     * Nigel Richards (University of Florida)
     * Dave Ritchie (Loria)
     * Gisbert Schneider (University of Frankfurt/Main)
     * Heinrich Sticht (University of Erlangen-N=FCrnberg)

In addition, the Claus-Wilhelm von der Lieth Medal will be awarded for=20
the first time at Model(l)ing 09 and the winner will present an award=20
lecture.

Details of the conference and online registration are now available=20
under http://www.modeling09.com/

We are looking forward to seeing you in Erlangen!

Kind regards,
-Harald Lanig

--=20
------------------------------------------------------------------------
  Dr. Harald Lanig            Universitaet Erlangen/Nuernberg
  Computer-Chemie-Centrum     Naegelsbachstr. 25, D-91052 Erlangen

  Phone +49(0)9131-85 26525   harald DOT lanig AT chemie.uni-erlangen.de
  Fax   +49(0)9131-85 26565   http://www.chemie.uni-erlangen.de/lanig
------------------------------------------------------------------------


From owner-chemistry@ccl.net Fri Mar 20 07:15:00 2009
From: "Marc Baaden baaden]*[smplinux.de" <owner-chemistry/a\server.ccl.net>
To: CCL
Subject: CCL: MM-PBSA calculation in Gromacs
Message-Id: <-38883-090320062933-21968-QZj2CAHtZ3QKbWW4Mo7tqQ/a\server.ccl.net>
X-Original-From: Marc Baaden <baaden%smplinux.de>
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Date: Fri, 20 Mar 2009 10:46:10 +0100
Mime-Version: 1.0


Sent to CCL by: Marc Baaden [baaden+/-smplinux.de]

Dear Neha Gandhi,

I have indeed been working on some scripts (derived from the original
Amber ones) to carry out mm-pbsa analysis with Gromacs. At the present
stage (sort of beta-testing) these scripts are not yet publicly available=
.
Anybody interested can contact me directly for more details.

Sincerely,
Marc Baaden

http://www.baaden.ibpc.fr


>>> =22Neha Gandhi n.gandhiau..gmail.com=22 said:
 >>=20
 >> Sent to CCL by: Neha Gandhi =5Bn.gandhiau=5Egmail.com=5D
 >> Hi,
 >>=20
 >> Did anyone tried running mm-pbsa using gromacs trajectories? Are ther=
e
 >> any scripts to run mm-pbsa calculations in gromacs?
 >>=20
 >> Kindly help=21
 >>=20
 >> --=20
 >> Regards,
 >> Neha Gandhi,
--=20
 Dr. Marc Baaden  - Institut de Biologie Physico-Chimique, Paris
 mailto:baaden=40smplinux.de      -      http://www.baaden.ibpc.fr
 FAX: +33 15841 5026  -  Tel: +33 15841 5176  ou  +33 609 843217


From owner-chemistry@ccl.net Fri Mar 20 08:48:01 2009
From: "Lucilla Angeli angeli10+*+unisi.it" <owner-chemistry:server.ccl.net>
To: CCL
Subject: CCL: Seventh European Workshop in Drug Design
Message-Id: <-38884-090319083612-25936-oab1k5oxj7QLCPJxQvmK3A:server.ccl.net>
X-Original-From: Lucilla Angeli <angeli10,,unisi.it>
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Date: Thu, 19 Mar 2009 13:37:43 +0100
MIME-version: 1.0


Sent to CCL by: Lucilla Angeli [angeli10{=}unisi.it]

The University of Siena is pleased to announce the Seventh European
                Workshop in Drug Design May 24-30, 2009

    This workshop, which follows up the six very successful previous
 editions, held respectively in Cortona on May 1995 and in Siena on May
1998, June 2001, May 2003, May 2005 and June 2007, will feature about 25
   well known researchers from the University and the Pharmaceutical
Industry, including directors of research, working with a maximum number
 of 65 workshop participants. Participants will be divided into teams,
each one led by a tutor, and will focus on solving concrete problems in
drug design using high level hardware and software tools. Talks and case
 studies will be interdisciplinary, touching uponligand/structure based
     drug design,in silico ADME-Tox,design and screening of virtual
                     libraries, molecular modelling
methodologies,cheminformatics/bioinformatics and synthetic feasibility,
                                  etc.

  With the purpose to stimulate helpful discussions, attendees will be
      invited to present a poster illustrating their own research.
Participation in the Seventh European Workshop in Drug Design is limited
   to 65 applicants, selected on the basis of individual experience.


                  For more info see: www.unisi.it/EWDD

  To apply, please submit your name, address, affiliation, and primary
 area of research, along with a curriculum vitae, by fax or mail/E-mail
                                  to:


Prof. Maurizio Botta, “Seventh European Workshop in Drug Design”,
Università di Siena 
Dipartimento Farmaco Chimico Tecnologico 
Via Aldo Moro 2, I-53100 Siena, Italy 
Fax: +39(0)577 234333 
email:botta]^[unisi.it


    Fee for participation (Euro 2,500.00) will include all meals and
participation in social events and hotel accommodation in two-bed rooms
 for seven nights (some single rooms are also available, supplementary
                           fee Euro 300.00). 

