From owner-chemistry@ccl.net Thu Sep 20 00:22:01 2012 From: "Dr. Lars Goerigk lars.goerigk###chem.usyd.edu.au" To: CCL Subject: CCL: Adding augmentation to the def2-TZVPP set Message-Id: <-47631-120919220021-10924-Y3+LkutTprQ10dlPkngi1Q]-[server.ccl.net> X-Original-From: "Dr. Lars Goerigk" Content-Type: multipart/alternative; boundary="------------030504060802050008000004" Date: Thu, 20 Sep 2012 12:00:14 +1000 MIME-Version: 1.0 Sent to CCL by: "Dr. Lars Goerigk" [lars.goerigk#%#chem.usyd.edu.au] This is a multi-part message in MIME format. --------------030504060802050008000004 Content-Type: text/plain; charset=ISO-8859-1; format=flowed Content-Transfer-Encoding: 7bit Dear Supriya, yes many publications show that it is no problem to combine Dunning's diffuse functions with Ahlrichs type basis sets. In fact, the benefit of Ahlrichs type basis sets is that they contain less primitives and are therefore computationally more efficient than Dunning sets. If you have def2-TZVPP, you should choose the diffuse functions from aug-cc-pVTZ. You will notice that the number of diffuse functions is large. Considering which type of system you are dealing with, you do not have to include all those frunctions. For example, for main group chemistry it is often sufficient to just include the s and p functions for first row elements and just the s function to hydrogen. The efficiency and accuracy of such an approach for the treatment of excited states can be e.g. seen in Fig. 2 of this paper, http://pubs.acs.org/doi/abs/10.1021/jp807366r For main group chemistry you can have a look at this one (diffuse functions were used for electron affinities and negatively charged water-hydroxylion clusters): http://pubs.rsc.org/en/Content/ArticleLanding/2011/CP/c0cp02984j But as I've said, there are several papers available following this approach and these are just two examples. This approach is therefore nothing "exotic". On a side note, five minutes before I saw your question, I had just finished a calculation with such a "mixed" basis set :) Sometimes people just take the lowest exponents of the respective functions and generate their own diffuse functions extending the geometric progression in the exponents. A third possibility you could try is to use F. Furche's new basis sets, e.g. def2-TZVPD. D. Rappoport and F. Furche; J. Chem. Phys. 133, 134105 (2010). Best wishes, Lars -- Dr. Lars Goerigk School of Chemistry (Building F11) The University of Sydney, NSW 2006 Australia www.researcherid.com/rid/D-3717-2009 --------------030504060802050008000004 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Dear Supriya,

yes many publications show that it is no problem to combine Dunning's diffuse functions with Ahlrichs type basis sets. In fact, the benefit of Ahlrichs type basis sets is that they contain less primitives and are therefore computationally more efficient than Dunning sets. If you have def2-TZVPP, you should choose the diffuse functions from aug-cc-pVTZ.
You will notice that the number of diffuse functions is large. Considering which type of system you are dealing with, you do not have to include all those frunctions.
For example, for main group  chemistry it is often sufficient to just include the s and p functions for first row elements and just the s function to hydrogen.

The efficiency and accuracy of such an approach for the treatment of excited states can be e.g. seen in Fig. 2 of this paper,
http://pubs.acs.org/doi/abs/10.1021/jp807366r

For main group chemistry you can have a look at this one (diffuse functions were used for electron affinities and negatively charged water-hydroxylion clusters):
http://pubs.rsc.org/en/Content/ArticleLanding/2011/CP/c0cp02984j

 But as I've said, there are several papers available following this approach and these are just two examples. This approach is therefore nothing "exotic".
On a side note, five minutes before I saw your question, I had just finished a calculation with such a "mixed" basis set :)

Sometimes people just take the lowest exponents of the respective functions and generate their own diffuse functions extending the geometric progression in the exponents.

A third possibility you could try is to use F. Furche's new basis sets, e.g. def2-TZVPD.
D. Rappoport and F. Furche; J. Chem. Phys. 133, 134105 (2010).

