From owner-chemistry@ccl.net Fri Mar 23 02:24:00 2012 From: "liu junjun ljjlp03,+,gmail.com" To: CCL Subject: CCL: about REMD simulation on sugar Message-Id: <-46553-120323010105-1085-jp64nWZS1c/ro17p/7t/JQ]~[server.ccl.net> X-Original-From: liu junjun Content-Type: multipart/alternative; boundary=f46d0442811efceb1004bbe1e83c Date: Fri, 23 Mar 2012 13:00:57 +0800 MIME-Version: 1.0 Sent to CCL by: liu junjun [ljjlp03:gmail.com] --f46d0442811efceb1004bbe1e83c Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: quoted-printable Thanks a lot for the reference! Best, Junjun On Thu, Mar 22, 2012 at 10:52 PM, Emmanuel Baribefe Naziga baribefe=3D-=3D gmail.com wrote: > Hello, > > I would say it depends on how high your simulation temperature is, see > > Conformational Flexibility of Soluble Cellulose Oligomers: > Chain Length and Temperature Dependence > Tongye Shen,=E2=80=A0,=E2=80=A1 Paul Langan,=C2=A7 Alfred D. French,=E2= =8A=A5 Glenn P. Johnson,=E2=8A=A5 and > S. Gnanakaran*,=E2=80=A0 > Theoretical Biology & Biophysics Group, Center for Nonlinear Studies, and > Biosciences, > > J. AM. CHEM. SOC. 2009, 131, 14786=E2=80=9314794 > > > Cheers > > Emmanuel > > On Wed, Mar 21, 2012 at 11:02 PM, liu junjun ljjlp03*o*gmail.com < > owner-chemistry{}ccl.net> wrote: > >> Hello all, >> >> I am trying to simulate a sugar system (disaccharide) to examine its >> conformation by performing Replica Exchange MD simulation (REMD). I >> notice that some chirality restraints are required to avoid non-physical >> chiralities at high temperature in the REMD simulation on peptide, as >> stated on AMBER tutorial ( >> http://ambermd.org/tutorials/advanced/tutorial7/) >> >> My question is, rather than for peptide, are the chirality >> restraints also required in the REMD simulation on disaccharide? In >> another word, is it possible that the disaccharide's chiralities change = at >> high temperature? >> >> Thanks in advance! >> >> Junjun >> > > --f46d0442811efceb1004bbe1e83c Content-Type: text/html; charset=UTF-8 Content-Transfer-Encoding: quoted-printable Thanks a lot for the reference!

Best,

Junjun

On Thu, Mar 22, 2012 at 10:= 52 PM, Emmanuel Baribefe Naziga baribefe=3D-=3Dgmail.com <owner-chemistry]|[ccl.net> wrote:

Hello,

I would say it dep= ends on how high your simulation temperature is, see

Conformational Flexibility of Soluble Cellulose Oligomers:
C= hain Length and Temperature Dependence

Tongye Shen,=E2=80=A0,=E2=80=A1 Paul Langan,=C2=A7 Alfred D. French,= =E2=8A=A5 Glenn P. Johnson,=E2=8A=A5 and
S. Gnanakaran*,=E2=80=A0=
Theoretical Biology & Biophysics Group, Center for Nonlinear= Studies, and Biosciences,

J. AM. CHEM. SOC. 2009, 131, 14786=E2=80=9314794

<= div>

Cheers

Emmanuel

On Wed, Mar 21, 2012 at 11:02 P= M, liu junjun ljjlp03*o*gmai= l.com <owner-chemistry{}ccl.net> wrote:

Hello all,

I am trying t= o simulate a sugar system (disaccharide) to examine its conformation by perform= ing Replica Exchange MD simulation (REMD).=C2=A0= I notice that some chirality restraints are required to avoid non-phy= sical chiralities at high temperature in the REMD simulation on peptide, as= stated on AMBER tutorial (http://ambermd.org/tutorials/advanced/tutori= al7/)

My question is, rather tha= n for peptide, are the=C2=A0chirality restraints=C2=A0also required i= n the REMD simulation on=C2=A0disaccharide? In another word, i= s it possible that the disaccharide's chiralities change at high temper= ature?=C2=A0

Th= anks in advance!

