From owner-chemistry@ccl.net Fri Oct 28 01:16:01 2011
From: "Arne Dieckmann adieckma(-)googlemail.com" <owner-chemistry * server.ccl.net>
To: CCL
Subject: CCL:G: DFT and dispersion
Message-Id: <-45753-111028011523-1370-V2krR9zCct+W7wrobbVq0A * server.ccl.net>
X-Original-From: Arne Dieckmann <adieckma###googlemail.com>
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Sent to CCL by: Arne Dieckmann [adieckma(-)googlemail.com]
Dear Lars, 

thanks for your immediate reply. I know about the differences between the Minnesota functionals and the DFT-D3 method. This is why I wanted to augment their mid-range dispersion with the long range dispersion your former group developed. Do you know if TPSS with D-corrections produces significantly different geometries than M06-2X without D-corrections? How much do geometries of molecules (>= 50 atoms) change in general? I am just wondering if it will be sufficient to optimize with M06-2X and apply the single point D-corrections. 

By the way, do you know how well DFT-D3 works with implicit solvation? I guess in this case the parameters would have to be solvent-dependent, right? 


Thanks again, 
Arne

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 
Dr. Arne Dieckmann
Houk Research Lab
University of California, Los Angeles 
email: adieckma()googlemail.com


On Oct 27, 2011, at 5:28 PM, Dr. Lars Goerigk lars.goerigk{}chem.usyd.edu.au wrote:

> 
> Sent to CCL by: "Dr. Lars Goerigk" [lars.goerigk(~)chem.usyd.edu.au]
> Dear Arne,
> 
> M06-2X was fitted to noncovalently bound systems in their equilibrium geometries and due to that fit it somehow incorporates medium-range dispersion interactions. However, as also discussed in the literature, it is expected that the asymptotic long-range behavior is still not correct and that it can also benefit from dispersion corrections.
> On the issue DFT-D3 in combination with the Minnesota functionals you can refer to PCCP 2011, 13, 6670. There, the parameters for DFT-D3 for those functionals were published and discussed.
> 
> DFT-D2 parameters for the Minnesota functionals were published by the Martin group in JPCA 2008, 112, 12868. The s6 had to be smaller than unity, though, which still does not give the correct asymptotics, opposed to DFT-D3, where it was fixed to unity.
> 
> If you have the Gaussian code available you could try to implement DFT-D3 (based on the code Stefan Grimme made available on his website).
> If you do not have the code, you would have to use DFT-D2. Please note that in G09 Rev A, DFT-D2 only works with B97-D and omega-B97X-D.
> That bug was fixed however and in Rev. B01 and higher you can now also use DFT-D2 for those functionals, which are mentioned in Grimme's DFT-D2 paper from 2006 (i.e. also for B3LYP, TPSS, PBE, BP86).
> You have to use the IOp(3/124=3) then. In combination with IOp33(3=3) you also get a printout to check, if the correct s6 value was applied.
> Other functionals are not supported and I do not know if it is possible to read in an s6 specified by the user (maybe you should contact the Gaussian support to find that out). IOp(3/124=1)  adds the dispersion correction to any functional, but only with an s6=1, which is too large for the Minnesota functionals.
> 
> If you can't use M06-2X, you could try TPSS in combination with D-corrections. Based on publications and my own experience, this gives very good structures.
> 
> Another possibility would be to get ORCA, which is for free. I am not 100% sure if DFT-D3 is already implemented; have a look at the ORCA website for that.
> You could also check if other programs have already implemented DFT-D3.
> 
> I hope these information could help you.
> 
> With best wishes,
> Lars
> 
> -- 
> Dr. Lars Goerigk
> School of Chemistry
> The University of Sydney
> Sydney, New South Wales 2006
> Australiahttp://www.ccl.net/chemistry/sub_unsub.shtml> 
>


From owner-chemistry@ccl.net Fri Oct 28 02:39:00 2011
From: "Dr. Lars Goerigk lars.goerigk:+:chem.usyd.edu.au" <owner-chemistry-#-server.ccl.net>
To: CCL
Subject: CCL:G: DFT and dispersion
Message-Id: <-45754-111028022713-23528-wEW770naM9eXKv/+v00s3g-#-server.ccl.net>
X-Original-From: "Dr. Lars Goerigk" <lars.goerigk%chem.usyd.edu.au>
Content-Transfer-Encoding: 7bit
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Date: Fri, 28 Oct 2011 17:26:51 +1100
MIME-Version: 1.0


Sent to CCL by: "Dr. Lars Goerigk" [lars.goerigk a chem.usyd.edu.au]
Dear Arne,

I guess it depends entirely on your system to decide whether a D 
correction with M06-2X has an impact on the geometries or not. As I do 
not know the system, I cannot say how much of the intramolecular 
dispersion effects are covered by M06-2X. I also do not have much 
experience with M06-2X-D3 geometry optimizations. However, I assume that 
a system of more than 50 atoms should show significant intramolecular 
dispersion effects, that of course also influence the relative energies 
between conformers.

Personally, I would always include a dispersion correction to be on the 
safe side. Maybe you could run a test calculation on one of the systems 
with M06-2X and another dipsersion-corrected functional (TPSS should be 
in general faster, of course). Then you can maybe see the effect on your 
system and can make a final decision.

But maybe other users, who are reading this, have already done such a 
comparison and can give you also some recommendations.

Cheers,
Lars

On 28/10/2011 4:15 PM, Arne Dieckmann adieckma(-)googlemail.com wrote:
> Sent to CCL by: Arne Dieckmann [adieckma(-)googlemail.com]
> Dear Lars,
>
> thanks for your immediate reply. I know about the differences between the Minnesota functionals and the DFT-D3 method. This is why I wanted to augment their mid-range dispersion with the long range dispersion your former group developed. Do you know if TPSS with D-corrections produces significantly different geometries than M06-2X without D-corrections? How much do geometries of molecules (>= 50 atoms) change in general? I am just wondering if it will be sufficient to optimize with M06-2X and apply the single point D-corrections.
>
> By the way, do you know how well DFT-D3 works with implicit solvation? I guess in this case the parameters would have to be solvent-dependent, right?
>
>
> Thanks again,
> Arne
>
> - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
> Dr. Arne Dieckmann
> Houk Research Lab
> University of California, Los Angeles
> email: adieckma+*+googlemail.com
>
>
> On Oct 27, 2011, at 5:28 PM, Dr. Lars Goerigk lars.goerigk{}chem.usyd.edu.au wrote:
>
>> Sent to CCL by: "Dr. Lars Goerigk" [lars.goerigk(~)chem.usyd.edu.au]
>> Dear Arne,
>>
>> M06-2X was fitted to noncovalently bound systems in their equilibrium geometries and due to that fit it somehow incorporates medium-range dispersion interactions. However, as also discussed in the literature, it is expected that the asymptotic long-range behavior is still not correct and that it can also benefit from dispersion corrections.
>> On the issue DFT-D3 in combination with the Minnesota functionals you can refer to PCCP 2011, 13, 6670. There, the parameters for DFT-D3 for those functionals were published and discussed.
>>
>> DFT-D2 parameters for the Minnesota functionals were published by the Martin group in JPCA 2008, 112, 12868. The s6 had to be smaller than unity, though, which still does not give the correct asymptotics, opposed to DFT-D3, where it was fixed to unity.
>>
>> If you have the Gaussian code available you could try to implement DFT-D3 (based on the code Stefan Grimme made available on his website).
>> If you do not have the code, you would have to use DFT-D2. Please note that in G09 Rev A, DFT-D2 only works with B97-D and omega-B97X-D.
>> That bug was fixed however and in Rev. B01 and higher you can now also use DFT-D2 for those functionals, which are mentioned in Grimme's DFT-D2 paper from 2006 (i.e. also for B3LYP, TPSS, PBE, BP86).
>> You have to use the IOp(3/124=3) then. In combination with IOp33(3=3) you also get a printout to check, if the correct s6 value was applied.
>> Other functionals are not supported and I do not know if it is possible to read in an s6 specified by the user (maybe you should contact the Gaussian support to find that out). IOp(3/124=1)  adds the dispersion correction to any functional, but only with an s6=1, which is too large for the Minnesota functionals.
>>
>> If you can't use M06-2X, you could try TPSS in combination with D-corrections. Based on publications and my own experience, this gives very good structures.
>>
>> Another possibility would be to get ORCA, which is for free. I am not 100% sure if DFT-D3 is already implemented; have a look at the ORCA website for that.
>> You could also check if other programs have already implemented DFT-D3.
>>
>> I hope these information could help you.
>>
>> With best wishes,
>> Lars
>>
>> -- 
>> Dr. Lars Goerigk
>> School of Chemistry
>> The University of Sydney
>> Sydney, New South Wales 2006
>> Australiahttp://www.ccl.net/chemistry/sub_unsub.shtml>
>


-- 
Dr. Lars Goerigk
School of Chemistry
The University of Sydney
Sydney, New South Wales 2006
Australia


From owner-chemistry@ccl.net Fri Oct 28 03:42:01 2011
From: "Neese, Frank frank.neese*mpi-mail.mpg.de" <owner-chemistry_+_server.ccl.net>
To: CCL
Subject: CCL:G: DFT and dispersion
Message-Id: <-45755-111028033948-32338-tZcOuntb3vVg6RwthIMQog_+_server.ccl.net>
X-Original-From: "Neese, Frank" <frank.neese _ mpi-mail.mpg.de>
Content-Transfer-Encoding: 8bit
Content-Type: text/plain;
	charset="us-ascii"
Date: Fri, 28 Oct 2011 09:39:09 +0200
MIME-Version: 1.0 (1.0)


Sent to CCL by: "Neese, Frank" [frank.neese^-^mpi-mail.mpg.de]
Just to briefly clarify what Lars eluded to: DFT-D3 *is* in ORCA and is also the default for dispersion corrected DFT.