Best wishes,
Lars

--
Dr. Lars Goerigk
School of Chemistry (Building F11)
The University of Sydney, NSW 2006
Australia
www.researcherid.com/rid/D-3717-2009
--------------030504060802050008000004-- From owner-chemistry@ccl.net Thu Sep 20 00:57:01 2012 From: "Savita Pundlik savita.pundlik-x-tcs.com" To: CCL Subject: CCL: Looking for MD program to model droplets Message-Id: <-47632-120919230501-27029-9I4OrvW01sFjQY0hFNRuaQ-x-server.ccl.net> X-Original-From: Savita Pundlik Content-Transfer-Encoding: quoted-printable Content-Type: text/html; charset="iso-8859-1" Date: Thu, 20 Sep 2012 08:34:49 +0530 MIME-Version: 1.0 Sent to CCL by: Savita Pundlik [savita.pundlik^-^tcs.com] Hello,

There are many parallel MD codes in open source.
We= have used LAMMPS and GROMACS though not for droplets so far.

= Good luck.
Regards,

Tata Consultancy Services
Mailto: savita.p= undlik===tcs.com
Website: http://www.tcs.com
__________________________= __________________
Experience certainty. IT Services
Business Solu= tions
Outsourcing
____________________________________________

-----owner-chemistry+savita.pundlik=3D= =3Dtcs.com===ccl.net wrote: -----
To: "Pundlik, Savita Sunil " <savita.pundlik===tcs.com&= gt;
From: "Peeter Burk peeter|a|chem.ut.ee" Sent by: owner-chemistry+savita.pundlik=3D=3Dtcs.com===ccl.net
Date: 09/1= 8/2012 12:45PM
Subject: CCL: Looking for MD program to model droplets
Sent to CCL by= : "Peeter  Burk" [peeter#,#chem.ut.ee]
Dear colleagues,

We a= re planning to extend our activities to the MD modeling of droplets in atmo= sphere. Could anyone suggest a suitable program, which can be used for MD m= odeling of water and also other solvent (e.g. acetonitrile, DMSO) droplets = containing some organic solutes (neutral and also cationic or anionic forms= ). The program should be capable of handling droplet of several thousand mo= lecules in a reasonable time. So far we have had some preliminary tries wit= h tinker and amoeba force field with some success, but tinker seems not to = be parallelized so I would like to inquire about other (faster, better, etc= .) options.