Ju= njun

--f46d0442811efceb1004bbe1e83c-- From owner-chemistry@ccl.net Fri Mar 23 07:42:00 2012 From: "John john:-:ccdc.cam.ac.uk" To: CCL Subject: CCL: Docking studies with multiple crystal structures of a protein Message-Id: <-46554-120323055005-8907-62q+mcOdTVhGie3Iq3WBzg]![server.ccl.net> X-Original-From: "John" Content-Language: en-gb Content-Type: multipart/alternative; boundary="----=_NextPart_000_0019_01CD08DA.4A227F80" Date: Fri, 23 Mar 2012 09:49:50 -0000 MIME-Version: 1.0 Sent to CCL by: "John" [john+*+ccdc.cam.ac.uk] This is a multi-part message in MIME format. ------=_NextPart_000_0019_01CD08DA.4A227F80 Content-Type: text/plain; charset="us-ascii" Content-Transfer-Encoding: 7bit Hello Prija, Greg and Vincent make good points regarding choice of appropriate structure. There are also tools available to superimpose and compare binding sites both visually and with metrics. For instance Relibase (which is free to academics) can be used to superimpose a set of PDB structures according to sequence and compare them visually . Relibase+ has a tool for superimposing and comparing binding sites according to the disposition of functionality in the binding site (i.e. independent of sequence). Using these tools would allow you to pick out a set of appropriate (perhaps most dissimilar) binding site structures for an ensemble docking approach. For more information on Relibase, Relibase+ and ensemble docking in GOLD you can access the links below http://www.ccdc.cam.ac.uk/free_services/relibase_free/ http://www.ccdc.cam.ac.uk/products/life_sciences/relibase/ http://www.ccdc.cam.ac.uk/products/life_sciences/gold/ http://www.ccdc.cam.ac.uk/case_studies/life_science/ensemble_docking.pdf regards John Liebeschuetz, CCDC > From: owner-chemistry+ccdc-announce==ccdc.cam.ac.uk:+:ccl.net [mailto:owner-chemistry+ccdc-announce==ccdc.cam.ac.uk:+:ccl.net] On Behalf Of Prija Ponnan prija.ponnan:-:gmail.com Sent: 21 March 2012 16:21 To: Rutland, Anne Subject: CCL: Docking studies with multiple crystal structures of a protein Hello all Its a general query not directly related to Autodock usage.I want to study interaction of certain coumarin molecules with INHA (Enoyl-[acyl-carrier-protein] reductase [NADH]) of Mycobacterium tuberculosis In PDB database 36 crystal structure entries of this protein is available.Can anyone please suggest as how should I choose any one/few crystal structure among them or am I supposed to dock my compounds with all the available 36 crystal structures of this protein. Thank you Prija Ponnan PhD Chemistry University of Delhi Delhi-110007,India LEGAL NOTICE Unless expressly stated otherwise, information contained in this message is confidential. If this message is not intended for you, please inform postmaster:+:ccdc.cam.ac.uk and delete the message. The Cambridge Crystallographic Data Centre is a company Limited by Guarantee and a Registered Charity. Registered in England No. 2155347 Registered Charity No. 800579 Registered office 12 Union Road, Cambridge CB2 1EZ. ------=_NextPart_000_0019_01CD08DA.4A227F80 Content-Type: text/html; charset="us-ascii" Content-Transfer-Encoding: quoted-printable

Hello Prija,

&nbs= p; Greg and = Vincent make good points regarding choice of appropriate structure. = There are also tools available to superimpose and compare binding sites = both visually and with metrics. For instance Relibase (which is free to academics) can = be used to superimpose a set of PDB structures according to sequence and = compare them visually . Relibase+ has a tool = for superimposing and comparing binding sites according to the = disposition of functionality in the binding site (i.e. independent of = sequence). Using these tools would allow you to pick out a set of = appropriate (perhaps most dissimilar) binding site structures for an = ensemble docking approach.

= For more information on Relibase, = Relibase+ and ensemble docking in GOLD you = can access the links = below

http://ww= w.ccdc.cam.ac.uk/free_services/relibase_free/

http://www.ccdc.cam.ac.uk/products/life_sciences/re= libase/

http://www.ccdc.cam.ac.uk/products/life_sciences/go= ld/

http://www.ccdc.cam.ac.uk/case_studies/life_science= /ensemble_docking.pdf =

&nbs= p; = regards

&nbs= p; = ; = John Liebeschuetz, = CCDC

From:<= font size=3D2 face=3DTahoma> = owner-chemistry+ccdc-announce=3D=3Dccdc.cam.ac.uk:+:ccl.net = [mailto:owner-chemistry+ccdc-announce=3D=3Dccdc.cam.ac.uk:+:ccl.net] = On Behalf Of Prija Ponnan = prija.ponnan:-:gmail.com
Sent: 21 March 2012 = 16:21
To: Rutland, = Anne
Subject: = CCL: Docking studies with multiple crystal structures of a = protein

Hello = all

Its a general query not directly = related to Autodock usage.I want to study interaction of certain = coumarin molecules with INHA

(Enoyl-[acyl-carrier-protei= n] reductase [NADH]) of Mycobacterium = tuberculosis

In = PDB database 36 crystal structure entries of this protein is = available.Can anyone please suggest as how should I choose any one/few = crystal structure among them or am I supposed to dock my compounds with = all the available 36 crystal structures of this = protein.