Best regards,
Frank



Am 28.10.2011 um 08:41 schrieb "Arne Dieckmann adieckma(-)googlemail.com" <owner-chemistry::ccl.net>:

> 
> Sent to CCL by: Arne Dieckmann [adieckma(-)googlemail.com]
> Dear Lars, 
> 
> thanks for your immediate reply. I know about the differences between the Minnesota functionals and the DFT-D3 method. This is why I wanted to augment their mid-range dispersion with the long range dispersion your former group developed. Do you know if TPSS with D-corrections produces significantly different geometries than M06-2X without D-corrections? How much do geometries of molecules (>= 50 atoms) change in general? I am just wondering if it will be sufficient to optimize with M06-2X and apply the single point D-corrections. 
> 
> By the way, do you know how well DFT-D3 works with implicit solvation? I guess in this case the parameters would have to be solvent-dependent, right? 
> 
> 
> Thanks again, 
> Arne
> 
> - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 
> Dr. Arne Dieckmann
> Houk Research Lab
> University of California, Los Angeles 
> email: adieckma+*+googlemail.com
> 
> 
> On Oct 27, 2011, at 5:28 PM, Dr. Lars Goerigk lars.goerigk{}chem.usyd.edu.au wrote:
> 
>> 
>> Sent to CCL by: "Dr. Lars Goerigk" [lars.goerigk(~)chem.usyd.edu.au]
>> Dear Arne,
>> 
>> M06-2X was fitted to noncovalently bound systems in their equilibrium geometries and due to that fit it somehow incorporates medium-range dispersion interactions. However, as also discussed in the literature, it is expected that the asymptotic long-range behavior is still not correct and that it can also benefit from dispersion corrections.
>> On the issue DFT-D3 in combination with the Minnesota functionals you can refer to PCCP 2011, 13, 6670. There, the parameters for DFT-D3 for those functionals were published and discussed.
>> 
>> DFT-D2 parameters for the Minnesota functionals were published by the Martin group in JPCA 2008, 112, 12868. The s6 had to be smaller than unity, though, which still does not give the correct asymptotics, opposed to DFT-D3, where it was fixed to unity.
>> 
>> If you have the Gaussian code available you could try to implement DFT-D3 (based on the code Stefan Grimme made available on his website).
>> If you do not have the code, you would have to use DFT-D2. Please note that in G09 Rev A, DFT-D2 only works with B97-D and omega-B97X-D.
>> That bug was fixed however and in Rev. B01 and higher you can now also use DFT-D2 for those functionals, which are mentioned in Grimme's DFT-D2 paper from 2006 (i.e. also for B3LYP, TPSS, PBE, BP86).
>> You have to use the IOp(3/124=3) then. In combination with IOp33(3=3) you also get a printout to check, if the correct s6 value was applied.
>> Other functionals are not supported and I do not know if it is possible to read in an s6 specified by the user (maybe you should contact the Gaussian support to find that out). IOp(3/124=1)  adds the dispersion correction to any functional, but only with an s6=1, which is too large for the Minnesota functionals.
>> 
>> If you can't use M06-2X, you could try TPSS in combination with D-corrections. Based on publications and my own experience, this gives very good structures.
>> 
>> Another possibility would be to get ORCA, which is for free. I am not 100% sure if DFT-D3 is already implemented; have a look at the ORCA website for that.
>> You could also check if other programs have already implemented DFT-D3.
>> 
>> I hope these information could help you.
>> 
>> With best wishes,
>> Lars
>> 
>> -- 
>> Dr. Lars Goerigk
>> School of Chemistry
>> The University of Sydney
>> Sydney, New South Wales 2006
>> Australiahttp://www.ccl.net/chemistry/sub_unsub.shtml> 
>


From owner-chemistry@ccl.net Fri Oct 28 04:17:00 2011
From: "Jan Kuras jan.kuras * chemistrycentral.com" <owner-chemistry(-)server.ccl.net>
To: CCL
Subject: CCL: Reminder: Syst chem biol & other systems approaches, ACS Meeting 2012
Message-Id: <-45756-111028035100-13490-lLDD5p21b5vedFt3UouwzA(-)server.ccl.net>
X-Original-From: "Jan  Kuras" <jan.kuras * chemistrycentral.com>
Date: Fri, 28 Oct 2011 03:50:57 -0400


Sent to CCL by: "Jan  Kuras" [jan.kuras]*[chemistrycentral.com]
Call for papers: deadline 31 October 2011

Session title: Systems chemical biology and other "systems" approaches in chemistry and biology research

243rd ACS National Meeting, San Diego, California, March 25-29, 2012 CINF Division

We are accepting submission of abstracts for consideration for an ACS Division of Chemical Information (CINF) Symposium on systems-based approaches in chemistry and biology research.

A systems approach to science aims to study complex networks rather than isolated entities.  This goal of this symposium is to review recent  developments in systems chemical biology, systems biology and systems chemistry, and examine links between them.

In systems biology large networks describing the regulation of entire genomes, metabolic pathways and signal transduction pathways are analyzed in their totality at different levels of biological organization.  The development of cheminformatics tools that can integrate chemical knowledge with this biological data has created an interest in systems chemical biology.  Systems chemistry provides another new research area moving beyond single molecular entities to multi-component, multi-functional chemical systems to create new functions from molecular components at different hierarchical levels or via molecular networks with emergent properties.  The development of these integrated systems-based approaches could improve our understanding of complex chemical and biological networks in areas as diverse as drug discovery and materials science.

Presentations will be 25-30 minutes, including time for questions. The deadline for submitting an abstract for consideration is October 31, 2011. Abstracts may be submitted via: http://abstracts.acs.org.

Please contact the co-organizers if you have any questions or to discuss a paper.

Thank you,
Tudor Oprea, Professor Biochemistry and Molecular Biology, University of New Mexico (toprea:_:salud.unm.edu)

Jan Kuras, Journal Publisher, Chemistry Central (jan.kuras:_:chemistrycentral.com)

______________________
Jan Kuras
Chemistry Central
236 Gray's Inn Road
London WC1X 8HB, UK
www.chemistrycentral.com


From owner-chemistry@ccl.net Fri Oct 28 04:51:01 2011
From: "Arne Dieckmann adieckma[-]googlemail.com" <owner-chemistry(0)server.ccl.net>
To: CCL
Subject: CCL:G: DFT and dispersion
Message-Id: <-45757-111028035243-15977-duMIk8V+4xYqEwBYy4cXyA(0)server.ccl.net>
X-Original-From: Arne Dieckmann <adieckma..googlemail.com>
Content-Transfer-Encoding: 8bit
Content-Type: text/plain; charset=iso-8859-1
Date: Fri, 28 Oct 2011 00:52:34 -0700
Mime-Version: 1.0 (Apple Message framework v1251.1)


Sent to CCL by: Arne Dieckmann [adieckma###googlemail.com]
Dear Lars, 

my systems resemble the active sites of enzymes, so dispersion effects will play a major role if a certain number of catalytic side chains are present. What other dispersion corrected functional would you recommend (apart from TPSS)? I guess you are more experienced with this than I am. 

Thanks, 
Arne

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 
Dr. Arne Dieckmann
Houk Research Lab
University of California, Los Angeles 
email: adieckma- -googlemail.com


On Oct 27, 2011, at 11:26 PM, Dr. Lars Goerigk lars.goerigk:+:chem.usyd.edu.au wrote:

> 
> Sent to CCL by: "Dr. Lars Goerigk" [lars.goerigk a chem.usyd.edu.au]
> Dear Arne,
> 
> I guess it depends entirely on your system to decide whether a D correction with M06-2X has an impact on the geometries or not. As I do not know the system, I cannot say how much of the intramolecular dispersion effects are covered by M06-2X. I also do not have much experience with M06-2X-D3 geometry optimizations. However, I assume that a system of more than 50 atoms should show significant intramolecular dispersion effects, that of course also influence the relative energies between conformers.
> 
> Personally, I would always include a dispersion correction to be on the safe side. Maybe you could run a test calculation on one of the systems with M06-2X and another dipsersion-corrected functional (TPSS should be in general faster, of course). Then you can maybe see the effect on your system and can make a final decision.
> 
> But maybe other users, who are reading this, have already done such a comparison and can give you also some recommendations.
> 
> Cheers,
> Lars
> 
> On 28/10/2011 4:15 PM, Arne Dieckmann adieckma(-)googlemail.com wrote:
>> Sent to CCL by: Arne Dieckmann [adieckma(-)googlemail.com]
>> Dear Lars,
>> 
>> thanks for your immediate reply. I know about the differences between the Minnesota functionals and the DFT-D3 method. This is why I wanted to augment their mid-range dispersion with the long range dispersion your former group developed. Do you know if TPSS with D-corrections produces significantly different geometries than M06-2X without D-corrections? How much do geometries of molecules (>= 50 atoms) change in general? I am just wondering if it will be sufficient to optimize with M06-2X and apply the single point D-corrections.
>> 
>> By the way, do you know how well DFT-D3 works with implicit solvation? I guess in this case the parameters would have to be solvent-dependent, right?
>> 
>> 
>> Thanks again,
>> Arne
>> 
>> - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
>> Dr. Arne Dieckmann
>> Houk Research Lab
>> University of California, Los Angeles
>> email: adieckma+*+googlemail.com
>> 
>> 
>> On Oct 27, 2011, at 5:28 PM, Dr. Lars Goerigk lars.goerigk{}chem.usyd.edu.au wrote:
>> 
>>> Sent to CCL by: "Dr. Lars Goerigk" [lars.goerigk(~)chem.usyd.edu.au]
>>> Dear Arne,
>>> 
>>> M06-2X was fitted to noncovalently bound systems in their equilibrium geometries and due to that fit it somehow incorporates medium-range dispersion interactions. However, as also discussed in the literature, it is expected that the asymptotic long-range behavior is still not correct and that it can also benefit from dispersion corrections.
>>> On the issue DFT-D3 in combination with the Minnesota functionals you can refer to PCCP 2011, 13, 6670. There, the parameters for DFT-D3 for those functionals were published and discussed.
>>> 
>>> DFT-D2 parameters for the Minnesota functionals were published by the Martin group in JPCA 2008, 112, 12868. The s6 had to be smaller than unity, though, which still does not give the correct asymptotics, opposed to DFT-D3, where it was fixed to unity.
>>> 
>>> If you have the Gaussian code available you could try to implement DFT-D3 (based on the code Stefan Grimme made available on his website).
>>> If you do not have the code, you would have to use DFT-D2. Please note that in G09 Rev A, DFT-D2 only works with B97-D and omega-B97X-D.
>>> That bug was fixed however and in Rev. B01 and higher you can now also use DFT-D2 for those functionals, which are mentioned in Grimme's DFT-D2 paper from 2006 (i.e. also for B3LYP, TPSS, PBE, BP86).
>>> You have to use the IOp(3/124=3) then. In combination with IOp33(3=3) you also get a printout to check, if the correct s6 value was applied.
>>> Other functionals are not supported and I do not know if it is possible to read in an s6 specified by the user (maybe you should contact the Gaussian support to find that out). IOp(3/124=1)  adds the dispersion correction to any functional, but only with an s6=1, which is too large for the Minnesota functionals.
>>> 
>>> If you can't use M06-2X, you could try TPSS in combination with D-corrections. Based on publications and my own experience, this gives very good structures.
>>> 
>>> Another possibility would be to get ORCA, which is for free. I am not 100% sure if DFT-D3 is already implemented; have a look at the ORCA website for that.
>>> You could also check if other programs have already implemented DFT-D3.
>>> 
>>> I hope these information could help you.
>>> 
>>> With best wishes,
>>> Lars
>>> 
>>> -- 
>>> Dr. Lars Goerigk
>>> School of Chemistry
>>> The University of Sydney
>>> Sydney, New South Wales 2006
>>> Australiahttp://www.ccl.net/chemistry/sub_unsub.shtml>
>> 
> 
> 
> -- 
> Dr. Lars Goerigk
> School of Chemistry
> The University of Sydney
> Sydney, New South Wales 2006
> Australiahttp://www.ccl.net/chemistry/sub_unsub.shtml> 
>


From owner-chemistry@ccl.net Fri Oct 28 05:26:00 2011
From: "Karol M. Langner karol.langner.^.gmail.com" <owner-chemistry^server.ccl.net>
To: CCL
Subject: CCL:G: Macro or something for Gaussian 03
Message-Id: <-45758-111028041958-15509-5yEiJFSpWRD6xA5X8eka8w^server.ccl.net>
X-Original-From: "Karol M. Langner" <karol.langner_._gmail.com>
Date: Fri, 28 Oct 2011 04:19:55 -0400


Sent to CCL by: "Karol M. Langner" [karol.langner*gmail.com]
Hi guys. As Geoff already wrote, cclib (cclib.sf.net) was created to do exactly this, in Python. It parses Gaussian logs, as well as logs from other programs, and serves the data as attributes of a Python object. Many of these attributes are multidimensional (MO coefficients, etc.), so NumPy is used heavily.

