From owner-chemistry@ccl.net Mon Feb 6 04:00:00 2012 From: "rafapa|-|us.es" To: CCL Subject: CCL:G: G03 does not read pseudo Message-Id: <-46247-120205035751-28067-lCr7hqhqnzmHOvDyivjsFA]|[server.ccl.net> X-Original-From: rafapa-*-us.es Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=UTF-8; format=flowed Date: Sun, 05 Feb 2012 09:57:33 +0100 MIME-Version: 1.0 Sent to CCL by: rafapa]|[us.es Dear Silvina, the basis set and pseudopotential should be input in the following format. C O H 0 6-311++G(d,p) **** Pt 0 mwb 60 **** Pt 0 mwb 60 Only one blank line after the basis and no asterix after the pseudo just another blank line. Sincerely, Dr. Rafael R. Pappalardo Physical Chemistry Dept., Univ. de Sevilla (Spain) On Sat, 4 Feb 2012 17:33:22 -0500, Silvina Bieza silvinabieza[*]gmail.com wrote: > Sent to CCL by: "Silvina Bieza" [silvinabieza^^gmail.com] > Hello list, > > I am experiencing some problems with a G03 calculation. This is my > input: > > %chk=primero.chk > #p b3lyp/genecp opt(maxcyc=100) scf(xqc,maxconventionalcyc=1000) freq > > Primero > > 0 1 > Pt > Pt 1 2.60928411 > Pt 1 2.60965373 2 63.48738392 > Pt 1 2.59752708 2 60.15835847 3 > -69.19506150 > H 3 B1 1 A1 4 > D1 > C 3 B2 1 A2 4 > D2 > O 6 B3 3 A3 1 > D3 > H 7 B4 6 A4 3 > D4 > H 3 B5 1 A5 4 > D5 > H 6 B6 3 A6 1 > D6 > > B1 2.61248506 > B2 1.76404071 > B3 1.43000000 > B4 0.96000000 > B5 1.94502428 > B6 1.07000000 > A1 96.31367000 > A2 98.08570784 > A3 134.48029962 > A4 158.58000000 > A5 108.58589901 > A6 69.84936514 > D1 -20.04613476 > D2 -2.52843005 > D3 174.01972651 > D4 -103.92385498 > D5 29.78441690 > D6 -163.49304823 > > C O H 0 > 6-311++G(d,p) > **** > Pt 0 > mwb 60 > **** > > > > Pt 0 > mwb 60 > **** > > > I believe that it is not reading the pseudopotential. When it reads > the basis (from the output): > > General basis read from cards: (5D, 7F) > Centers: 6 7 5 8 9 10 > 6-311++G(d,p) > **** > Centers: 1 2 3 4 > mwb60 > **** > > But then... > > 1 78 > 2.680048 -1.455240 1.060615 > No pseudopotential on this center. > > > And. This the warning I get in the output: > > Warning! Pt atom 1 has 78 valence electrons but only 36 basis > functions. > This is less than a minimal basis set! > > I think there is something wrong in the input. Can you help me? > Thank you very much, > Silvina > > > > -= This is automatically added to each message by the mailing script > =- > To recover the email address of the author of the message, please > change> Conferences: > http://server.ccl.net/chemistry/announcements/conferences/ From owner-chemistry@ccl.net Mon Feb 6 08:16:00 2012 From: "Massimiliano Porrini M.Porrini#,#ed.ac.uk" To: CCL Subject: CCL: Proline backbone nitrogen pKa/pKb Message-Id: <-46248-120206074842-11754-zWXnxciit+WExMXENSovUw/a\server.ccl.net> X-Original-From: Massimiliano Porrini Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=ISO-8859-1 Date: Mon, 6 Feb 2012 12:48:29 +0000 MIME-Version: 1.0 Sent to CCL by: Massimiliano Porrini [M.Porrini[a]ed.ac.uk] Hi all, I hope my following question is not that far from the scope of this mailing list. Does anybody know any reference where I could get the value of the pK_a (or related pK_b) of the backbone nitrogen of proline residue as a part of a peptide/protein (not the lone proline) ? Any hint would be really appreciated. Best, -- Dr Massimiliano Porrini Institute for Condensed Matter and Complex Systems School of Physics & Astronomy The University of Edinburgh James Clerk Maxwell Building The King's Buildings Mayfield Road Edinburgh EH9 3JZ Tel +44-(0)131-650-5229 E-mails : M.Porrini~!~ed.ac.uk              mozz76~!~gmail.com              maxp~!~iesl.forth.gr From owner-chemistry@ccl.net Mon Feb 6 08:51:00 2012 From: "Stan van Gisbergen vangisbergen]*[scm.com" To: CCL Subject: CCL: ADF2012 release of Amsterdam Density Functional (ADF) software suite Message-Id: <-46249-120206082349-10121-MnPY/Jhf2STiXIsAFjJ1Hg]~[server.ccl.net> X-Original-From: Stan van Gisbergen Content-Type: multipart/alternative; boundary=Apple-Mail-427-187654610 Date: Mon, 6 Feb 2012 14:24:49 +0100 Mime-Version: 1.0 (Apple Message framework v1084) Sent to CCL by: Stan van Gisbergen [vangisbergen * scm.com] --Apple-Mail-427-187654610 Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset=windows-1252 Dear CCL subscribers, =20 SCM proudly announces a new major release, ADF2012, of our suite of = chemical modeling programs. =20 The Slater-based LCAO Density Functional Theory codes for molecules = (ADF) and periodic systems (BAND) feature all-electron basis sets for = the entire periodic table and relativistic effects through ZORA with = spin-orbit coupling. Both codes offer a very broad range of spectroscopy = calculations and are popular tools for structure and reactivity studies = in chemistry and material science. =20 Apart from our flagship DFT programs, SCM now also offers a = density-functional based tight-binding (DFTB) code for fast approximate = DFT calculations of molecules or periodic systems with molecular = dynamics capabilities and full GUI support for Dr. Stewart's = semi-empirical MOPAC2009 program. =20 Reactive molecular dynamics calculations can be run and analyzed with = the reactive force field program ReaxFF. The post-ADF COSMO-RS module, = with a database of almost 1900 compounds, predicts thermodynamic = properties of mixed fluids and solutions. =20 An integrated graphical user interface seamlessly switches between = modules and allows for cross-platform preparation, execution and = analysis. GUI tutorials make the codes easy to learn and use. The = programs run out of the box in parallel on all major computer platforms = (Windows, Mac, Linux, UNIX). =20 A snapshot of new features in ADF2012: * latest xc functionals, including (hybrid)metaGGAs and dispersion = corrections=20 * electronic transport properties with non-self-consistent Green=92s = functions * homogeneous electric fields for surfaces, flexible unit cells, phonons * fast DFTB code for molecules and periodic systems, including DFTB3 and = dispersion corrections * PyMD python interface to perform complex molecular dynamics: QM/MM, = adaptive, metadynamics * ReaxFF reactive force field for molecular dynamics studies of complex = systems =20 More details: http://www.scm.com/News/ADF2012.html Authors: http://www.scm.com/About/AboutAuthors Our free 30-day trial contains full functionality as well as support. = Sign up now at: http://www.scm.com/trial =20 Best regards, Stan van Gisbergen, on behalf of the SCM team. =20 Dr. S.J.A. van Gisbergen Chief Executive Officer Scientific Computing & Modelling NV Theoretical Chemistry, Vrije Universiteit De Boelelaan 1083 1081 HV Amsterdam The Netherlands vangisbergen===scm.com http://www.scm.com T: +31-20-5987626 F: +31-20-5987629= --Apple-Mail-427-187654610 Content-Transfer-Encoding: quoted-printable Content-Type: text/html; charset=windows-1252
SCM proudly announces a = new major release, ADF2012, of our suite of chemical modeling = programs.