Thank = you

Prija = Ponnan
PhD Chemistry
University of = Delhi
Delhi-110007,India

------=_NextPart_000_0019_01CD08DA.4A227F80-- From owner-chemistry@ccl.net Fri Mar 23 10:16:00 2012 From: "Michel Petitjean petitjean.chiral * gmail.com" To: CCL Subject: CCL: Docking studies with multiple crystal structures of a protein Message-Id: <-46555-120323101029-15254-DcLZ7yM/kzDFN/rwjvF1hw_._server.ccl.net> X-Original-From: Michel Petitjean Content-Type: multipart/alternative; boundary=047d7b339ca5976cc504bbe99573 Date: Fri, 23 Mar 2012 15:10:18 +0100 MIME-Version: 1.0 Sent to CCL by: Michel Petitjean [petitjean.chiral|,|gmail.com] --047d7b339ca5976cc504bbe99573 Content-Type: text/plain; charset=ISO-8859-1 Hi, If you do not know the input pairwise correspondence (existence of gaps, etc.), you can use the CSR freeware: http://petitjeanmichel.free.fr/itoweb.petitjean.freeware.html CSR computes the pairwise correspondence, the optimal superposition, its RMSD, etc. Eventually, extract the set of C-alphas with the grep command brfaure running CSR. Best, Michel. Michel Petitjean MTi, INSERM UMR-S 973, University Paris 7, 35 rue Helene Brion, 75205 Paris Cedex 13, France. Phone: +331 5727 8434; Fax: +331 5727 8372 E-mail: petitjean.chiral_+_gmail.com (preferred), michel.petitjean_+_univ-paris-diderot.fr http://petitjeanmichel.free.fr/itoweb.petitjean.html 2012/3/23 John john:-:ccdc.cam.ac.uk > Hello Prija,**** > > Greg and Vincent make good points regarding choice of > appropriate structure. There are also tools available to superimpose and > compare binding sites both visually and with metrics. For instance > Relibase (which is free to academics) can be used to superimpose a set > of PDB structures according to sequence and compare them visually . > Relibase+ has a tool for superimposing and comparing binding sites > according to the disposition of functionality in the binding site (i.e. > independent of sequence). Using these tools would allow you to pick out a > set of appropriate (perhaps most dissimilar) binding site structures for an > ensemble docking approach.**** > > ** ** > > For more information on Relibase, Relibase+ and ensemble docking > in GOLD you can access the links below**** > > ** ** > > http://www.ccdc.cam.ac.uk/free_services/relibase_free/**** > > http://www.ccdc.cam.ac.uk/products/life_sciences/relibase/**** > > http://www.ccdc.cam.ac.uk/products/life_sciences/gold/**** > > http://www.ccdc.cam.ac.uk/case_studies/life_science/ensemble_docking.pdf > **** > > ** ** > > regards**** > > ** ** > > John Liebeschuetz, CCDC**** > > ** ** > > > --047d7b339ca5976cc504bbe99573 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Hi,
If you do not know the input pairwise correspondence (existence of g= aps, etc.),
you can use the CSR freeware:
http://petitjeanmichel.free.= fr/itoweb.petitjean.freeware.html
CSR computes the pairwise correspondence, the optimal superposition, its RM= SD, etc.
Eventually, extract the set of C-alphas with the grep command = brfaure running CSR.
Best,
Michel.

Michel Petitjean
MTi, IN= SERM UMR-S 973, University Paris 7,
35 rue Helene Brion, 75205 Paris Cedex 13, France.
Phone: +331 5727 8434= ; Fax: +331 5727 8372
E-mail: petitjean.chiral_+_gmail.com (preferred), michel.petitjean_+_univ-paris-diderot.fr http://pet= itjeanmichel.free.fr/itoweb.petitjean.html

2012/3/23 John john:-:ccdc.cam.ac.u= k <owne= r-chemistry_+_ccl.net>

Hello Prija,<= /font>

=A0=A0=A0=A0=A0=A0=A0=A0=A0 =A0=A0=A0=A0= Greg and Vincent make good points regarding choice of appropriate st= ructure. There are also tools available to superimpose and compare binding = sites both visually and with metrics. For instance Relibase =A0(which is free to academics) can be used to superimpose a set= of PDB structures according to sequence and compare them visually . = Relibase+ has a tool for superimposing and comparing binding sites a= ccording to the disposition of functionality in the binding site (i.e. inde= pendent of sequence). Using these tools would allow you to pick out a set o= f appropriate (perhaps most dissimilar) binding site structures for an ense= mble docking approach.