Anyway, you might find that cclib already parses the things you want. If not, we'd be happy to integrate any scripts that people have for Gaussian or other programs. Just visit the mailing list.

Best,
Karol

> "Edward Holland hollandej-x-Cardiff.ac.uk"  wrote:
> 
> Sent to CCL by: Edward Holland [hollandej]_[Cardiff.ac.uk]
> 
> Would it be possible to publish this on-line somewhere? I'm currently in =
> the progress	 of writing similar python scripts and it seems foolish =
> to duplicate efforts!
> 
> Yours
> 
> Ed Holland
> 
> On 24 Oct 2011, at 16:14, Jo=E3o Henriques jmhenriques!A!fc.ul.pt wrote:
> > I wouldn't mind sending you a Python program I wrote to extract a
> > comprehensive amount of data from gaussian03/09 logs. It has no
> > integration with Excel though. I store all my data in txt files.
> > Whenever I want to plot data, I just run gnuplot on them...
>
> > Best regards,
>
> > On Wed, Oct 19, 2011 at 7:56 PM, Serdar Badoglu sbadoglu##gazi.edu.tr
> >> Do any of you have / know an excel macro / a little program to =
> extract
> >> calculated frequencies, infrared intensities, and Raman activities =
> > from
> >> Gaussian log file? I don't need the complete spectrum generated, I =
> only need
> >> the mentioned data of vibrational modes. I'm really tired of =
> switching between
> >> windows and reading and typing the data into spreadsheets.


From owner-chemistry@ccl.net Fri Oct 28 08:12:00 2011
From: "Andras Borosy andras.borosy[]givaudan.com" <owner-chemistry*_*server.ccl.net>
To: CCL
Subject: CCL:G: DFT and dispersion
Message-Id: <-45759-111028024444-25779-cvuh8jkdr8gukmXmXD4pJg*_*server.ccl.net>
X-Original-From: Andras Borosy <andras.borosy++givaudan.com>
Content-Transfer-Encoding: 8bit
Content-type: text/plain; charset=UTF-8
Date: Fri, 28 Oct 2011 08:44:35 +0200
MIME-Version: 1.0


Sent to CCL by: Andras Borosy [andras.borosy%a%givaudan.com]



You may find answers to your questions in

Comprehensive Benchmarking of a Density-Dependent Dispersion Correction
http://pubs.acs.org/doi/abs/10.1021/ct200602x

Best wishes,

Dr. András Péter Borosy
Scientific Modelling Expert

Fragrance Research
Givaudan Schweiz AG  -  Ueberlandstrasse 138  -  CH-8600  -  Dübendorf  -
Switzerland
T:+41-44-824 2164  -  F:+41-44-8242926    -  http://www.givaudan.com




> From:	"Arne Dieckmann adieckma(-)googlemail.com"
            <owner-chemistry%ccl.net>
To:	"Borosy, Andras " <andras.borosy%givaudan.com>
Date:	28.10.2011 07:46
Subject:	CCL:G: DFT and dispersion
Sent by:	owner-chemistry+andras.borosy==givaudan.com%ccl.net




Sent to CCL by: Arne Dieckmann [adieckma(-)googlemail.com]
Dear Lars,

thanks for your immediate reply. I know about the differences between the
Minnesota functionals and the DFT-D3 method. This is why I wanted to
augment their mid-range dispersion with the long range dispersion your
former group developed. Do you know if TPSS with D-corrections produces
significantly different geometries than M06-2X without D-corrections? How
much do geometries of molecules (>= 50 atoms) change in general? I am just
wondering if it will be sufficient to optimize with M06-2X and apply the
single point D-corrections.

By the way, do you know how well DFT-D3 works with implicit solvation? I
guess in this case the parameters would have to be solvent-dependent,
right?


Thanks again,
Arne

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Dr. Arne Dieckmann
Houk Research Lab
University of California, Los Angeles
email: adieckma+*+googlemail.com


On Oct 27, 2011, at 5:28 PM, Dr. Lars Goerigk lars.goerigk
{}chem.usyd.edu.au wrote:

>
> Sent to CCL by: "Dr. Lars Goerigk" [lars.goerigk(~)chem.usyd.edu.au]
> Dear Arne,
>
> M06-2X was fitted to noncovalently bound systems in their equilibrium
geometries and due to that fit it somehow incorporates medium-range
dispersion interactions. However, as also discussed in the literature, it
is expected that the asymptotic long-range behavior is still not correct
and that it can also benefit from dispersion corrections.
> On the issue DFT-D3 in combination with the Minnesota functionals you can
refer to PCCP 2011, 13, 6670. There, the parameters for DFT-D3 for those
functionals were published and discussed.
>
> DFT-D2 parameters for the Minnesota functionals were published by the
Martin group in JPCA 2008, 112, 12868. The s6 had to be smaller than unity,
though, which still does not give the correct asymptotics, opposed to
DFT-D3, where it was fixed to unity.
>
> If you have the Gaussian code available you could try to implement DFT-D3
(based on the code Stefan Grimme made available on his website).
> If you do not have the code, you would have to use DFT-D2. Please note
that in G09 Rev A, DFT-D2 only works with B97-D and omega-B97X-D.
> That bug was fixed however and in Rev. B01 and higher you can now also
use DFT-D2 for those functionals, which are mentioned in Grimme's DFT-D2
paper from 2006 (i.e. also for B3LYP, TPSS, PBE, BP86).
> You have to use the IOp(3/124=3) then. In combination with IOp33(3=3) you
also get a printout to check, if the correct s6 value was applied.
> Other functionals are not supported and I do not know if it is possible
to read in an s6 specified by the user (maybe you should contact the
Gaussian support to find that out). IOp(3/124=1)  adds the dispersion
correction to any functional, but only with an s6=1, which is too large for
the Minnesota functionals.
>
> If you can't use M06-2X, you could try TPSS in combination with
D-corrections. Based on publications and my own experience, this gives very
good structures.
>
> Another possibility would be to get ORCA, which is for free. I am not
100% sure if DFT-D3 is already implemented; have a look at the ORCA website
for that.
> You could also check if other programs have already implemented DFT-D3.
>
> I hope these information could help you.
>
> With best wishes,
> Lars
>
> --
> Dr. Lars Goerigk
> School of Chemistry
> The University of Sydney
> Sydney, New South Wales 2006
> Australiahttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt

From owner-chemistry@ccl.net Fri Oct 28 09:27:00 2011
From: "S P lcqsigi : hotmail.com" <owner-chemistry .. server.ccl.net>
To: CCL
Subject: CCL: CAS number to 3D XYZ
Message-Id: <-45760-111028092347-32704-WDDRBac+2owD1JKRRtyKCw .. server.ccl.net>
X-Original-From: "S  P" <lcqsigi|a|hotmail.com>
Date: Fri, 28 Oct 2011 09:23:44 -0400


Sent to CCL by: "S  P" [lcqsigi..hotmail.com]
Dear CCL,

Is there any unix/linux tool that can take a CAS number of a given molecular structure and convert it into a 3D-xyz coordinates representation?

Thanks,


From owner-chemistry@ccl.net Fri Oct 28 10:34:00 2011
From: "Wolf Ihlenfeldt wdi,xemistry.com" <owner-chemistry[A]server.ccl.net>
To: CCL
Subject: CCL: CAS number to 3D XYZ
Message-Id: <-45761-111028102713-9618-weeGOPwCfwQUt8xRq4/Ejg[A]server.ccl.net>
X-Original-From: Wolf Ihlenfeldt <wdi-*-xemistry.com>
Content-Type: multipart/alternative; boundary=00163683265cf374d604b05cae36
Date: Fri, 28 Oct 2011 16:27:05 +0200
MIME-Version: 1.0


Sent to CCL by: Wolf Ihlenfeldt [wdi|-|xemistry.com]
--00163683265cf374d604b05cae36
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You can do that (to the degree that the CAS number has escaped into the wil=
d
and is now for example captured in the NCI Resolver) with the Corina-enable=
d
version of CACTVS

Here is a minimal script:

-- snip ---
molfile write benzene.xyz [ens create 71-43-2]
--- snip ---

Note: the free academic version of the toolkit at
www.xemistry.com/academicdoes *not* contain the Corina module which
relies on IP of Molecular
Networks, you will need to get either their approval or a standard Corina
license to get access to this enhanced version.

With the standard toolkit version, you are still, for example, able to fetc=
h
3D structures from PubChem after mapping the CAS number to the PubChem CID.