   Financial aid will be available by request for a limited number of
                              applicants.


             Deadline for applications is March 31st, 2009


Organizing Secretariat: 

Dr.Suvi Rajamäki
Dipartimento Farmaco Chimico Tecnologico—Università degli studi di Siena
Via Aldo Moro 2, I-53100 Siena, Italy
email:rajamaki]^[unisi.it




-- 
*********************************
Dr.Lucilla Angeli
Dip. Farmaco Chimico Tecnologico
Universita' degli Studi Di Siena
Via Aldo Moro
I-53100 Siena, Italy
Phone:  ++39 0577 234256
Fax:    ++39 0577 234333
e-mail  angeli10]^[unisi.it
**********************************


From owner-chemistry@ccl.net Fri Mar 20 10:38:01 2009
From: "=?gb2312?B?yqnBvA==?= shiliang{}mail.ustc.edu.cn" <owner-chemistry###server.ccl.net>
To: CCL
Subject: CCL:G: Regarding the C-NO2 BDE calculations
Message-Id: <-38885-090320103639-30858-LZX5rjU6WeuiJitTQimYNQ###server.ccl.net>
X-Original-From: "=?gb2312?B?yqnBvA==?=" <shiliang::mail.ustc.edu.cn>
Content-Type: text/plain
Date: Fri, 20 Mar 2009 22:05:59 +0800


Sent to CCL by: "=?gb2312?B?yqnBvA==?=" [shiliang[#]mail.ustc.edu.cn]
Dear CCLers:

In my calculated systems, some molecules have the nitro groups connected to the
carbon atoms. I intend to investigate the relationships of the C-N bond
dissociation enthalpies (BDE) and its bond lengths. But unfortunately I find the
DFT methods and MP2 fails to reproduce the experimental values of C-NO2 BDEs
accurately. Moreover, in the chain compounds and aromatic compounds the
performances of DFT are different: Some predict chain compounds well while some
predict aromatic compounds well. Could some one tell me what the problem is in my
computation? I optimized the geometry using b3lyp in Gaussian03. Thank you for
your attention and kind help!


Best wishes,

Liang Shi


From owner-chemistry@ccl.net Fri Mar 20 11:58:00 2009
From: "Tai Ba Truong truong.batai{:}chem.kuleuven.be" <owner-chemistry-,-server.ccl.net>
To: CCL
Subject: CCL:G: Please help me to obtain separate pi and sigma orbitals?
Message-Id: <-38886-090320094902-23892-WLlGBxvHT6TfP8CDsCn3jw-,-server.ccl.net>
X-Original-From: "Tai Ba Truong" <truong.batai*_*chem.kuleuven.be>
Date: Fri, 20 Mar 2009 09:48:59 -0400


Sent to CCL by: "Tai Ba Truong" [truong.batai()chem.kuleuven.be]
Dear Sir/Madam

I am trying to plot ELFs for metal clusters. I would like to plot pi and sigma ELF separately to identify thier aromaticity.
The problem is that I donnot know how to separate pi and sigma orbital in wavefunction to plot ELFs. I am using Gaussian03 softwave and topmod for plot ELFs. Could anyone know how to do it?

I will apreciate very mcuh for your help.

Thank you very much indeed


From owner-chemistry@ccl.net Fri Mar 20 12:38:01 2009
From: "Jose R. Valverde jrvalverde]|[cnb.csic.es" <owner-chemistry!=!server.ccl.net>
To: CCL
Subject: CCL:G: QM/MM question
Message-Id: <-38887-090318064432-7448-lqcYtQU6pCDssK4bWuJCYQ!=!server.ccl.net>
X-Original-From: "Jose R. Valverde" <jrvalverde:+:cnb.csic.es>
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Date: Wed, 18 Mar 2009 10:41:59 +0100
Mime-Version: 1.0


Sent to CCL by: "Jose R. Valverde" [jrvalverde]=[cnb.csic.es]

On Fri, 6 Mar 2009 01:08:53 -0500
"Maurizzio m.argonni[]gmail.com" <owner-chemistry]_[ccl.net> wrote:
> Dear CCL'ers:
> 
> I would like to perform some QM/MM calculations but I don't seem to be able
> to find adequate software for it that is free for academic use. Are the
> choices really so limited? So far, I am aware of GAMESS interfaced to a very
> dated version of Tinker and then QMMM software from Dr. Truhlar's lab that
> is able to use also GAMESS and Tinker albeit in a limited way because of
> limitations in GAMESS.
> 

You can try GAMESS-US directly using EFF.

You can try NWchem using mixed models and ONIOM.

You can try EGO-VIII with CPMD (but it and its documentation are somewhat 
hidden).

Gromacs interfaces seem to be also getting outdated (sigh) but work.

Ghemical has some degree of support but it's undocumented.