=A0
<= font face=3D"Calibri" color=3D"#1f497d">= =A0=A0=A0=A0=A0=A0 For more information on Relibase, Relibase+ and ensemble docking in GOLD you can access the = =A0links below

=A0
<= font face=3D"Calibri" color=3D"#1f497d">http://www.ccdc.cam.ac.uk/free_services/relibase_free/=

http://www.ccdc.cam.ac.uk/products/life_scien= ces/relibase/

http://www.ccdc.cam.ac.uk/products/life_sciences/= gold/

http://www.ccdc.cam.ac.uk/case_= studies/life_science/ensemble_docking.pdf=A0

=A0
<= font face=3D"Calibri" color=3D"#1f497d">= =A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0 regards

=A0
<= font face=3D"Calibri" color=3D"#1f497d">= =A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0= =A0=A0=A0=A0=A0=A0=A0 John Liebeschuetz,=A0=A0 CCDC<= /u>

=A0
<= font face=3D"Calibri" color=3D"#1f497d">=A0

--047d7b339ca5976cc504bbe99573-- From owner-chemistry@ccl.net Fri Mar 23 13:09:00 2012 From: "Brian Masek brian.masek]_[certara.com" To: CCL Subject: CCL: SYBYL-X 2.0 release now available Message-Id: <-46556-120323130746-28996-2vGP9xSDdykErxznrQ88Lw]*[server.ccl.net> X-Original-From: "Brian Masek" Date: Fri, 23 Mar 2012 13:07:44 -0400 Sent to CCL by: "Brian Masek" [brian.masek]|[certara.com] SYBYL-X 2.0 release now available - with new Molecular Data Explorer, QSAR enhancements, and updates for Surflex-Sim and Surflex-Dock to make performing your CADD modeling studies more intuitive and efficient. The Molecular Data Explorer is a multi-component tool for molecular data analysis and visualization, and early testers tell us they obtain insights into their dataset in minutes that previously would have taken days. The MDE includes: A newly re-vamped molecular spreadsheet, a molecular grid viewer, graphing and charts. Structure similarity maps that provide a visual structural clustering to show activity/selectivity islands and cliffs at a glance. One click browsing of both data and 3D structure. Tightly coupled selection between components, allowing you to get insights from data in minutes For example:Selecting a set of highly active compounds in the molecular spreadsheet highlights these same structures in the structure similarity map and allows you to identify whether your highly active compounds reside in one or more chemotypes. Support for importing and merging data from files in a wide variety of formats. For example, merge chemical structure information in SMILES format with biological data in csv or tsv format SYBYL-X 2.0 also includes enhancements to QSAR workflows, adding the ability to create both CoMSIA and EVA QSAR models using the QSAR Project Manager. Additionally, the most recent versions of Surflex-Sim and Surflex-Dock are included, providing command line access to new functionality: Surflex-Sim o Log-Odds data fusion calculations allow multiple predictions to be combined to improve overall prediction o Important for both On Target and Off Target prediction Surflex-Dock o Fast and Convenient Protein Alignment o Binding site shape comparison analysis If youre a SYBYL or SYBYL-X customer with a current support contract, download SYBYL-X 2.0 at www.tripos.com/download today (youll need to have created a profile for the site). If youd like more information about the SYBYL-X Suite of CADD tools, contact me at brian.masek . certara.com Sincerely, Brian B. Masek, Ph.D. Product Manager and Lead Scientist From owner-chemistry@ccl.net Fri Mar 23 14:24:01 2012 From: "ili jordak ilijordak*yahoo.fr" To: CCL Subject: CCL: Bader Analysis Message-Id: <-46557-120323141945-3738-BZ2PDxfzDubKuc1+M4m0qQ . server.ccl.net> X-Original-From: "ili jordak" Date: Fri, 23 Mar 2012 14:19:42 -0400 Sent to CCL by: "ili jordak" [ilijordak%%yahoo.fr] I would like to make a calculation by the theory of Bader (with the AIM2000 software) to obtain direct evidence of interaction between two atoms. Could you help me to create a file (*.aim or *.wfn) or tell me how I can do to make this calculation ?. From owner-chemistry@ccl.net Fri Mar 23 15:08:01 2012 From: "Jing Kong jkong:q-chem.com" To: CCL Subject: CCL:G: Workshop on Electronic Structure Calculations Preceding MWTCC 2012 Message-Id: <-46558-120323144510-10418-5cY3l86rit5A2Rgsg74OWQ]![server.ccl.net> X-Original-From: "Jing Kong" Content-Language: en-us Content-Type: multipart/related; boundary="----=_NextPart_000_02E2_01CD0903.81F6F610" Date: Fri, 23 Mar 2012 14:44:51 -0400 MIME-Version: 1.0 Sent to CCL by: "Jing Kong" [jkong,q-chem.com] This is a multi-part message in MIME format. ------=_NextPart_000_02E2_01CD0903.81F6F610 Content-Type: multipart/alternative; boundary="----=_NextPart_001_02E3_01CD0903.81F6F610" ------=_NextPart_001_02E3_01CD0903.81F6F610 Content-Type: text/plain; charset="us-ascii" Content-Transfer-Encoding: 7bit Dear Colleague, Q-Chem would like to invite you to a workshop in conjunction with the 44th Midwest Theoretical Chemistry Conference (MWTCC) in Madison, Wisconsin. The workshop is in the afternoon of June 7th, immediately preceding the conference which starts in the evening. Q-Chem is a comprehensive ab initio package and the recent release of Q-Chem 4.0 includes many of the latest developments in quantum methodology. The workshop will highlight some of the features in the new Q-Chem 4.0 software package and provide hands-on tutorials of how to use the Q-Chem Program. Please bring your own laptop computers for the tutorials. All workshop participants will receive a free four-month license for unlimited use of Q-Chem 4.0. Please register by May 15th on our website (http://www.q-chem.com/qchem-website/wsmtcc_hh.html). Q-Chem 4.0 represents the state-of-the-art of methodology from the highest performance DFT/HF calculations to high level post-HF correlation methods: . Dispersion-corrected and double hybrid DFT functionals; . Faster algorithms for DFT, HF and coupled-cluster calculations; . Structures and vibrations of excited states with TD-DFT; . Methods for mapping complicated potential energy surfaces; . Efficient valence space models for strong correlation; . More choices for excited states, solvation and charge-transfer; . Effective Fragment Potential and QM/MM for large systems; . Shared-memory for multicores and implementations for GPU's. . For a complete list of new features, please visit our website http://www.q-chem.com/index.htm. Happy Computing, Jing Kong, PhD CEO and Chief Scientist Q-Chem, Inc. This message was sent from Q-Chem WAnnouncement to jkong]![q-chem.com. It was sent from: Q-Chem Inc., 5001 Baum Blvd., Pittsburgh, Pa 15213. You can modify/update your subscription via the link below. q-chem.com Manage Your Subscription http://click.icptrack.com/icp/track.php?msgid=1089435&act=2L3L&r=79619953&c= 378887 ------=_NextPart_001_02E3_01CD0903.81F6F610 Content-Type: text/html; charset="us-ascii" Content-Transfer-Encoding: quoted-printable