On Fri, Oct 28, 2011 at 3:23 PM, S P lcqsigi : hotmail.com <
owner-chemistry]^[ccl.net> wrote:

>
> Sent to CCL by: "S  P" [lcqsigi..hotmail.com]
> Dear CCL,
>
> Is there any unix/linux tool that can take a CAS number of a given
> molecular structure and convert it into a 3D-xyz coordinates representati=
on?
>
> Thanks,
>
>
>
> -=3D This is automatically added to each message by the mailing script =
=3D->
>
>


--=20
Wolf-D. Ihlenfeldt -  Xemistry GmbH - wdi]^[xemistry.com
Phone: +49 6174 201455 - Fax +49 6174 209665
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Address: Hainholzweg 11, D-61462 K=C3=B6nigstein, Germany
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<br>You can do that (to the degree that the CAS number has escaped into the=
 wild and is now for example captured in the NCI Resolver) with the Corina-=
enabled version of CACTVS <br><br>Here is a minimal script:<br><br>-- snip =
---<br>
molfile write benzene.xyz [ens create 71-43-2]<br>--- snip ---<br><br>Note:=
 the free academic version of the toolkit at <a href=3D"http://www.xemistry=
.com/academic">www.xemistry.com/academic</a> does *not* contain the Corina =
module which relies on IP of Molecular Networks, you will need to get eithe=
r their approval or a standard Corina license to get access to this enhance=
d version.<br>
<br>With the standard toolkit version, you are still, for example, able to =
fetch 3D structures from PubChem after mapping the CAS number to the PubChe=
m CID.<br><br><br><br><br><div class=3D"gmail_quote">On Fri, Oct 28, 2011 a=
t 3:23 PM, S P lcqsigi : <a href=3D"http://hotmail.com">hotmail.com</a> <sp=
an dir=3D"ltr">&lt;<a href=3D"mailto:owner-chemistry]^[ccl.net">owner-chemist=
ry]^[ccl.net</a>&gt;</span> wrote:<br>
<blockquote class=3D"gmail_quote" style=3D"margin: 0pt 0pt 0pt 0.8ex; borde=
r-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;"><br>
Sent to CCL by: &quot;S =C2=A0P&quot; [lcqsigi..<a href=3D"http://hotmail.c=
om" target=3D"_blank">hotmail.com</a>]<br>
Dear CCL,<br>
<br>
Is there any unix/linux tool that can take a CAS number of a given molecula=
r structure and convert it into a 3D-xyz coordinates representation?<br>
<br>
Thanks,<br>
<br>
<br>
<br>
-=3D This is automatically added to each message by the mailing script =3D-=
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E-mail to subscribers: <a href=3D"mailto:CHEMISTRY]^[ccl.net">CHEMISTRY]^[ccl.n=
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</blockquote></div><br><br clear=3D"all"><br>-- <br>Wolf-D. Ihlenfeldt -=C2=
=A0 Xemistry GmbH - <a href=3D"mailto:wdi]^[xemistry.com" target=3D"_blank">w=
di]^[xemistry.com</a><br>Phone: +49 6174 201455 - Fax +49 6174 209665<br>---<=
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Address: Hainholzweg 11, D-61462 K=C3=B6nigstein, Germany<br>HR K=C3=B6nigs=
tein B7522 : Ust/VAT ID DE215316329 : DUNS 34-400-1719<br><br>

--00163683265cf374d604b05cae36--


From owner-chemistry@ccl.net Fri Oct 28 11:08:00 2011
From: "sitzmann _ helix.nih.gov" <owner-chemistry]=[server.ccl.net>
To: CCL
Subject: CCL: CAS number to 3D XYZ
Message-Id: <-45762-111028105200-14215-hG58VXazQpuDwbExVCaUvw]=[server.ccl.net>
X-Original-From: <sitzmann]![helix.nih.gov>
Content-Transfer-Encoding: 8bit
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Date: Fri, 28 Oct 2011 10:51:51 -0400
MIME-Version: 1.0


Sent to CCL by: [sitzmann(a)helix.nih.gov]
This is not a program, but a web service (Chemical Identifier Resolver):

http://cactus.nci.nih.gov/chemical/structure/50-00-0/file?format=xyz

You can find more information at the Resolver's start page:

http://cactus.nci.nih.gov/chemical/structure

Markus


>
> Sent to CCL by: "S  P" [lcqsigi..hotmail.com]
> Dear CCL,
>
> Is there any unix/linux tool that can take a CAS number of a given
> molecular structure and convert it into a 3D-xyz coordinates
> representation?
>
> Thanks,>
>


From owner-chemistry@ccl.net Fri Oct 28 11:43:01 2011
From: "Stefan Grimme grimme]![thch.uni-bonn.de" <owner-chemistry * server.ccl.net>
To: CCL
Subject: CCL: DFT and dispersion
Message-Id: <-45763-111028071708-22520-oRX/Z90C31m27zPSkQ0Tgw * server.ccl.net>
X-Original-From: "Stefan  Grimme" <grimme%thch.uni-bonn.de>
Date: Fri, 28 Oct 2011 07:16:37 -0400


Sent to CCL by: "Stefan  Grimme" [grimme _ thch.uni-bonn.de]
>By the way, do you know how well DFT-D3 works with implicit solvation? I guess in this case the >parameters would have to be solvent    -dependent, right?
 
One important comment on this point: DFT-D3 (and similarly other dispersion corrections) are constructed to yield accurate isolated molecule (gas phase) energies and geometries. These can be combined with any kind of solvation model and when this model accurately accounts for solvent-solute dispersion,
everything is consistent. What could be done in principle as suggested (to modify the intramolecular dispersion to implicitly account for solvent-solute dispersion) is theoretically not justified in my opinion.
DFT-D3 has been developed to reproduce CCSD(T)/CBS as closely as possible and should not be used as an empirical tool to balance inter- and intra-molecular effects. 
A further note in this context: this balance of intramolecular and intermolecular dispersion is also the reason why in some cases dispersion-UNcorrected DFT seemingly provides better results compared to experimental solution data than physically correct methods. But when one wants to get the right result for the right reason I would prefer to first treat the gas phase system as accurately as possible and then to add the best available condensed phase corrections. And this holds for DFT as well as WFT methods.

Best wishes
Stefan Grimme
grimme-,-thch.uni-bonn.de


From owner-chemistry@ccl.net Fri Oct 28 12:51:01 2011
From: "Arne Dieckmann adieckma**googlemail.com" <owner-chemistry{}server.ccl.net>
To: CCL
Subject: CCL: DFT and dispersion
Message-Id: <-45764-111028124925-19206-id/b+IpiyAG83YmFaZ91/A{}server.ccl.net>
X-Original-From: Arne Dieckmann <adieckma ~~ googlemail.com>
Content-Transfer-Encoding: 8bit
Content-Type: text/plain; charset=us-ascii
Date: Fri, 28 Oct 2011 09:49:15 -0700
Mime-Version: 1.0 (Apple Message framework v1251.1)


Sent to CCL by: Arne Dieckmann [adieckma[A]googlemail.com]
First, I would like to thank all of you for your comments and help. I strongly believe in the principle of getting the right answers for the right reasons, which is why I want to make sure I am using methods in the context they were developed for. With regards to solution corrections: As the DFT-D3 model is only geometry-dependent, I guess the following procedure would be valid: 

1. Optimize the geometry in the gas phase 
2. Calculate energy in solution (e.g. using SMD) 
3. Add DFT-D3 dispersion correction 
4. Add thermal corrections 

Would you agree? 


Cheers, 
Arne


On Oct 28, 2011, at 4:16 AM, Stefan Grimme grimme]![thch.uni-bonn.de wrote:

> 
> Sent to CCL by: "Stefan  Grimme" [grimme _ thch.uni-bonn.de]
>> By the way, do you know how well DFT-D3 works with implicit solvation? I guess in this case the >parameters would have to be solvent    -dependent, right?
> 
> One important comment on this point: DFT-D3 (and similarly other dispersion corrections) are constructed to yield accurate isolated molecule (gas phase) energies and geometries. These can be combined with any kind of solvation model and when this model accurately accounts for solvent-solute dispersion,
> everything is consistent. What could be done in principle as suggested (to modify the intramolecular dispersion to implicitly account for solvent-solute dispersion) is theoretically not justified in my opinion.
> DFT-D3 has been developed to reproduce CCSD(T)/CBS as closely as possible and should not be used as an empirical tool to balance inter- and intra-molecular effects. 
> A further note in this context: this balance of intramolecular and intermolecular dispersion is also the reason why in some cases dispersion-UNcorrected DFT seemingly provides better results compared to experimental solution data than physically correct methods. But when one wants to get the right result for the right reason I would prefer to first treat the gas phase system as accurately as possible and then to add the best available condensed phase corrections. And this holds for DFT as well as WFT methods.
> 
> Best wishes
> Stefan Grimme
> grimme],[thch.uni-bonn.de> 
>


From owner-chemistry@ccl.net Fri Oct 28 13:25:00 2011
From: "karthikeyan m.karthikeyan%a%ncl.res.in" <owner-chemistry ~ server.ccl.net>
To: CCL
Subject: CCL: CAS number to 3D XYZ
Message-Id: <-45765-111028103012-15801-Ci8DjKVIDYduKQerNn+ZkA ~ server.ccl.net>
X-Original-From: karthikeyan <m.karthikeyan],[ncl.res.in>
Content-Transfer-Encoding: 8bit
Content-Type: text/plain; charset="ISO-8859-1"; format=flowed
Date: Fri, 28 Oct 2011 19:57:30 +0530
MIME-Version: 1.0


Sent to CCL by: karthikeyan [m.karthikeyan#ncl.res.in]
I am really feeling sorry for this question. Unfortunately the answer is NO.
Only way to get CAS number into 3D structure is to search  through
SCIFINDER (Windows/Linux/Web) subscription

Look up for CASRN to Structure (some of the cas numbers are assigned for
mixtures , compositions etc.,)
a) Get the image or 2d structure
b) use tools of scifinder or Chemaxon MarvinView to create 3D (optimized
/ rapid) structure.

CAS RN to Structure tools not yet available for free.

e.g., for example CASRN for dyes
548-62-9    C.I. Basic Violet 3 with  0.1% of Michler's ketone
91315-45-6    C.I. Pigment White 25
91432-92-7    C.I. Solvent Red 96
915026-98-1    C.I. Reactive Red 264
916900-16-8    C.I. Disperse Blue 183:1
99549-42-5    C.I. Fluorescent Brightener 263

CASRN for mixtures..
Tail gas (petroleum), gas recovery plant deethanizer    68308-05-4
Fuel gases, refinery    68308-27-0
Alkanes, C1-2    68475-57-0
Alkanes, C2-3    68475-58-1
Alkanes, C3-4    68475-59-2
Alkanes, C4-5    68475-60-5

Wish you goodluck
M.Karthikeyan
http://moltable.ncl.res.in


On 10/28/2011 6:53 PM, S P lcqsigi : hotmail.com wrote:
> Sent to CCL by: "S  P" [lcqsigi..hotmail.com]
> Dear CCL,
>
> Is there any unix/linux tool that can take a CAS number of a given molecular structure and convert it into a 3D-xyz coordinates representation?
>
> Thanks,>
>
> .
>


Disclaimer:

This message and the information contained herein is proprietary and confidential and subject to the policy statement of the National Chemical Laboratory, Pune, India. You may review the policy at http://www.ncl-india.org/common/webmailDisclaimer.htm


From owner-chemistry@ccl.net Fri Oct 28 14:00:01 2011
From: "karthikeyan m.karthikeyan#ncl.res.in" <owner-chemistry,,server.ccl.net>
To: CCL
Subject: CCL: CAS number to 3D XYZ
Message-Id: <-45766-111028113947-25021-1rivS2WCoojV8OKI6LgONA,,server.ccl.net>
X-Original-From: karthikeyan <m.karthikeyan],[ncl.res.in>
Content-Transfer-Encoding: 8bit
Content-Type: text/plain; charset="ISO-8859-1"; format=flowed
Date: Fri, 28 Oct 2011 21:07:05 +0530
MIME-Version: 1.0


Sent to CCL by: karthikeyan [m.karthikeyan*o*ncl.res.in]
Unfortunately the direct answer to your question is NO.
There is no software available other than Scifinder to fetch 2D/3D of
molecules from their databases.