The Slater-based LCAO = Density Functional Theory codes for molecules (ADF) and periodic systems = (BAND) feature all-electron basis sets for the entire periodic table and = relativistic effects through ZORA with spin-orbit coupling. Both codes = offer a very broad range of spectroscopy calculations and are popular = tools for structure and reactivity studies in chemistry and material = science.

Apart from our flagship = DFT programs, SCM now also offers a density-functional based = tight-binding (DFTB) code for fast approximate DFT calculations of = molecules or periodic systems with molecular dynamics capabilities and = full GUI support for Dr. Stewart's semi-empirical MOPAC2009 = program.

Reactive molecular = dynamics calculations can be run and analyzed with the reactive force = field program ReaxFF. The post-ADF COSMO-RS module, with a database of = almost 1900 compounds, predicts thermodynamic properties of mixed fluids = and solutions.

An integrated graphical = user interface seamlessly switches between modules and allows for = cross-platform preparation, execution and analysis. GUI tutorials make = the codes easy to learn and use. The programs run out of the box in = parallel on all major computer platforms (Windows, Mac, Linux, = UNIX).

A snapshot of new = features in ADF2012:

* latest xc = functionals, including (hybrid)metaGGAs and dispersion = corrections* electronic transport = properties with non-self-consistent Green=92s = functions
* homogeneous electric = fields for surfaces, flexible unit cells, = phonons
* fast DFTB code for = molecules and periodic systems, including DFTB3 and dispersion = corrections
* PyMD python interface = to perform complex molecular dynamics: QM/MM, adaptive, = metadynamics
* ReaxFF reactive force = field for molecular dynamics studies of complex = systems

More = details: http://www.scm.com/News/ADF2= 012.html

http://www.scm.com/About/Ab= outAuthors
Our free 30-day trial = contains full functionality as well as support. Sign up now = at: Best = regards,