Dear = Colleague,

Q-Chem would like to invite you to a = workshop in conjunction with the 44th Midwest Theoretical Chemistry = Conference (MWTCC) in Madison, Wisconsin.

The workshop = is in the afternoon of June 7th, immediately preceding the conference = which starts in the evening. Q-Chem is a comprehensive ab initio = package and the recent release of Q-Chem 4.0 includes many of the latest = developments in quantum methodology. The workshop will highlight = some of the features in the new Q-Chem 4.0 software package and provide = hands-on tutorials of how to use the Q-Chem = Program.

Please bring your own laptop computers = for the tutorials. All workshop participants will receive a free = four-month license for unlimited use of Q-Chem 4.0. Please = register by May 15th on our website (http://www.q-= chem.com/qchem-website/wsmtcc_hh.html).

Q-Chem 4.0 = represents the state-of-the-art of methodology from the highest = performance DFT/HF calculations to high level post-HF correlation = methods:

• Dispersion-corrected and double hybrid = DFT functionals;

• Faster algorithms for DFT, HF = and coupled-cluster calculations;

• Structures = and vibrations of excited states with TD-DFT;

• = Methods for mapping complicated potential energy = surfaces;

• Efficient valence space models for = strong correlation;

• More choices for excited = states, solvation and charge-transfer;

• = Effective Fragment Potential and QM/MM for large = systems;

• Shared-memory for multicores and = implementations for GPU's.

• For a complete list = of new features, please visit our website http://www.q-chem.com/index.htm<= /a>.

Happy Computing,
Jing Kong, PhD
CEO and = Chief Scientist
Q-Chem, Inc.

This = message was sent from Q-Chem WAnnouncement to jkong]![q-chem.com. It was sent from: = Q-Chem Inc., 5001 Baum Blvd., Pittsburgh, Pa 15213. You can = modify/update your subscription via the link = below.

Manage Your Subscription =

Hi,

You should first create a WFN (or a WFX f= ile for working with AIMAll program package) file. The way that you obtain = the WFN files depends on the software that you are using; so cast a look on= the manual of your software to see how you can create the WFN file.=

Now you can simply open the WFN in the AIM2000 and analyse= the electron density. First find critical points ((3,-3), (3,-1), (3,+1) a= nd (3,+3) points) then you can find the atomic interaction lines and integr= ate the atomic basins to obtain atomic properties...

By sa= ving your job in the AIM2000 you will have an *.AIM file.

I = have two recommendations for you in addition.

1) I= suggest working with AIMAll instead of AIM2000, it is more accurate and much faster.

2) for studying the interaction between atoms d= o not just rely on the critical point properties. Check the delocalization = index as well. See this paper; J. Mol. Struct. THEOCHEM, 2009, 901, 243. Yo= u may use the paper as a template for your study.

= Good luck,

Cina Foroutan-Nejad, Ph. D.