Only way to get CAS number into 3D structure is to search  through
SCIFINDER (Windows/Linux/Web) subscription

Look up for CASRN to Structure (some of the cas numbers are assigned for
mixtures , compositions etc.,)
a) Get the image or 2d structure
b) use tools of scifinder or Chemaxon MarvinView to create 3D (optimized
/ rapid) structure.

CAS RN to Structure tools not yet available for free.

e.g., for example CASRN for dyes
548-62-9    C.I. Basic Violet 3 with  0.1% of Michler's ketone
91315-45-6    C.I. Pigment White 25
91432-92-7    C.I. Solvent Red 96
915026-98-1    C.I. Reactive Red 264
916900-16-8    C.I. Disperse Blue 183:1
99549-42-5    C.I. Fluorescent Brightener 263

CASRN for mixtures..
Tail gas (petroleum), gas recovery plant deethanizer    68308-05-4
Fuel gases, refinery    68308-27-0
Alkanes, C1-2    68475-57-0
Alkanes, C2-3    68475-58-1
Alkanes, C3-4    68475-59-2
Alkanes, C4-5    68475-60-5

Wish you goodluck
M.Karthikeyan
moltable (dot) ncl (dot) res (dot) in

Disclaimer:

This message and the information contained herein is proprietary and confidential and subject to the policy statement of the National Chemical Laboratory, Pune, India. You may review the policy at http://www.ncl-india.org/common/webmailDisclaimer.htm


From owner-chemistry@ccl.net Fri Oct 28 14:35:00 2011
From: "Dr M Karthikeyan karthincl-.-gmail.com" <owner-chemistry ~ server.ccl.net>
To: CCL
Subject: CCL: CAS number to 3D XYZ
Message-Id: <-45767-111028113808-20527-lNRRgAoSyrTgHw28gOE41w ~ server.ccl.net>
X-Original-From: Dr M Karthikeyan <karthincl===gmail.com>
Content-Transfer-Encoding: 7bit
Content-Type: text/plain; charset=ISO-8859-1; format=flowed
Date: Fri, 28 Oct 2011 21:05:28 +0530
MIME-Version: 1.0


Sent to CCL by: Dr M Karthikeyan [karthincl()gmail.com]
Unfortunately the direct answer to your question is NO.
There is no software available other than Scifinder to fetch 2D/3D of 
molecules from their databases.

Only way to get CAS number into 3D structure is to search  through
SCIFINDER (Windows/Linux/Web) subscription

Look up for CASRN to Structure (some of the cas numbers are assigned for 
mixtures , compositions etc.,)
a) Get the image or 2d structure
b) use tools of scifinder or Chemaxon MarvinView to create 3D (optimized 
/ rapid) structure.

CAS RN to Structure tools not yet available for free.

e.g., for example CASRN for dyes
548-62-9    C.I. Basic Violet 3 with  0.1% of Michler's ketone
91315-45-6    C.I. Pigment White 25
91432-92-7    C.I. Solvent Red 96
915026-98-1    C.I. Reactive Red 264
916900-16-8    C.I. Disperse Blue 183:1
99549-42-5    C.I. Fluorescent Brightener 263

CASRN for mixtures..
Tail gas (petroleum), gas recovery plant deethanizer    68308-05-4
Fuel gases, refinery    68308-27-0
Alkanes, C1-2    68475-57-0
Alkanes, C2-3    68475-58-1
Alkanes, C3-4    68475-59-2
Alkanes, C4-5    68475-60-5

Wish you goodluck
M.Karthikeyan
moltable (dot) ncl (dot) res (dot) in

On 10/28/2011 6:53 PM, S P lcqsigi : hotmail.com wrote:
> Sent to CCL by: "S  P" [lcqsigi..hotmail.com]
> Dear CCL,
>
> Is there any unix/linux tool that can take a CAS number of a given molecular structure and convert it into a 3D-xyz coordinates representation?
>
> Thanks,>
>
> .
>


From owner-chemistry@ccl.net Fri Oct 28 15:10:00 2011
From: "Chris Swain swain^mac.com" <owner-chemistry!=!server.ccl.net>
To: CCL
Subject: CCL: CAS number to 3D XYZ
Message-Id: <-45768-111028110608-6192-Ymz8G3Q15w1PQGkqpXPbtA!=!server.ccl.net>
X-Original-From: Chris Swain <swain],[mac.com>
Content-type: multipart/alternative;
 boundary="Boundary_(ID_ecV6gI8xbh+4blxuOCY+3Q)"
Date: Fri, 28 Oct 2011 16:05:48 +0100
MIME-version: 1.0


Sent to CCL by: Chris Swain [swain(!)mac.com]

--Boundary_(ID_ecV6gI8xbh+4blxuOCY+3Q)
Content-type: text/plain; CHARSET=US-ASCII
Content-transfer-encoding: 7BIT

Hi,

http://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pccompound&term=64318-79-2

should return the PubChem CID

If you can get the PubChem CID then you can use a URL like this to download.

http://pubchem.ncbi.nlm.nih.gov/summary/summary.cgi?cid=5960&disopt=3DSaveSDF

Cheers

Chris


Dr Chris Swain BA MA (Cantab) PhD CChem FRSC
Macinchem
Insanely Great Science
swain ~~ mac.com
http://www.macinchem.org


On 28 Oct 2011, at 14:23, S P lcqsigi : hotmail.com wrote:

> 
> Sent to CCL by: "S  P" [lcqsigi..hotmail.com]
> Dear CCL,
> 
> Is there any unix/linux tool that can take a CAS number of a given molecular structure and convert it into a 3D-xyz coordinates representation?
> 
> Thanks,> 
> 


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Content-type: text/html; CHARSET=US-ASCII
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<html><head></head><body style=3D"word-wrap: break-word; =
-webkit-nbsp-mode: space; -webkit-line-break: after-white-space; =
">Hi,<div><br></div><div><div style=3D"margin-top: 0px; margin-right: =
0px; margin-bottom: 0px; margin-left: 115.2px; text-indent: -115.2px; =
font: normal normal normal 12px/normal Courier; color: rgb(145, 25, =
147); "><a =
href=3D"http://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=3Dpcc=
ompound&amp;term=3D64318-79-2">http://eutils.ncbi.nlm.nih.gov/entrez/eutil=
s/esearch.fcgi?db=3Dpccompound&amp;term=3D64318-79-2</a></div><div =
style=3D"margin-top: 0px; margin-right: 0px; margin-bottom: 0px; =
margin-left: 115.2px; text-indent: -115.2px; font: normal normal normal =
12px/normal Courier; color: rgb(145, 25, 147); "><br></div><div =
style=3D"margin-top: 0px; margin-right: 0px; margin-bottom: 0px; =
margin-left: 115.2px; text-indent: -115.2px; font: normal normal normal =
12px/normal Courier; color: rgb(145, 25, 147); ">should return the =
PubChem CID</div><div><br></div><div>If you can get the PubChem CID then =
you can use a URL like this to download.</div><div><br></div><div><a =
href=3D"http://pubchem.ncbi.nlm.nih.gov/summary/summary.cgi?cid=3D5960&amp=
;disopt=3D3DSaveSDF">http://pubchem.ncbi.nlm.nih.gov/summary/summary.cgi?c=
id=3D5960&amp;disopt=3D3DSaveSDF</a></div><div><br></div><div>Cheers</div>=
<div><br></div><div>Chris</div><div><br></div><div><br><div>
<div style=3D"font-size: 12px; ">Dr Chris Swain BA MA (Cantab) PhD CChem =
FRSC</div><div style=3D"font-size: 12px; ">Macinchem</div><div =
style=3D"font-size: 12px; ">Insanely Great Science</div><div =
style=3D"font-size: 12px; "><a =
href=3D"mailto:swain ~~ mac.com">swain ~~ mac.com</a></div><div =
style=3D"font-size: 12px; "><a =
href=3D"http://www.macinchem.org">http://www.macinchem.org</a></div><span =
class=3D"Apple-style-span" style=3D"font-size: 12px; "><br =
class=3D"Apple-interchange-newline"></span>
</div>
<br><div><div>On 28 Oct 2011, at 14:23, S P lcqsigi : <a =
href=3D"http://hotmail.com">hotmail.com</a> wrote:</div><br =
class=3D"Apple-interchange-newline"><blockquote =
type=3D"cite"><div><br>Sent to CCL by: "S &nbsp;P" =
[lcqsigi..hotmail.com]<br>Dear CCL,<br><br>Is there any unix/linux tool =
that can take a CAS number of a given molecular structure and convert it =
into a 3D-xyz coordinates =
representation?<br><br>Thanks,<br><br><br><br>-=3D This is automatically =
added to each message by the mailing script =3D-<br>To recover the email =
address of the author of the message, please change<br>the strange =
characters on the top line to the  ~~  sign. You can also<br>look up the =
X-Original-From: line in the mail header.<br><br>E-mail to subscribers: =
<a href=3D"mailto:CHEMISTRY ~~ ccl.net">CHEMISTRY ~~ ccl.net</a> or use:<br> =
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;<a =
href=3D"http://www.ccl.net/cgi-bin/ccl/send_ccl_message">http://www.ccl.ne=
t/cgi-bin/ccl/send_ccl_message</a><br><br>E-mail to administrators: <a =
href=3D"mailto:CHEMISTRY-REQUEST ~~ ccl.net">CHEMISTRY-REQUEST ~~ ccl.net</a> =
or use<br> &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;<a =
href=3D"http://www.ccl.net/cgi-bin/ccl/send_ccl_message">http://www.ccl.ne=
t/cgi-bin/ccl/send_ccl_message</a><br><br<br> =
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;<a =
href=3D"http://www.ccl.net/chemistry/sub_unsub.shtml">http://www.ccl.net/c=
hemistry/sub_unsub.shtml</a><br><br>Before posting, check wait time at: =
<a href=3D"http://www.ccl.net">http://www.ccl.net</a><br><br>Job: <a =
href=3D"http://www.ccl.net/jobs">http://www.ccl.net/jobs</a> =
<br>Conferences: <a =
href=3D"http://server.ccl.net/chemistry/announcements/conferences/">http:/=
/server.ccl.net/chemistry/announcements/conferences/</a><br><br>Search =
Messages: <a =
href=3D"http://www.ccl.net/chemistry/searchccl/index.shtml">http://www.ccl=
.net/chemistry/searchccl/index.shtml</a><br><br>If your mail bounces =
> from CCL with 5.7.1 error, check:<br> &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;<a =
href=3D"http://www.ccl.net/spammers.txt">http://www.ccl.net/spammers.txt</=
a><br><br>RTFI: <a =
href=3D"http://www.ccl.net/chemistry/aboutccl/instructions/">http://www.cc=
l.net/chemistry/aboutccl/instructions/</a><br><br><br></div></blockquote><=
/div><br></div></div></body></html>=

--Boundary_(ID_ecV6gI8xbh+4blxuOCY+3Q)--


From owner-chemistry@ccl.net Fri Oct 28 15:45:01 2011
From: "Berger Raphael berger-,-chem.helsinki.fi" <owner-chemistry###server.ccl.net>
To: CCL
Subject: CCL: CAS number to 3D XYZ
Message-Id: <-45769-111028132855-20595-LKS4kLc43BJ4hAWsHrF4Qg###server.ccl.net>
X-Original-From: Berger Raphael <berger^^chem.helsinki.fi>
Content-Type: TEXT/PLAIN; charset=US-ASCII; format=flowed
Date: Fri, 28 Oct 2011 20:28:46 +0300 (EEST)
MIME-Version: 1.0


Sent to CCL by: Berger Raphael [berger^chem.helsinki.fi]
But be aware, the CAS number refers to a chemically pure substance, rather 
than "a molecule". For instance racemic limonene has got a CAS number, and 
D-limonene has another one and an arbitrary mixture od D- and L-limonene 
again a completely different CAS number.