Dr. S.J.A. van = Gisbergen

F: = +31-20-5987629

= --Apple-Mail-427-187654610-- From owner-chemistry@ccl.net Mon Feb 6 09:26:00 2012 From: "Jim Kress ccl_nospam_-_kressworks.com" To: CCL Subject: CCL:G: Memory and CPU Time Message-Id: <-46250-120206081729-15926-B4jnB1a3r92AZNFFflyiRw(-)server.ccl.net> X-Original-From: "Jim Kress" Content-Language: en-us Content-Type: multipart/alternative; boundary="----=_NextPart_000_0022_01CCE4A7.B9ECB170" Date: Mon, 6 Feb 2012 08:17:11 -0500 MIME-Version: 1.0 Sent to CCL by: "Jim Kress" [ccl_nospam*kressworks.com] This is a multipart message in MIME format. ------=_NextPart_000_0022_01CCE4A7.B9ECB170 Content-Type: text/plain; charset="us-ascii" Content-Transfer-Encoding: 7bit > Or try ORCA.. very efficient and free.. I agree. Jim > From: owner-chemistry+ccl_nospam==kressworks.com%x%ccl.net [mailto:owner-chemistry+ccl_nospam==kressworks.com%x%ccl.net] On Behalf Of John McKelvey jmmckel||gmail.com Sent: Sunday, February 05, 2012 9:16 PM To: Kress, Jim Subject: CCL:G: Memory and CPU Time Or try ORCA.. very efficient and free.. On Sun, Feb 5, 2012 at 8:07 AM, Max J Prendergast eneas.:.usal.es wrote: Sent to CCL by: "Max J Prendergast" [eneas-*-usal.es] How to know that a particular JOB will take how much memory and CPU time in gaussian 03/09 program ? Is there any keyword to calculate the same without performing calculation. I know that how to define the memory and diskspace in gaussian But need to know how much value should put there. Thanks in advance. If your are managing calculations in personal computers, Gaussian is a very annoying software. However, is best for run in parallel. There are a table about memory space in the Gaussian website about parameters to optimaze properly the calculation, nevertheless, its terrible if you try to run in single machines I strongly recommend use jaguar: is better than gaussian and you donthave to manage CPU and space memory. Cheers
 ------=_NextPart_000_0022_01CCE4A7.B9ECB170-- From owner-chemistry@ccl.net Mon Feb 6 10:17:00 2012 From: "Arindam Ganguly arindamganguly(~)gmail.com" To: CCL Subject: CCL: Open Source Toxicity Prediction and QSAR Software Message-Id: <-46251-120206101500-7979-rIiCCnFuDsqIIdIWZd4AHQ/./server.ccl.net> X-Original-From: "Arindam Ganguly" Date: Mon, 6 Feb 2012 10:14:58 -0500 Sent to CCL by: "Arindam Ganguly" [arindamganguly%%gmail.com] Dear CCl users, Good morning and hope you all had a great weekend. I am asking 2 questions, as I understand, and please correct me if I have mis- phrased the question. I am seeking information on OpenSource Software available for Toxicity prediction, preferably with a GUIs and on Windows Platform. I guess, the software will accept a chemical structure and utilize QSAR for predicting toxicity and compare it with published experimental results. Thank you very much for sharing your thoughts and comments. Sincerely, Arindam From owner-chemistry@ccl.net Mon Feb 6 11:40:00 2012 From: "David Gallagher gallagher.da^^^gmail.com" To: CCL Subject: CCL: Open Source Toxicity Prediction and QSAR Software Message-Id: <-46252-120206113853-22303-TTv3DcpCgZwBb8M8qdVVzQ:+:server.ccl.net> X-Original-From: David Gallagher Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Mon, 06 Feb 2012 08:38:38 -0800 MIME-Version: 1.0 Sent to CCL by: David Gallagher [gallagher.da*o*gmail.com] Hi Arindam, One option to consider is the OpenTox project at http://opentox.org/ which was funded by the EU from 2008-2011. An example of a prototype toxicity predictor built with OpenTox is available at http://apps.ideaconsult.net:8080/ToxPredict , and a prototype tool to automatically build