Best regards
Peeter Burk
University of Tartu, Esto= nia
burk{=3D}ut.ee



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From owner-chemistry@ccl.net Thu Sep 20 01:31:01 2012 From: "Daniel Fernando Coimbra danielfcoimbra|*|gmail.com" To: CCL Subject: CCL: Adding augmentation to the def2-TZVPP set Message-Id: <-47633-120920001518-23332-p4e7ts1SMOJ0mQ/IclkCJw{:}server.ccl.net> X-Original-From: Daniel Fernando Coimbra Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Thu, 20 Sep 2012 01:15:08 -0300 MIME-Version: 1.0 Sent to CCL by: Daniel Fernando Coimbra [danielfcoimbra_._gmail.com] The Def2-TZVPPD basis set already contains additional diffuse functions and is available at EMSL. Em 19/09/2012 20:08, Supriya Shrestha shrestha.gsas#%#gmail.com escreveu: > Sent to CCL by: "Supriya Shrestha" [shrestha.gsas{}gmail.com] > Hello CCLers! > > I got the def2-TZVPP set from the Basis set exchange and now I want to add augmentation to it. I am getting the augmentation part from the dunning basis set but I am unsure which augmented dunning set should I use: aug-cc-pVDZ or aug-cc-pVTZ. Since def2-TZVPP is a triple zeta basis set, I am guessing that the augmentation from aug-cc-pVTZ. Are there any specific/standard rules on how to add augmentation to a basis set?> > From owner-chemistry@ccl.net Thu Sep 20 08:01:00 2012 From: "Hans De Winter hans!=!silicos-it.com" To: CCL Subject: CCL: Filter-it 1.0.1 released Message-Id: <-47634-120920075803-26265-Ii1/JNW9XCKJtAQwiGP20A ~~ server.ccl.net> X-Original-From: "Hans De Winter" Date: Thu, 20 Sep 2012 07:58:02 -0400 Sent to CCL by: "Hans De Winter" [hans-.-silicos-it.com] Hi all, I am pleased to announce the release of Filter-it version 1.0.1. Filter-it is an open source program for filtering out molecules with unwanted properties. It is build on top of OpenBabel open source C++ API for rapid calculation of molecular properties. This version includes a number of bugfixes and improvements: - The input/output parameters and program logic have been improved. - Corrected a bug in the SIMILARITY_STACK property (molecules with space-containing molecular titles were handled incorrectly); - Documentation has been updated and more information on the logic and use of standard output and standard error has been included. The new version can be downloaded from www.silicos-it.com Happy filtering! Hans From owner-chemistry@ccl.net Thu Sep 20 08:35:00 2012 From: "Goedele Roos groos=vub.ac.be" To: CCL Subject: CCL: BASIC CHEMICAL THERMODYNAMICS (book) Message-Id: <-47635-120920082033-2434-8ljlRIh6mwTIORMEjY+i+w*server.ccl.net> X-Original-From: Goedele Roos Date: Thu, 20 Sep 2012 14:20:25 +0200 Sent to CCL by: Goedele Roos [groos%x%vub.ac.be] Dear list, is this a good book? or can anyone recommend one on chemical thermodynamics? BASIC CHEMICAL THERMODYNAMICS (Fifth Edition), ISBN: 978-1-86094-445-1 by E Brian Smith (Former Master of St Catherine's College, Oxford, UK & Vice-Chancellor of Cardiff University, UK) Thank you in advance, Goedele _____________________________ Goedele Roos, PhD Department of General Chemistry http://we.vub.ac.be/~algc/ VIB, Department of Structural Biology, Vrije Universiteit Brussel | http://www.structuralbiology.be/ Brussels Center for Redox Biology | http://redox.vub.ac.be/ Vrije Universiteit Brussel, Building G, room 10G714 Pleinlaan 2, 1050 Brussels,Belgium phone: +32 2 6293312 fax: +32 2 6293317 E-mail: groos%a%vub.ac.be From owner-chemistry@ccl.net Thu Sep 20 09:10:00 2012 From: "Andrew Voronkov drugdesign-$-yandex.ru" To: CCL Subject: CCL: question on free energy/constant of dissociation estimation for protein-ligand complex (X-ray) Message-Id: <-47636-120919170346-27764-snUTr400/J6rMkt+IXXq+Q*o*server.ccl.net> X-Original-From: Andrew Voronkov Content-Transfer-Encoding: 7bit Content-Type: text/plain Date: Thu, 20 Sep 2012 01:03:24 +0400 MIME-Version: 1.0 Sent to CCL by: Andrew Voronkov [drugdesign : yandex.ru] Dear CCL users, there is plethora of methods for estimation of the free energy of protein-ligand binding. Which software among the fastest is most accurate in evaluation of the free energy of binding for a given protein-ligand complex (X-ray). I need to thoeretically calculate constant of protein-ligand complex dissociation. Best regards, Andrew From owner-chemistry@ccl.net Thu Sep 20 11:36:00 2012 From: "Sayan Ghosh sayan.rana1990{:}gmail.com" To: CCL Subject: CCL: Appropriate Functional for Chromium Message-Id: <-47637-120920083610-10198-LZ2rMSFqNfbGPHSqPG9IrQ .. server.ccl.net> X-Original-From: "Sayan Ghosh" Date: Thu, 20 Sep 2012 08:36:09 -0400 Sent to CCL by: "Sayan Ghosh" [sayan.rana1990[#]gmail.com] Dear Members, I am using B3LYP functional to optimize some Chromium complex and in some cases i have found out that the optimized structures are hugely deviating from the experimentally determined(crystal structure) geometry. Now this may be because of crystal packing effect(i.e intermolecular forces). I want to know which is the best functional for Chromium complexes and please give me some references. Thanks in advance. Regards. Sayan sayan.rana1990===gmail.com From owner-chemistry@ccl.net Thu Sep 20 12:11:00 2012 From: "J D Whitfield jdwhitfield(0)gmail.com" To: CCL Subject: CCL: BASIC CHEMICAL THERMODYNAMICS (book) Message-Id: <-47638-120920091014-24707-9J/w6p7JMO8ejdcqRLj7Hg(!)server.ccl.net> X-Original-From: J D Whitfield Content-Type: multipart/alternative; boundary=20cf3079b8987cf39c04ca21d7d9 Date: Thu, 20 Sep 2012 15:10:04 +0200 MIME-Version: 1.0 Sent to CCL by: J D Whitfield [jdwhitfield]_[gmail.com] --20cf3079b8987cf39c04ca21d7d9 Content-Type: text/plain; charset=ISO-8859-1 I like this book and also Fermi's Thermodynamics which although dated is a quick clear introduction to thermodynamics. JDW -- Dr. J. D. Whitfield VCQ Postdoctoral Fellow Vienna Center for Quantum Science and Technology email: james.whitfield_-_univie.ac.at On Thu, Sep 20, 2012 at 2:20 PM, Goedele Roos groos=vub.ac.be < owner-chemistry_-_ccl.net> wrote: > > Sent to CCL by: Goedele Roos [groos%x%vub.ac.be] > Dear list, > > is this a good book? or can anyone recommend one on chemical > thermodynamics? > > BASIC CHEMICAL THERMODYNAMICS (Fifth Edition), ISBN: 978-1-86094-445-1 > by E Brian Smith (Former Master of St Catherine's College, Oxford, UK & > Vice-Chancellor of Cardiff University, UK) > > Thank you in advance, > Goedele > _____________________________ > > Goedele Roos, PhD > > Department of General Chemistry http://we.vub.ac.be/~algc/ > VIB, Department of Structural Biology, Vrije Universiteit Brussel | > http://www.structuralbiology.be/ > Brussels Center for Redox Biology | http://redox.vub.ac.be/ > > Vrije Universiteit Brussel, Building G, room 10G714 > Pleinlaan 2, 1050 Brussels,Belgium > phone: +32 2 6293312 > fax: +32 2 6293317 > E-mail: groos!=!vub.ac.be> > > --20cf3079b8987cf39c04ca21d7d9 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable I like this book and also Fermi's Thermodynamics which although dated i= s a quick clear introduction to thermodynamics.