On Fri, 28 Oct 2011, sitzmann _ helix.nih.gov wrote:

>
> Sent to CCL by: [sitzmann(a)helix.nih.gov]
> This is not a program, but a web service (Chemical Identifier Resolver):
>
> http://cactus.nci.nih.gov/chemical/structure/50-00-0/file?format=xyz
>
> You can find more information at the Resolver's start page:
>
> http://cactus.nci.nih.gov/chemical/structure
>
> Markus
>
>
>>
>> Sent to CCL by: "S  P" [lcqsigi..hotmail.com]
>> Dear CCL,
>>
>> Is there any unix/linux tool that can take a CAS number of a given
>> molecular structure and convert it into a 3D-xyz coordinates
>> representation?
>>
>> Thanks,>
>
>


From owner-chemistry@ccl.net Fri Oct 28 16:20:00 2011
From: "Venable, Richard (NIH/NHLBI) E venabler()nhlbi.nih.gov" <owner-chemistry() server.ccl.net>
To: CCL
Subject: CCL: best Linux for clusters
Message-Id: <-45770-111028150311-1587-+RisPBQKKCFoEoonnB5ekA() server.ccl.net>
X-Original-From: "Venable, Richard (NIH/NHLBI) [E]" <venabler . nhlbi.nih.gov>
Content-Language: en-US
Content-Transfer-Encoding: 8bit
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Date: Fri, 28 Oct 2011 15:02:54 -0400
MIME-Version: 1.0


Sent to CCL by: "Venable, Richard (NIH/NHLBI) [E]" [venabler#%#nhlbi.nih.gov]

We have been re-evaluating the choice of CentOS for our cluster, and would like solicit comments on which freely available Linux flavor seems to be the best for scientific computing, in terms of performance, stability, ease of administration, and support for more commercial software (QM packages, Matlab, etc.) and hardware (Qlogic Infiniband boards and driver software).

Besides CentOS, we are looking at Scientific Linux and Debian, but comments on other distributions are welcome.  If you (or someone in your group) can provide some detailed remarks noting good or bad features of specific Linux distributions, please send them to me and I will summarize to the list.

Thank you.

--
Rick Venable     5635 FL/T906
Membrane Biophysics Section
NIH/NHLBI Lab. of Computational Biology
Bethesda, MD  20892-9314   U.S.A.
(301) 496-1905   venabler AT nhlbi*nih*gov


From owner-chemistry@ccl.net Fri Oct 28 17:27:00 2011
From: "David A Mannock dmannock-.-ualberta.ca" <owner-chemistry%server.ccl.net>
To: CCL
Subject: CCL: best Linux for clusters
Message-Id: <-45771-111028172441-11787-IH+vapOhCu6OTPSzpaz0Xg%server.ccl.net>
X-Original-From: David A Mannock <dmannock---ualberta.ca>
Content-Type: multipart/alternative; boundary=000e0cd574eeedea7604b062830b
Date: Fri, 28 Oct 2011 15:24:33 -0600
MIME-Version: 1.0


Sent to CCL by: David A Mannock [dmannock]-[ualberta.ca]
--000e0cd574eeedea7604b062830b
Content-Type: text/plain; charset=ISO-8859-1

I find that Ubuntu 10.04 is a good stable GUI OS which has no problem with
the QC packages that I am running on AMD opteron processors/Supemicro dual
1207 motherboard. Dave

On Fri, Oct 28, 2011 at 1:02 PM, Venable, Richard (NIH/NHLBI) E venabler()
nhlbi.nih.gov <owner-chemistry^-^ccl.net> wrote:

>
> Sent to CCL by: "Venable, Richard (NIH/NHLBI) [E]" [venabler#%#
> nhlbi.nih.gov]
>
> We have been re-evaluating the choice of CentOS for our cluster, and would
> like solicit comments on which freely available Linux flavor seems to be the
> best for scientific computing, in terms of performance, stability, ease of
> administration, and support for more commercial software (QM packages,
> Matlab, etc.) and hardware (Qlogic Infiniband boards and driver software).
>
> Besides CentOS, we are looking at Scientific Linux and Debian, but comments
> on other distributions are welcome.  If you (or someone in your group) can
> provide some detailed remarks noting good or bad features of specific Linux
> distributions, please send them to me and I will summarize to the list.
>
> Thank you.
>
> --
> Rick Venable     5635 FL/T906
> Membrane Biophysics Section
> NIH/NHLBI Lab. of Computational Biology
> Bethesda, MD  20892-9314   U.S.A.
> (301) 496-1905   venabler AT nhlbi*nih*gov>
>
>

--000e0cd574eeedea7604b062830b
Content-Type: text/html; charset=ISO-8859-1
Content-Transfer-Encoding: quoted-printable

I find that Ubuntu 10.04 is a good stable GUI OS which has no problem with =
the QC packages that I am running on AMD opteron processors/Supemicro dual =
1207 motherboard. Dave<br><br><div class=3D"gmail_quote">On Fri, Oct 28, 20=
11 at 1:02 PM, Venable, Richard (NIH/NHLBI) E venabler()<a href=3D"http://n=
hlbi.nih.gov">nhlbi.nih.gov</a> <span dir=3D"ltr">&lt;<a href=3D"mailto:own=
er-chemistry^-^ccl.net">owner-chemistry^-^ccl.net</a>&gt;</span> wrote:<br>
<blockquote class=3D"gmail_quote" style=3D"margin:0 0 0 .8ex;border-left:1p=
x #ccc solid;padding-left:1ex;"><br>
Sent to CCL by: &quot;Venable, Richard (NIH/NHLBI) [E]&quot; [venabler#%#<a=
 href=3D"http://nhlbi.nih.gov" target=3D"_blank">nhlbi.nih.gov</a>]<br>
<br>
We have been re-evaluating the choice of CentOS for our cluster, and would =
like solicit comments on which freely available Linux flavor seems to be th=
e best for scientific computing, in terms of performance, stability, ease o=
f administration, and support for more commercial software (QM packages, Ma=
tlab, etc.) and hardware (Qlogic Infiniband boards and driver software).<br=
>

<br>
Besides CentOS, we are looking at Scientific Linux and Debian, but comments=
 on other distributions are welcome. =A0If you (or someone in your group) c=
an provide some detailed remarks noting good or bad features of specific Li=
nux distributions, please send them to me and I will summarize to the list.=
<br>

<br>
Thank you.<br>
<br>
--<br>
Rick Venable =A0 =A0 5635 FL/T906<br>
Membrane Biophysics Section<br>
NIH/NHLBI Lab. of Computational Biology<br>
Bethesda, MD =A020892-9314 =A0 U.S.A.<br>
<a href=3D"tel:%28301%29%20496-1905" value=3D"+13014961905">(301) 496-1905<=
/a> =A0 venabler AT nhlbi*nih*gov<br>
<br>
<br>
<br>
-=3D This is automatically added to each message by the mailing script =3D-=
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<br>
<br>
</blockquote></div><br>

--000e0cd574eeedea7604b062830b--


From owner-chemistry@ccl.net Fri Oct 28 18:02:00 2011
From: "Sujit Kumar Mondal sujitharvard|*|gmail.com" <owner-chemistry{=}server.ccl.net>
To: CCL
Subject: CCL:G: IRC-TS-PES
Message-Id: <-45772-111028175123-3716-LJgLj/7dwXr1ZdmbYo8ROw{=}server.ccl.net>
X-Original-From: Sujit Kumar Mondal <sujitharvard^gmail.com>
Content-Type: multipart/alternative; boundary=bcaec520efa746517004b062e3ed
Date: Fri, 28 Oct 2011 16:51:13 -0500
MIME-Version: 1.0


Sent to CCL by: Sujit Kumar Mondal [sujitharvard-.-gmail.com]
--bcaec520efa746517004b062e3ed
Content-Type: text/plain; charset=ISO-8859-1

Dear Prof Dan
 Thank you for your kind reply and I will remember not to hit button twice
next time sending message to CCL. I am glad that you have explain me a
lot. I learned a lot from your email but i have already figured it out what
to do next, i performed the calculation and also finalize my TS.
1) Earlier, I was interested to extract every geometry of IRC path to
evaluate the ring delocalization of the ligand molecule. I found out that
whole IRC pathway the ligand(heterocylce moleule) will have different
delocalization and ring delocalization can be measured to predict the
critical bonding stage...bong formation at the product side.

2) Also I figured it out about looking at the TS and of course noeigen test
Gaussian will keep
searching/optimizing even if no imaginary frequency was found or the Hessian
has two or more imaginary negative eigenvalues. I learned my mistake and I
checked the negative hessian eigen values. Now i have confirmed my TS with
imaginary frequency. No problem at all. Thanks for your advice.

3) I hope i will be able to perform the scan and i look into the link.
Thanks once again.