School of Chemis= try, University College of Science,

University of Tehran, Tehran,= Iran.

http://independent.academia.edu/CinaForoutanNejad

=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D

From: ili jordak ilijordak*yahoo.fr <owner-chemistry _ ccl.net>
To: "Foroutan-Nejad, Cina " <canys= lopus _ yahoo.co.uk>
Sent: Friday, 23 March 2012, 22:19
Subject: CCL: Bader Analysis

Sent = to CCL by: "ili jordak" [ilijordak%%yahoo.fr]
I would like to make= a calculation by the theory of Bader (with the AIM2000 software) to obtain= direct evidence of interaction between two atoms.
Could you help me to= create a file (*.aim or *.wfn) or tell me how I can do to make this calcul= ation ?.

-=3D This is automatically added to each message by= the mailing script =3D-
To recover the email address of the author of t= he message, please change
the strange characters on the top line to the = _ sign. You can also
E-mail to subscribers: CHEMISTRY _ ccl.net or use:
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Before posting, check wait= time at: http://www.ccl.n= et

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RTFI: http://www.ccl.net/c= hemistry/aboutccl/instructions/

--505732852-1173082768-1332531172=:84179-- From owner-chemistry@ccl.net Fri Mar 23 16:17:00 2012 From: "Jaime Martell jaime_martell[a]cbu.ca" To: CCL Subject: CCL: Bader Analysis Message-Id: <-46560-120323153544-31763-RnzkHXnIK5vnEab3YjDTPQ- -server.ccl.net> X-Original-From: "Jaime Martell" Content-class: urn:content-classes:message Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="us-ascii" Date: Fri, 23 Mar 2012 16:35:33 -0300 MIME-Version: 1.0 Sent to CCL by: "Jaime Martell" [jaime_martell/a\cbu.ca] AIM2000 contains a Help function and online tutorials to help you with this. Jaime -----Original Message----- > From: owner-chemistry+jaime_martell==cbu.ca()ccl.net [mailto:owner-chemistry+jaime_martell==cbu.ca()ccl.net] On Behalf Of ili jordak ilijordak*yahoo.fr Sent: March-23-12 3:20 PM To: Jaime Martell Subject: CCL: Bader Analysis Sent to CCL by: "ili jordak" [ilijordak%%yahoo.fr] I would like to make a calculation by the theory of Bader (with the AIM2000 software) to obtain direct evidence of interaction between two atoms. Could you help me to create a file (*.aim or *.wfn) or tell me how I can do to make this calculation ?.http://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 Mar 23 16:52:00 2012 From: "Tymofii Nikolaienko tim_mail::ukr.net" To: CCL Subject: CCL:G: Bader Analysis Message-Id: <-46561-120323161227-6017-yrhtZP1z/pBBSa4AE+cWiA*_*server.ccl.net> X-Original-From: "Tymofii Nikolaienko" Date: Fri, 23 Mar 2012 16:12:24 -0400 Sent to CCL by: "Tymofii Nikolaienko" [tim_mail-#-ukr.net] Dear Dr. Jordak! Technically it is simple enough: if you use Gaussian just add output=wfn (and density=current if you use non-SCF method in your calculation) option to your route section and append an empty line followed with the line containing the name_of_file.wfn after geometry description section in your .gjf file. In such way after calculation is finished you obtain the .wfn file, containing the reduced first-order density matrix, which is the source for obtaining spatial electron density distribution. Next you just have to run AIM2000, select File->New wavefuntion and open your .wfn file. Next, select Calculation -> Critical Points, click on ...nuclear positions button, and then - on ...mean values of maxima pairs. You obtain critical point data. Next, select Calculation -> Molecular graph and click on Paths uphill from (3,-1) critical points. AIM2000 will generate molecular graph and now you may save it as .aim file for delayed review. However, these steps will not solve your task :) I mean, that yes, you will make the Bader analysis successfully and obtain all the critical points and bond paths present in your molecule. But, strictly speaking, this gives you nothing but just a hint in answering the question about "evidence of interaction between two atoms"!!! Remember, that ALL atoms in the molecule DO interact when they are closer than infinity (i.e., non isolated completely) ! You may ask me then, why people say that AIM shows H-bonds etc? My answer is that Quantum theory of atoms in molecules is NOT the tool to analyze interactions, but a JUST tool to partition your molecule into spatial domains, called topological atoms. Afterwards, you may refer to your chemical experience and say that in MANY CASES these spatial domains behave themselves as that things that chemists call 'atoms', so, when they behave so, you say, that the interaction between neighboring spatial domains is the most strong, so there might be some kind of bonding. So, this is only multiple phenomenological observations on that spatial domains bounded by zero-flux surfaces properties that gives you some sure that QTAIM may give you a GUESS about preferential interactions in your molecule. Remember, that to obtain an "evidence" you should use another approaches (NBO, vibrational spectroscopy etc) along with AIM. Perhaps, "multi-method" approach is the only way that may give you enough data to make yourself sure to claim that there is some bonding in the molecule. Regards, Tymofii Nikolaienko Taras Shevchenko National University of Kyiv, Faculty of Physics, Molecular Physics Department http://timn.ho.ua/ccs 23.03.2012 20:19, ili jordak ilijordak*yahoo.fr wrote: > Sent to CCL by: "ili jordak" [ilijordak%%yahoo.fr] > I would like to make a calculation by the theory of Bader (with the AIM2000 software) to obtain direct evidence of interaction between two atoms. > Could you help me to create a file (*.aim or *.wfn) or tell me how I can do to make this calculation ?.