JDW

--

Dr. J. D. Whitfield
VCQ Postdoctoral Fellow
Vienna Center for Quantum Science an= d Technology





On Thu, Sep 20, 2012 at 2:20 PM, Goedele= Roos groos=3Dvub.ac.be = <owner-chem= istry_-_ccl.net> wrote:

Sent to CCL by: Goedele Roos [groos%x%vub.ac.be]
Dear list,

is this a good book? or can anyone recommend one on chemical thermodynamics= ?

BASIC CHEMICAL THERMODYNAMICS (Fifth Edition), ISBN: 978-1-86094-445-1
by E Brian Smith (Former Master of St Catherine's College, Oxford, UK &= amp; Vice-Chancellor of Cardiff University, UK)

Thank you in advance,
Goedele
_____________________________

Goedele Roos, PhD

Department of General Chemistry http://we.vub.ac.be/~algc/
VIB, Department of Structural Biology, Vrije Universiteit Brussel | http://www.structur= albiology.be/
Brussels Center for Redox Biology | http://redox.vub.ac.be/

Vrije Universiteit Brussel, Building G, room 10G714
Pleinlaan 2, 1050 Brussels,Belgium
phone: +32 2 6293= 312
fax: +32 2 629331= 7
E-mail: groos!=3D!vub.ac.be<= /a>