Sujit





On Wed, Oct 26, 2011 at 5:28 AM, Dan Maftei dan.maftei---uaic.ro <
owner-chemistry,,ccl.net> wrote:

>
> Sent to CCL by: Dan Maftei [dan.maftei:uaic.ro]
> Dear Sujit,
>
> First, I'd recommend not to double-click the send button when writing to
> CCL. Your message will appear twice.
>
> 1) Second, why optimizing the IRC geometries? It's pointless, really.
> Starting from those 21 geometries found after a significant
> computational effort for locating the TS then for performing the IRC,
> you'll end up with 2 final geometries, one corresponding to the
> reactants and the other to the products. To verify that TS corresponds
> to THAT reaction pathway, a visual inspection of the IRC geometries is
> usually enough. Even in the TS, after a frequency run, you should be
> able to predict the reaction course by inspecting the displacement
> vector which is the Hessian eigenvector corresponding to the Hessian
> negative eigenvalue (imaginary frequency).
>
> To extract, however, the geometries for each IRC step, you may find
> useful the GAUSSTOOL package (a pack of C-shell scripts written by Cu G.
> Phung,
> http://www.ccl.net/cca/software/UNIX/gaussian-utilities/README.shtml) on
> Linux/UNIX or, if using Windows, GaussView.
>
> 2) Third (I mean second), if the job for finding the TS yielded ONE (and
> ONLY one) imaginary frequency, the final geometry calculated IS a
> transition state, at the level or theory you are doing the computations.
> I suggest to check you output file carefully, as the noeigentest
> parameter for the OPT keyword will make Gaussian to keep
> searching/optimizing even if no imaginary frequency (oe negative Hessian
> eigenvalue) was found or the Hessian has two or more imaginary negative
> eigenvalues. However, if you've been able to perform IRC calculations,
> the TS may be the one of interest...
> Also it is not uncommon after a geometry optimization to obtain a
> different geometry with respect to the initial one. Otherwise, why
> running geometry optimization?
> What did you mean by delocalization inside a ring? Your TS geometry does
> not display "aromatic" bonds inside the ring? This doesn't mean the
> chemistry of your geometry has changed! That's why I hate visualization
> software which displays multiple bonds. Any visualization program will
> display single, aromatic, double or triple bonds based on some values
> and tolerances hardcoded. If you give a ethane molecule as input, with
> about 2.0 angstroms between the carbon atoms, it will display as two CH3
> groups. It doesn't mean it's chemistry has changed. You've only
> elongated a bond. It will be displayed broken as the bond length is
> sufficiently larger than the one the program knows or has been told.
>
> Finally, I don't know if that's the case in your TS geometry, but if it
> is, you may use the above considerations.
>
> 3) If looking towards PES scans and use Gaussian for that, first
> identify your coordinates of interest (those beings scanned) and
> "freeze" them to some equidistant values while optimizing (relaxing) the
> rest of the structure. The Gaussian keyword(s) for that is
> opt(z-matrix,...) or opt(modredundant,...). Both are well documented in
> the user guide (online, http://www.gaussian.com/g_tech/g_ur/k_opt.htm).
>
> Regards,
> Dan
>
>
> On 10/25/2011 10:43 PM, Sujit Kumar Mondal sujitharvard|,|gmail.com wrote:
> > Hi
> > I am working on Intrinsic Reaction Co-ordinate for hetero cycle organic
> > molecules and transition metal system. I performed IRC calculation which
> > produced 21 step of a reaction profile path, I would like to optimized
> > all the 21 structures obtained in IRC path including the transition
> > state individually.
> > 1) Can any one tell me the keywords for optimizing all the structures
> > obtained in IRC? I do not know how to do that, please help me out.
> >
> > 2) secondly, I tried to optimize my transition state using keywords
> > opt=(Calcfc,TS,noeigentest,maxcycle=200) Scf=(conver=5,maxcycle=200)
> > but I found that my optimized transition state has changed all the
> > atomic property including delocalization inside the 5membered ring
> > compare to the transition state I build up (as input file). Can anyone
> > tell me what should be done here?
> > i need help......
> >
> > 3) I would like to perform a potential energy scan, could someone tell
> > me the keywords for a potential energy scan of a particular system?
> >
> > Looking forward for your reply
> > Sujit
> >
> >
>
>
> --
> Dan Maftei,
> Assistant Professor,
> Faculty of Chemistry/Department of Chemistry
> University Alexandru Ioan Cuza Iasi
> Bd. Carol 1, Nr. 11, 700506 Iasi, Romania
>
> Tel: +40 232 201307
> E-mail(s):
> dan.maftei]![chem.uaic.ro
> dan.maftei]![uaic.ro>
>
>

--bcaec520efa746517004b062e3ed
Content-Type: text/html; charset=ISO-8859-1
Content-Transfer-Encoding: quoted-printable

<div>Dear Prof Dan</div>
<div>=A0Thank you for your kind reply and I will remember not to hit button=
 twice next time sending message to CCL. I am glad that you have explain me=
 a lot.=A0I learned a lot from your email but=A0i have already figured it o=
ut what to do next, i performed the calculation and also finalize my TS.</d=
iv>

<div>1) Earlier, I was interested to extract every geometry of IRC path to =
evaluate the ring delocalization of the=A0ligand molecule.=A0I found out=A0=
that whole IRC pathway the ligand(heterocylce moleule) will have different =
delocalization and ring delocalization can be measured to predict the criti=
cal bonding=A0stage...bong formation at the product side. </div>

<div>=A0</div>
<div>2) Also I figured it out about looking at the TS and of course noeigen=
 test Gaussian=A0will keep<br>searching/optimizing even if no imaginary fre=
quency=A0was found or the Hessian has two or more imaginary negative eigenv=
alues.=A0I learned my mistake and=A0I checked the negative hessian eigen va=
lues. Now i have confirmed my TS with imaginary frequency. No problem at al=
l. Thanks for your advice.</div>

<div>=A0</div>
<div>3)=A0I hope i will be able to perform the scan and i look into the lin=
k. Thanks once again.</div>
<div>=A0</div>
<div>Sujit</div>
<div>=A0</div>
<div>=A0</div>
<div>=A0</div>
<div>=A0</div>
<div>=A0</div>
<div class=3D"gmail_quote">On Wed, Oct 26, 2011 at 5:28 AM, Dan Maftei <a h=
ref=3D"http://dan.maftei---uaic.ro">dan.maftei---uaic.ro</a> <span dir=3D"l=
tr">&lt;<a href=3D"mailto:owner-chemistry,,ccl.net">owner-chemistry,,ccl.net<=
/a>&gt;</span> wrote:<br>

<blockquote style=3D"BORDER-LEFT: #ccc 1px solid; MARGIN: 0px 0px 0px 0.8ex=
; PADDING-LEFT: 1ex" class=3D"gmail_quote"><br>Sent to CCL by: Dan Maftei [=
dan.maftei:<a href=3D"http://uaic.ro/" target=3D"_blank">uaic.ro</a>]<br>De=
ar Sujit,<br>
<br>First, I&#39;d recommend not to double-click the send button when writi=
ng to<br>CCL. Your message will appear twice.<br><br>1) Second, why optimiz=
ing the IRC geometries? It&#39;s pointless, really.<br>Starting from those =
21 geometries found after a significant<br>
computational effort for locating the TS then for performing the IRC,<br>yo=
u&#39;ll end up with 2 final geometries, one corresponding to the<br>reacta=
nts and the other to the products. To verify that TS corresponds<br>to THAT=
 reaction pathway, a visual inspection of the IRC geometries is<br>
usually enough. Even in the TS, after a frequency run, you should be<br>abl=
e to predict the reaction course by inspecting the displacement<br>vector w=
hich is the Hessian eigenvector corresponding to the Hessian<br>negative ei=
genvalue (imaginary frequency).<br>
<br>To extract, however, the geometries for each IRC step, you may find<br>=
useful the GAUSSTOOL package (a pack of C-shell scripts written by Cu G.<br=
>Phung,<br><a href=3D"http://www.ccl.net/cca/software/UNIX/gaussian-utiliti=
es/README.shtml" target=3D"_blank">http://www.ccl.net/cca/software/UNIX/gau=
ssian-utilities/README.shtml</a>) on<br>
Linux/UNIX or, if using Windows, GaussView.<br><br>2) Third (I mean second)=
, if the job for finding the TS yielded ONE (and<br>ONLY one) imaginary fre=
quency, the final geometry calculated IS a<br>transition state, at the leve=
l or theory you are doing the computations.<br>
I suggest to check you output file carefully, as the noeigentest<br>paramet=
er for the OPT keyword will make Gaussian to keep<br>searching/optimizing e=
ven if no imaginary frequency (oe negative Hessian<br>eigenvalue) was found=
 or the Hessian has two or more imaginary negative<br>
eigenvalues. However, if you&#39;ve been able to perform IRC calculations,<=
br>the TS may be the one of interest...<br>Also it is not uncommon after a =
geometry optimization to obtain a<br>different geometry with respect to the=
 initial one. Otherwise, why<br>
running geometry optimization?<br>What did you mean by delocalization insid=
e a ring? Your TS geometry does<br>not display &quot;aromatic&quot; bonds i=
nside the ring? This doesn&#39;t mean the<br>chemistry of your geometry has=
 changed! That&#39;s why I hate visualization<br>
software which displays multiple bonds. Any visualization program will<br>d=
isplay single, aromatic, double or triple bonds based on some values<br>and=
 tolerances hardcoded. If you give a ethane molecule as input, with<br>
about 2.0 angstroms between the carbon atoms, it will display as two CH3<br=
>groups. It doesn&#39;t mean it&#39;s chemistry has changed. You&#39;ve onl=
y<br>elongated a bond. It will be displayed broken as the bond length is<br=
>
sufficiently larger than the one the program knows or has been told.<br><br=
>Finally, I don&#39;t know if that&#39;s the case in your TS geometry, but =
if it<br>is, you may use the above considerations.<br><br>3) If looking tow=
ards PES scans and use Gaussian for that, first<br>
identify your coordinates of interest (those beings scanned) and<br>&quot;f=
reeze&quot; them to some equidistant values while optimizing (relaxing) the=
<br>rest of the structure. The Gaussian keyword(s) for that is<br>opt(z-mat=
rix,...) or opt(modredundant,...). Both are well documented in<br>
the user guide (online, <a href=3D"http://www.gaussian.com/g_tech/g_ur/k_op=
t.htm" target=3D"_blank">http://www.gaussian.com/g_tech/g_ur/k_opt.htm</a>)=
.<br><br>Regards,<br>Dan<br><br><br>On 10/25/2011 10:43 PM, Sujit Kumar Mon=
dal sujitharvard|,|<a href=3D"http://gmail.com/" target=3D"_blank">gmail.co=
m</a> wrote:<br>
&gt; Hi<br>&gt; I am working on Intrinsic Reaction Co-ordinate for hetero c=
ycle organic<br>&gt; molecules and transition metal system. I performed IRC=
 calculation which<br>&gt; produced 21 step of a reaction profile path, I w=
ould like to optimized<br>
&gt; all the 21 structures obtained in IRC path including the transition<br=
>&gt; state individually.<br>&gt; 1) Can any one tell me the keywords for o=
ptimizing all the structures<br>&gt; obtained in IRC? I do not know how to =
do that, please help me out.<br>
&gt;<br>&gt; 2) secondly, I tried to optimize my transition state using key=
words<br>&gt; opt=3D(Calcfc,TS,noeigentest,maxcycle=3D200) Scf=3D(conver=3D=
5,maxcycle=3D200)<br>&gt; but I found that my optimized transition state ha=
s changed all the<br>
&gt; atomic property including delocalization inside the 5membered ring<br>=
&gt; compare to the transition state I build up (as input file). Can anyone=
<br>&gt; tell me what should be done here?<br>&gt; i need help......<br>
&gt;<br>&gt; 3) I would like to perform a potential energy scan, could some=
one tell<br>&gt; me the keywords for a potential energy scan of a particula=
r system?<br>&gt;<br>&gt; Looking forward for your reply<br>&gt; Sujit<br>
&gt;<br>&gt;<br><br><br>--<br>Dan Maftei,<br>Assistant Professor,<br>Facult=
y of Chemistry/Department of Chemistry<br>University Alexandru Ioan Cuza Ia=
si<br>Bd. Carol 1, Nr. 11, 700506 Iasi, Romania<br><br>Tel: <a href=3D"tel:=
%2B40%20232%20201307" value=3D"+40232201307">+40 232 201307</a><br>
E-mail(s):<br>dan.maftei]![<a href=3D"http://chem.uaic.ro/" target=3D"_blan=
k">chem.uaic.ro</a><br>dan.maftei]![<a href=3D"http://uaic.ro/" target=3D"_=
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--bcaec520efa746517004b062e3ed--