> I have no money to pay for Gaussian or Schrodinger's Qsite and I sort of
> refuse to pay 500 UK Pounds for Chemshell on the basis that I am not British
> (not to mention that most of the software they use as a base for theirs is
> free and/or developed elsewhere).
> 
> Anyway, I would appreciate any insights into what choices I have for  QM/MM
> software that would allow me to do calculations like geometry optimizations,
> transition states, etc. in protein systems. Thanks for the help!
> 
> Maurizzio


-- 
			EMBnet/CNB
		Scientific Computing Service
	Solving all your computer needs for Scientific
			Research.

		http://bioportal.cnb.csic.es
		  http://www.es.embnet.org


From owner-chemistry@ccl.net Fri Mar 20 13:42:01 2009
From: "John McKelvey jmmckel[-]gmail.com" <owner-chemistry:+:server.ccl.net>
To: CCL
Subject: CCL:G: Regarding the C-NO2 BDE calculations
Message-Id: <-38888-090320124041-26513-fKHVTPYXK0WcnWtsMditwA:+:server.ccl.net>
X-Original-From: John McKelvey <jmmckel,gmail.com>
Content-Type: multipart/alternative; boundary=000e0cd2442249590f04658f92b5
Date: Fri, 20 Mar 2009 12:40:15 -0400
MIME-Version: 1.0


Sent to CCL by: John McKelvey [jmmckel%gmail.com]
--000e0cd2442249590f04658f92b5
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Try googling "DFT bond dissociation"  I got many hits..

John McKelvey

2009/3/20 $B;\NI(B shiliang{}mail.ustc.edu.cn <owner-chemistry~!~ccl.net>

>
> Sent to CCL by: "=?gb2312?B?yqnBvA==?=" [shiliang[#]mail.ustc.edu.cn]
> Dear CCLers:
>
> In my calculated systems, some molecules have the nitro groups connected to
> the
> carbon atoms. I intend to investigate the relationships of the C-N bond
> dissociation enthalpies (BDE) and its bond lengths. But unfortunately I
> find the
> DFT methods and MP2 fails to reproduce the experimental values of C-NO2
> BDEs
> accurately. Moreover, in the chain compounds and aromatic compounds the
> performances of DFT are different: Some predict chain compounds well while
> some
> predict aromatic compounds well. Could some one tell me what the problem is
> in my
> computation? I optimized the geometry using b3lyp in Gaussian03. Thank you
> for
> your attention and kind help!
>
>
> Best wishes,
>
> Liang Shi>
>
>

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--000e0cd2442249590f04658f92b5--


From owner-chemistry@ccl.net Fri Mar 20 16:23:01 2009
From: "Gustavo Seabra gustavo.seabra() gmail.com" <owner-chemistry#%#server.ccl.net>
To: CCL
Subject: CCL:G: QM/MM question
Message-Id: <-38889-090320160110-15671-MpVT5GWsqZ1k0NgZCcSLdQ#%#server.ccl.net>
X-Original-From: Gustavo Seabra <gustavo.seabra|a|gmail.com>
Content-Transfer-Encoding: quoted-printable
Content-Type: text/plain; charset=ISO-8859-1
Date: Fri, 20 Mar 2009 16:00:36 -0400
MIME-Version: 1.0


Sent to CCL by: Gustavo Seabra [gustavo.seabra : gmail.com]
Hi,

What kind of QM/MM calculations do you want to do?

If semi-empirical methods are ok, I'd recommend that you use Amber.
Granted, it's not free, but the fee is small compared to other
programs (just US$400 for academic users). Also, depending on your
situation, the fee may be reduced or even waived:

http://ambermd.org
http://ambermd.org/#obtain

If you need ab-initio or dft methods, I'd recommend that you take a
look at the PUPIL interface. It is free and open source, and can
interface different MM and QM packages. The latest release allows you
to use Amber or DLPOLY as the MD driver, and Gaussian, MNDO or SIESTA
as the QM program, and other interfaces are currently being developed.
If the program you want is not there, then you could suggest the
developers of that program to consider providing a PUPIL interface.

http://pupil.sourceforge.net

HTH,
Gustavo Seabra
Postdoctoral Associate
Quantum Theory Project - University of Florida
Gainesville - Florida - USA



On Fri, Mar 6, 2009 at 2:08 AM, Maurizzio m.argonni[]gmail.com
<owner-chemistry]=[ccl.net> wrote:
> Dear CCL'ers:
>
> I would like to perform some QM/MM calculations but I don't seem to be ab=
le
> to find adequate software for it that is free for academic use. Are the
> choices really so limited? So far, I am aware of GAMESS interfaced to a v=
ery
> dated version of Tinker and then QMMM software from Dr. Truhlar's lab tha=
t
> is able to use also GAMESS and Tinker albeit in a limited way because of
> limitations in GAMESS.
>
> I have no money to pay for Gaussian or Schrodinger's Qsite and I sort of
> refuse to pay 500 UK Pounds for Chemshell on the basis that I am not Brit=
ish
> (not to mention that most of the software they use as a base for theirs i=
s
> free and/or developed elsewhere).
>
> Anyway, I would appreciate any insights into what choices I have for=A0 Q=
M/MM
> software that would allow me to do calculations like geometry optimizatio=
ns,
> transition states, etc. in protein systems. Thanks for the help!
>
> Maurizzio
>
>
>