-=3D This is automatically added to each message by the mailing script =3D-=
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--20cf3079b8987cf39c04ca21d7d9-- From owner-chemistry@ccl.net Thu Sep 20 12:46:00 2012 From: "John Shelley john.shelley : schrodinger.com" To: CCL Subject: CCL: Looking for MD program to model droplets Message-Id: <-47639-120920101237-6205-8p3/62L4ZFLtKBdTWfs0pA*_*server.ccl.net> X-Original-From: John Shelley Content-Type: multipart/alternative; boundary=bcaec54b5004cb451f04ca22b6e1 Date: Thu, 20 Sep 2012 07:12:31 -0700 MIME-Version: 1.0 Sent to CCL by: John Shelley [john.shelley(!)schrodinger.com] --bcaec54b5004cb451f04ca22b6e1 Content-Type: text/plain; charset=ISO-8859-1 Another possibility for a code that runs well in parallel is Desmond. Desmond and its source code are available without cost for non-commercial use by universities and other not-for-profit research institutions: http://www.deshawresearch.com/resources_desmond.html -- John Shelley, Ph.D. Schrodinger Fellow --bcaec54b5004cb451f04ca22b6e1 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Another possibility for a code that runs well in parallel is Desmond.=A0 De= smond and its source code are available without cost for non-commercial use by universities and other not-for-profit research institutions:
http://www.des= hawresearch.com/resources_desmond.html
--
John Shelley, Ph.D. Schrodinger Fellow
--bcaec54b5004cb451f04ca22b6e1-- From owner-chemistry@ccl.net Thu Sep 20 13:20:00 2012 From: "Sergio Manzetti sergio.manzetti[-]gmx.com" To: CCL Subject: CCL:G: Torsion angles Message-Id: <-47640-120920120524-28409-SYDJ03d/5BHVm8EDcoDvKA(-)server.ccl.net> X-Original-From: "Sergio Manzetti" Content-Type: multipart/alternative; boundary="========GMXBoundary167021348156909687974" Date: Thu, 20 Sep 2012 18:01:49 +0200 MIME-Version: 1.0 Sent to CCL by: "Sergio Manzetti" [sergio.manzetti!^!gmx.com] --========GMXBoundary167021348156909687974 Content-Type: text/plain; charset="utf-8" Content-Transfer-Encoding: 8bit Dear CCLrs can you recommend a program that can easily report the torsion angles of given atoms in a Gaussian output file? Thanks Best wishes Sergio --========GMXBoundary167021348156909687974 Content-Type: text/html; charset="utf-8" Content-Transfer-Encoding: quoted-printable Dear CCL= rs can you recommend a program that can easily report the torsion angles of= given atoms in a Gaussian output file?
=20
=20 Thanks
=20
=20 Best wishes
=20
=20 Sergio --========GMXBoundary167021348156909687974-- From owner-chemistry@ccl.net Thu Sep 20 13:55:00 2012 From: "steinbrt]-[rci.rutgers.edu" To: CCL Subject: CCL: question on free energy/constant of dissociation estimation for protein-ligand complex (X-ray) Message-Id: <-47641-120920103315-12393-x+qlvR4iHXLAHxW+hDs8HA|*|server.ccl.net> X-Original-From: steinbrt*rci.rutgers.edu Content-Transfer-Encoding: 8bit Content-Type: text/plain;charset=iso-8859-1 Date: Thu, 20 Sep 2012 10:33:08 -0400 (EDT) MIME-Version: 1.0 Sent to CCL by: steinbrt]^[rci.rutgers.edu Hi Andrew, there is a large variety of methods available and unfortunately there is a trade-off between the fastest and most accurate methods. If your protein-ligand complex structure is known, you can conduct free energy calculations of the thermodynamic integration, jarzynski pulling or umbrella sampling variants, depending on your system. All these can often predict the binding free energy for a complex to within 1-2 kcal/mol, but there remain many pitfalls and problems in doing the simulations right. A simpler and quicker approach would use endpoint methods like MM-PBSA or the linear interaction energy method which still need long MD simulations and sometimes show severe convergence problems. The fastest methods to predict binding energies are ligand docking tools, like FlexX, Autodock, Gold, Glide, Flexscreen etc. These tend to give good binding modes but docking scores are rarely very reliable predictions of absolute binding free energies. Computing a ligand's binding affinity is a tricky thing to do as many reviews on