From owner-chemistry@ccl.net Fri Oct 28 18:37:00 2011
From: "Adam Tenderholt atenderholt-,-gmail.com" <owner-chemistry^-^server.ccl.net>
To: CCL
Subject: CCL:G: best Linux for clusters
Message-Id: <-45773-111028180747-1412-zx+w+ZUe5URv62Rqd1oWAg^-^server.ccl.net>
X-Original-From: Adam Tenderholt <atenderholt-*-gmail.com>
Content-Transfer-Encoding: 8bit
Content-Type: text/plain; charset=ISO-8859-1
Date: Fri, 28 Oct 2011 15:07:36 -0700
MIME-Version: 1.0


Sent to CCL by: Adam Tenderholt [atenderholt^gmail.com]
Hi Richard,

I built and managed a Rocks cluster (based on CentOS) a couple of
years ago, and found it quite easy to work with. Once the head node
has been setup properly, compute nodes are added via network
boot/install. Propagating new users to the compute nodes involves
issuing a single command, software is shared over a NFS drive, and
multiple queuing packages are available. The only commercial packages
we used were Gaussian and ADF, and we had no special hardware.

 Adam


On Fri, Oct 28, 2011 at 12:02 PM, Venable, Richard (NIH/NHLBI) E
venabler()nhlbi.nih.gov <owner-chemistry*ccl.net> wrote:
>
> Sent to CCL by: "Venable, Richard (NIH/NHLBI) [E]" [venabler#%#nhlbi.nih.gov]
>
> We have been re-evaluating the choice of CentOS for our cluster, and would like solicit comments on which freely available Linux flavor seems to be the best for scientific computing, in terms of performance, stability, ease of administration, and support for more commercial software (QM packages, Matlab, etc.) and hardware (Qlogic Infiniband boards and driver software).
>
> Besides CentOS, we are looking at Scientific Linux and Debian, but comments on other distributions are welcome.  If you (or someone in your group) can provide some detailed remarks noting good or bad features of specific Linux distributions, please send them to me and I will summarize to the list.
>
> Thank you.
>
> --
> Rick Venable     5635 FL/T906
> Membrane Biophysics Section
> NIH/NHLBI Lab. of Computational Biology
> Bethesda, MD  20892-9314   U.S.A.
> (301) 496-1905   venabler AT nhlbi*nih*gov>      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 Fri Oct 28 19:13:00 2011
From: "Joseph Han jhh3851 . yahoo.com" <owner-chemistry/./server.ccl.net>
To: CCL
Subject: CCL: best Linux for clusters
Message-Id: <-45774-111028182203-15551-IzrrMKdTDfXTv5SN35uc8A/./server.ccl.net>
X-Original-From: Joseph Han <jhh3851^yahoo.com>
Content-Type: multipart/alternative; boundary="886285840-2024974128-1319840512=:76310"
Date: Fri, 28 Oct 2011 15:21:52 -0700 (PDT)
MIME-Version: 1.0


Sent to CCL by: Joseph Han [jhh3851 .. yahoo.com]
--886285840-2024974128-1319840512=:76310
Content-Type: text/plain; charset=iso-8859-1
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I have not been too=A0satisfied=A0with the release schedule of CentOS of la=
te. =A0Also, there seem to have been some release process issues that give =
me concern about using CentOS 6.x. =A0
We'll likely move over to Scientific Linux for the 6.x branch as it's close=
 enough to CentOS/RHEL plus it has the added benefit of being used widely f=
or scientific computing.
For some ISV codes, we sometimes have to edit /etc/redhat-release, but usua=
lly that's it. =A0
Joseph

--- On Fri, 10/28/11, Venable, Richard (NIH/NHLBI) E venabler()nhlbi.nih.go=
v <owner-chemistry/./ccl.net> wrote:

> From: Venable, Richard (NIH/NHLBI) E venabler()nhlbi.nih.gov <owner-chemist=
ry/./ccl.net>
Subject: CCL: best Linux for clusters
To: "Han, Joseph " <jhh3851/./yahoo.com>
Date: Friday, October 28, 2011, 12:02 PM


Sent to CCL by: "Venable, Richard (NIH/NHLBI) [E]" [venabler#%#nhlbi.nih.go=
v]

We have been re-evaluating the choice of CentOS for our cluster, and would =
like solicit comments on which freely available Linux flavor seems to be th=
e best for scientific computing, in terms of performance, stability, ease o=
f administration, and support for more commercial software (QM packages, Ma=
tlab, etc.) and hardware (Qlogic Infiniband boards and driver software).

Besides CentOS, we are looking at Scientific Linux and Debian, but comments=
 on other distributions are welcome.=A0 If you (or someone in your group) c=
an provide some detailed remarks noting good or bad features of specific Li=
nux distributions, please send them to me and I will summarize to the list.

Thank you.

--
Rick Venable=A0 =A0=A0=A05635 FL/T906
Membrane Biophysics Section
NIH/NHLBI Lab. of Computational Biology
Bethesda, MD=A0 20892-9314=A0=A0=A0U.S.A.
(301) 496-1905=A0=A0=A0venabler AT nhlbi*nih*gov



-=3D This is automatically added to each message by the mailing script =3D-=A0 =A0 =A0=A0 =A0 =A0Subscribe/Unsubscribe:=20
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<table cellspacing=3D"0" cellpadding=3D"0" border=3D"0" ><tr><td valign=3D"=
top" style=3D"font: inherit;"><font class=3D"Apple-style-span" face=3D"aria=
l" size=3D"2">I have not been too&nbsp;satisfied&nbsp;with the release sche=
dule of CentOS of late. &nbsp;Also, there seem to have been some release pr=
ocess issues that give me concern about using CentOS 6.x. &nbsp;</font><div=
><font class=3D"Apple-style-span" face=3D"arial" size=3D"2"><br></font></di=
v><div><font class=3D"Apple-style-span" face=3D"arial" size=3D"2">We'll lik=
ely move over to Scientific Linux for the 6.x branch as it's close enough t=
o CentOS/RHEL plus it has the added benefit of being used widely for scient=
ific computing.</font></div><div><font class=3D"Apple-style-span" face=3D"a=
rial" size=3D"2"><br></font></div><div><font class=3D"Apple-style-span" fac=
e=3D"arial" size=3D"2">For some ISV codes, we sometimes have to edit /etc/r=
edhat-release, but usually that's it. &nbsp;</font></div><div><font class=
=3D"Apple-style-span" face=3D"arial"
 size=3D"2"><br></font></div><div><font class=3D"Apple-style-span" face=3D"=
arial" size=3D"2">Joseph</font></div><div><font class=3D"Apple-style-span" =
face=3D"arial" size=3D"2"><br></font><br><font class=3D"Apple-style-span" f=
ace=3D"arial" size=3D"2">--- On </font><b style=3D"font-family: arial; font=
-size: 10pt; ">Fri, 10/28/11, Venable, Richard (NIH/NHLBI) E venabler()nhlb=
i.nih.gov <i>&lt;owner-chemistry/./ccl.net&gt;</i></b><font class=3D"Apple-st=
yle-span" face=3D"arial" size=3D"2"> wrote:</font><br><blockquote style=3D"=
font-family: arial; font-size: 10pt; border-left-width: 2px; border-left-st=
yle: solid; border-left-color: rgb(16, 16, 255); margin-left: 5px; padding-=
left: 5px; "><br>From: Venable, Richard (NIH/NHLBI) E venabler()nhlbi.nih.g=
ov &lt;owner-chemistry/./ccl.net&gt;<br>Subject: CCL: best Linux for clusters=
<br>To: "Han, Joseph " &lt;jhh3851/./yahoo.com&gt;<br>Date: Friday, O=
ctober 28, 2011, 12:02 PM<br><br><div class=3D"plainMail"><br>Sent to CCL b=
y: "Venable, Richard
 (NIH/NHLBI) [E]" [venabler#%#nhlbi.nih.gov]<br><br>We have been re-evaluat=
ing the choice of CentOS for our cluster, and would like solicit comments o=
n which freely available Linux flavor seems to be the best for scientific c=
omputing, in terms of performance, stability, ease of administration, and s=
upport for more commercial software (QM packages, Matlab, etc.) and hardwar=
e (Qlogic Infiniband boards and driver software).<br><br>Besides CentOS, we=
 are looking at Scientific Linux and Debian, but comments on other distribu=
tions are welcome.&nbsp; If you (or someone in your group) can provide some=
 detailed remarks noting good or bad features of specific Linux distributio=
ns, please send them to me and I will summarize to the list.<br><br>Thank y=
ou.<br><br>--<br>Rick Venable&nbsp; &nbsp;&nbsp;&nbsp;5635 FL/T906<br>Membr=
ane Biophysics Section<br>NIH/NHLBI Lab. of Computational Biology<br>Bethes=
da, MD&nbsp; 20892-9314&nbsp;&nbsp;&nbsp;U.S.A.<br>(301)
 496-1905&nbsp;&nbsp;&nbsp;venabler AT nhlbi*nih*gov<br><br><br><br>-=3D Th=
is is automatically added to each message by the mailing script =3D-<br>To =
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iv></blockquote></div></td></tr></table>
--886285840-2024974128-1319840512=:76310--