> > > > > From owner-chemistry@ccl.net Fri Mar 23 17:27:00 2012 From: "Julia Rice julia- -almaden.ibm.com" To: CCL Subject: CCL: 2012 Computational Chemistry GRC July 22-27 Mount Snow, VT Message-Id: <-46562-120323151606-9220-L0OZXJMfQcRyJW4rvWCKQg=-=server.ccl.net> X-Original-From: "Julia Rice" Date: Fri, 23 Mar 2012 15:16:03 -0400 Sent to CCL by: "Julia Rice" [julia^-^almaden.ibm.com] The Gordon Research Conferences are pleased to announce the 2012 Computational Chemistry GRC to be held at Mount Snow, Vermont from July 22 - July 27, 2012. Session themes (discussion leads; speakers) include Reactions in the Condensed Phase (Ken Houk / Walter Thiel) Condensed Phase Quantum Chemistry I (Hai Lin; Christian Ochsenfeld / Roland Lindh / Benadette Mennucci) Condensed Phase Quantum Chemistry II (Chris-Kriton Skylaris; Emily Carter / Thomas Miller) Water Structure and Dynamics (Ken Jordan;Sotiris Xantheas / Giulia Galli / Teresa Head-Gordon) Force Field Developments I (John Chodera;Alex MacKerell / William Noid) Force Field Developments II (Christopher Bayly; Pengyu Ren / Matthew Habgood / Adri van Duin) Astrochemistry (Timothy Lee / Lou Allamandola / Daniel Crawford / Helen Fraser) Biomolecular Simulations (Adrian Mulholland / Adrian Roitberg / Darrin York / Riccardo Baron) Industrial Applications (Jed Pitera; Hans-Joerg Limbach / William Swope / Agnes Derecskei) There are some travel awards still available for students, post-docs and young investigators. More details on the program may be found at http://www.grc.org/programs.aspx?year=2012&program=compchem Any questions, please contact julia:_:almaden.ibm.com (Chair, 2012 Computational Chemistry GRC) From owner-chemistry@ccl.net Fri Mar 23 18:02:01 2012 From: "Alex Henderson blueobelisk4alex++gmail.com" To: CCL Subject: CCL: Simple Matlab Question Message-Id: <-46563-120323153405-30116-Bl9ALGYG3m+t8Zz/bUm/ng(0)server.ccl.net> X-Original-From: Alex Henderson Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Fri, 23 Mar 2012 19:34:12 +0000 MIME-Version: 1.0 Sent to CCL by: Alex Henderson [blueobelisk4alex#%#gmail.com] Hi Bradley, The cftool GUI has a 'Print to Figure' option on the File menu. This will create your chart in a standard axes window. From there select 'Save As...' from the File menu and change the 'Save as type:' option to a format of your choice. If you're planning a poster then you'll need to make the figure much bigger than you would expect for a word processor document. There are two types of image format; vector and raster. Vector formats scale nicely while raster formats get pixelated. Consider a line in an image. A raster format says there are a number of coloured pixels next to one another, a vector format says draw a line from here to there. On scaling the rastered dots get bigger and the line looks jagged while the vector version just redraws the line at the appropriate resolution. Not all software packages accept all formats so decide on a format that your poster production software can import. Vector formats: Illustrator EPS EMF (also SVG, but not an option in my version of MATLAB) Raster formats: Bitmap JPEG Paintbrush PNG TIFF Hope your conference goes well. Best wishes, Alex On 22/03/2012 19:00, Bradley Welch bwelch5_._slu.edu wrote: > Sent to CCL by: "Bradley Welch" [bwelch5- -slu.edu] > Dear all, > > I have a simple matlab question that will probably get me laughed at. > > I'm using the curve fitting tool function (cftool for short). I have my curve and the graph. My question is how do I export this graph to say word or open office? My graphs look very nice and I want to use them for my poster at an upcoming local conference. > > Thank you, > > Bradley Welch > Saint Louis University> > From owner-chemistry@ccl.net Fri Mar 23 18:37:00 2012 From: "Tymofii Nikolaienko tim_mail**ukr.net" To: CCL Subject: CCL:G: Bader Analysis Message-Id: <-46564-120323160656-799-rJ6uWjhxiWd+5G17dcRIog+*+server.ccl.net> X-Original-From: Tymofii Nikolaienko Content-Type: multipart/alternative; boundary="------------090701030408060902030104" Date: Fri, 23 Mar 2012 22:06:34 +0200 MIME-Version: 1.0 Sent to CCL by: Tymofii Nikolaienko [tim_mail-$-ukr.net] This is a multi-part message in MIME format. --------------090701030408060902030104 Content-Type: text/plain; charset=windows-1251; format=flowed Content-Transfer-Encoding: 7bit Dear Dr. Jordak! Technicaly it is simple enough: if you use Gaussian just add /output=wfn/ (and /density=current/ if you use non-SCF method in your calculation) option to your route section and append an empty line followed with the line containing the name_of_file.wfn after geometry description section in your .gjf file. In such way after calculation is finished you obtain the .wfn file, containing the reduced first-order density matrix, which is the source for obtaining spatial electron density distribituion. Next you just have to run AIM2000, select File->New wavefuntion and open your .wfn file. Next, select Calculation -> Critical Points, click on ...nuclear positions button, and then - on ...mean values of maxima pairs. You obtain critical point data. Next, select Calculation -> Molecular graph and click on Paths uphil > from (3,-1) critical points. AIM2000 will generate molecular graph and now you may save it as .aim file for delayed review. However, these steps will not solve your task :) I mean, that yes, you will make the Bader analysis successfully and obtain all the critical points and bond paths present in your molecule. But, strictly speaking, this gives you nothing but just a hint in answering the question about "evidence of interaction between two atoms"!!! Remember, that ALL atoms in the molecule DO interact when they are closer than infinity (i.e., non isolated completely) ! You may ask me then, why people say that AIM shows H-bonds etc? My answer is that Quantum theory of atoms in molecules is NOT the tool to analyze interactions, but a JUST tool to partition your molecule into spatial domains, called topological atoms. Afterwards, you may reffer to your chemical experience and say that in MANY CASES these spatial domains behave themselves as that things that chemists call 'atoms', so, when they behave so, you say, that the interaction between neighboring spatial domains is the most strong, so there might be some kind of bonding. So, this is only multiple phenomenological observations on that spatial domains bounded by zero-flux surfaces properties that gives you some sure that QTAIM may give you a GUESS about preferential interactions in your molecule. Remember, that to obtain an "evidence" you should use another approaches (NBO, vibrational spectroscopy etc) along with AIM. Perhaps, "multi-method" approach is the only way that may give you enough data to make yourself sure to claim that there is some bonding in the molecule. Regards, Tymofii Nikolaienko Taras Shevchenko National University of Kyiv, Faculty of Physics, Molecular Physics Department http://timn.ho.ua/ccs 23.03.2012 20:19, ili jordak ilijordak*yahoo.fr wrote: > Sent to CCL by: "ili jordak" [ilijordak%%yahoo.fr] > I would like to make a calculation by the theory of Bader (with the AIM2000 software) to obtain direct evidence of interaction between two atoms. > Could you help me to create a file (*.aim or *.wfn) or tell me how I can do to make this calculation ?.> > > > > --------------090701030408060902030104 Content-Type: text/html; charset=windows-1251 Content-Transfer-Encoding: 8bit Dear Dr. Jordak!