the topic will tell you, so be prepared to spend a lot of time on validating your approach. Kind Regards, Thomas On Wed, September 19, 2012 5:03 pm, Andrew Voronkov drugdesign-$-yandex.ru wrote: > > Sent to CCL by: Andrew Voronkov [drugdesign : yandex.ru] > Dear CCL users, there is plethora of methods for estimation of the free > energy of protein-ligand binding. Which software among the fastest is most > accurate in evaluation of the free energy of binding for a given > protein-ligand complex (X-ray). I need to thoeretically calculate constant > of protein-ligand complex dissociation. > > Best regards, > Andrew> > > Dr. Thomas Steinbrecher formerly at the BioMaps Institute Rutgers University 610 Taylor Rd. Piscataway, NJ 08854 From owner-chemistry@ccl.net Thu Sep 20 14:31:01 2012 From: "Vincent Leroux vincent.leroux:+:loria.fr" To: CCL Subject: CCL: question on free energy/constant of dissociation estimation for protein-ligand complex (X-ray) Message-Id: <-47642-120920125204-32292-MnBHrtrGKrx3ioJ2o5B+3Q[a]server.ccl.net> X-Original-From: Vincent Leroux Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=ISO-8859-1 Date: Thu, 20 Sep 2012 18:51:53 +0200 (CEST) MIME-Version: 1.0 Sent to CCL by: Vincent Leroux [vincent.leroux#,#loria.fr] Hi Andrew If it is just for evaluating X-ray-derived structures or previously-docked models, I would recommend Szybki (OpenEye, free for academics) as a good choice regarding the relevance/calculation speed ratio. You will probably not get very precise predictions matching experimental measurements, yet this (through MM/PBSA minimization within a simple general forcefield) may be the best you can get without resorting to forcefield parameterization, complex free energy perturbation protocols, and quantum mechanics. If you are not facing "difficult" systems, you may find Szybki is "good enough". Regards VL ----- Mail original ----- > De: "Andrew Voronkov drugdesign-$-yandex.ru" > À: "Vincent Leroux " > Envoyé: Mercredi 19 Septembre 2012 23:03:24 > Objet: CCL: question on free energy/constant of dissociation estimation for protein-ligand complex (X-ray) > > > Sent to CCL by: Andrew Voronkov [drugdesign : yandex.ru] > Dear CCL users, there is plethora of methods for estimation of the > free energy of protein-ligand binding. Which software among the > fastest is most accurate in evaluation of the free energy of binding > for a given protein-ligand complex (X-ray). I need to thoeretically > calculate constant of protein-ligand complex dissociation. > > Best regards, > Andrew > > > > -= 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 Thu Sep 20 15:05:00 2012 From: "Supriya Shrestha sshrestha_+_fas.harvard.edu" To: CCL Subject: CCL: Adding augmentation to the def2-TZVPP set Message-Id: <-47643-120920133558-5609-Nls8E6YQvCyos4L8WG9zDA*o*server.ccl.net> X-Original-From: Supriya Shrestha Content-Type: text/plain; charset=ISO-8859-1 Date: Thu, 20 Sep 2012 13:35:31 -0400 MIME-Version: 1.0 Sent to CCL by: Supriya Shrestha [sshrestha||fas.harvard.edu] Thank you everyone for the response. It was very helpful! On Thu, Sep 20, 2012 at 12:15 AM, Daniel Fernando Coimbra danielfcoimbra|*|gmail.com wrote: > > Sent to CCL by: Daniel Fernando Coimbra [danielfcoimbra_._gmail.com] > The Def2-TZVPPD basis set already contains additional diffuse functions and > is available at EMSL. > > Em 19/09/2012 20:08, Supriya Shrestha shrestha.gsas#%#gmail.com escreveu: > >> Sent to CCL by: "Supriya Shrestha" [shrestha.gsas{}gmail.com] >> Hello CCLers! >> >> I got the def2-TZVPP set from the Basis set exchange and now I want to add >> augmentation to it. I am getting the augmentation part from the dunning >> basis set but I am unsure which augmented dunning set should I use: >> aug-cc-pVDZ or aug-cc-pVTZ. Since def2-TZVPP is a triple zeta basis set, I >> am guessing that the augmentation from aug-cc-pVTZ. Are there any >> specific/standard rules on how to add augmentation to a basis set?http://www.ccl.net/chemistry/sub_unsub.shtmlConferences: > http://server.ccl.net/chemistry/announcements/conferences/> >