predictive models from your own training data is posted at http://www.toxcreate.org/create . An overview of the OpenTox project was presented at ACS last year: http://www.softconference.com/ACSchem/sessionDetail.asp?SID=250349 Regards, David Gallagher CACheResearch.com On 2/6/2012 7:14 AM, Arindam Ganguly arindamganguly(~)gmail.com wrote: > Sent to CCL by: "Arindam Ganguly" [arindamganguly%%gmail.com] > Dear CCl users, > Good morning and hope you all had a great weekend. > > I am asking 2 questions, as I understand, and please correct me if I have mis- > phrased the question. > > I am seeking information on OpenSource Software available for Toxicity > prediction, preferably with a GUIs and on Windows Platform. I guess, the > software will accept a chemical structure and utilize QSAR for predicting > toxicity and compare it with published experimental results. > > Thank you very much for sharing your thoughts and comments. > > Sincerely, > Arindam> > > From owner-chemistry@ccl.net Mon Feb 6 12:46:00 2012 From: "Arindam Ganguly arindamganguly(0)gmail.com" To: CCL Subject: CCL: Open Source Toxicity Prediction and QSAR Software Message-Id: <-46253-120206124439-20294-AmL0+hymCLtlUNXMoHsyGA,+,server.ccl.net> X-Original-From: Arindam Ganguly Content-Type: multipart/alternative; boundary=20cf303f6d6a010a0c04b84f376b Date: Mon, 6 Feb 2012 12:44:31 -0500 MIME-Version: 1.0 Sent to CCL by: Arindam Ganguly [arindamganguly _ gmail.com] --20cf303f6d6a010a0c04b84f376b Content-Type: text/plain; charset=ISO-8859-1 Hi David, Thank you for your suggestions. Sincerely, Arindam On Mon, Feb 6, 2012 at 11:38 AM, David Gallagher gallagher.da^^^gmail.com < owner-chemistry||ccl.net> wrote: > > Sent to CCL by: David Gallagher [gallagher.da*o*gmail.com] > Hi Arindam, > > One option to consider is the OpenTox project at http://opentox.org/which was funded by the EU from 2008-2011. An example of a prototype > toxicity predictor built with OpenTox is available at > http://apps.ideaconsult.net:**8080/ToxPredict, and a prototype tool to automatically build predictive models from your > own training data is posted at http://www.toxcreate.org/**create. > > An overview of the OpenTox project was presented at ACS last year: > http://www.softconference.com/**ACSchem/sessionDetail.asp?SID=**250349 > > Regards, > David Gallagher > CACheResearch.com > > > > On 2/6/2012 7:14 AM, Arindam Ganguly arindamganguly(~)gmail.com wrote: > >> Sent to CCL by: "Arindam Ganguly" [arindamganguly%%gmail.com] >> Dear CCl users, >> Good morning and hope you all had a great weekend. >> >> I am asking 2 questions, as I understand, and please correct me if I have >> mis- >> phrased the question. >> >> I am seeking information on OpenSource Software available for Toxicity >> prediction, preferably with a GUIs and on Windows Platform. I guess, the >> software will accept a chemical structure and utilize QSAR for predicting >> toxicity and compare it with published experimental results. >> >> Thank you very much for sharing your thoughts and comments. >> >> Sincerely, >> Arindam> http://www.ccl.net/cgi-bin/**ccl/send_ccl_message http://www.ccl.net/cgi-bin/**ccl/send_ccl_message chemistry/announcements/**conferences/ > > Search Messages: http://www.ccl.net/chemistry/**searchccl/index.shtml http://www.ccl.net/spammers.**txt > > RTFI: http://www.ccl.net/chemistry/**aboutccl/instructions/ > > > -- Arindam Ganguly, Ph.D. Scientist, USP Applied Compendial Research-Spectrometry Laboratory http://www.linkedin.com/in/arindamganguly --20cf303f6d6a010a0c04b84f376b Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Hi David,
Thank you for your suggestions.

Sinc= erely,
Arindam

On Mon, Feb 6, 2012 at = 11:38 AM, David Gallagher gallagher.da^^^gmail= .com <o= wner-chemistry||ccl.net> wrote:

Sent to CCL by: David Gallagher [gallagher.da*o*gmail.com]
Hi Arindam,

One option to consider is the OpenTox project at http://opentox.org/ which was funded by the EU = > from 2008-2011. =A0An example of a prototype toxicity predictor built with = OpenTox is available at http://apps.ideaconsult.net:8080/ToxPredict , and a prototype tool to automatically build predictive models from you= r own training data is posted at http://www.toxcreate.org/create .

An overview of the OpenTox project was presented at ACS last year:
http://www.softconference.com/ACSchem/sessio= nDetail.asp?SID=3D250349

Regards,
David Gallagher
CACheResearch.com



On 2/6/2012 7:14 AM, Arindam Ganguly arindamganguly(~)gmail.com wrote:
Sent to CCL by: "Arindam =A0 Ganguly" [arindamganguly%%gmail.com]
Dear CCl users,
Good morning and hope you all had a great weekend.

I am asking 2 questions, as I understand, and please correct me if I have m= is-
phrased the question.

I am seeking information on OpenSource Software available for Toxicity
prediction, preferably with a GUIs and on Windows Platform. I guess, the software will accept a chemical structure and utilize QSAR for predicting toxicity and compare it with published experimental results.

Thank you very much for sharing your thoughts and comments.

Sincerely,
Arindam>





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--
=

Arindam Ganguly, Ph.D.
Scientist, USP
Applied Compendial Research-= Spectrometry Laboratory
http://www.linkedin.com/in/arindamganguly


--20cf303f6d6a010a0c04b84f376b--

> Or try ORCA..  very efficient = and free..

I agree.

 

Jim

 

From:= = owner-chemistry+ccl_nospam=3D=3Dkressworks.com%x%ccl.net = [mailto:owner-chemistry+ccl_nospam=3D=3Dkressworks.com%x%ccl.net] On = Behalf Of John McKelvey jmmckel||gmail.com
Sent: Sunday, = February 05, 2012 9:16 PM
To: Kress, Jim =
Subject: CCL:G: Memory and CPU = Time

 

Or try ORCA..  very efficient and = free..

On Sun, Feb 5, 2012 at = 8:07 AM, Max J Prendergast eneas.:.usal.es <owner-chemistry.:.ccl.net&g= t; wrote:


Sent to CCL by: "Max J = Prendergast" [eneas-*-usal.es]
How to know that a particular JOB will = take how much memory and CPU
time in gaussian 03/09 program ? Is = there any keyword to calculate the same
without performing = calculation. I know that how to define the memory and
diskspace in = gaussian But need to know how much value should put there.
  =  Thanks in advance.

If your are managing calculations in = personal computers, Gaussian is a very annoying software. However, is = best for run in parallel. There are a table about memory space in the = Gaussian website about parameters to optimaze properly the calculation, = nevertheless, its terrible if you try to run in single machines

I = strongly recommend use jaguar: is better than gaussian and you donthave = to manage CPU and space memory.

Cheers



-=3D This = is automatically added to each message by the mailing script = =3D-<br


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--
John McKelvey
10819 Middleford Pl
Ft Wayne, = IN 46818
260-489-2160
jmmckel.:.gmail.com