Technicaly it is simple enough: if you use Gaussian just add output=wfn (and density=current if you use non-SCF method in your calculation) option
to your route section and append an empty line followed with the line containing the name_of_file.wfn after geometry description section in your .gjf file.
In such way after calculation is finished you obtain the .wfn file, containing the reduced first-order density matrix, which is the source for obtaining spatial electron density
distribituion.
Next you just have to run AIM2000, select File->New wavefuntion and open your .wfn file.
Next, select Calculation -> Critical Points, click on ...nuclear positions button, and then - on ...mean values of maxima pairs.
You obtain critical point data.
Next, select Calculation -> Molecular graph and click on Paths uphil from (3,-1) critical points.
AIM2000 will generate molecular graph
and now you may save it as .aim file for delayed review.

However, these steps will not solve your task :)
I mean, that yes, you will make the Bader analysis successfully and obtain all the critical points and bond paths present in your molecule.
But, strictly speaking, this gives you nothing but just a hint in answering the question about "evidence of interaction between two atoms"!!!
Remember, that ALL atoms in the molecule DO interact when they are closer than infinity (i.e., non isolated completely) !
You may ask me then, why people say that AIM shows H-bonds etc?
My answer is that Quantum theory of atoms in molecules is NOT the tool to analyze interactions, but a JUST tool to partition your molecule
into spatial domains, called topological atoms. Afterwards, you may reffer to your chemical experience and say that in MANY CASES
these spatial domains behave themselves as that things that chemists call 'atoms', so, when they behave so, you say, that the interaction between
neighboring spatial domains is the most strong, so there might be some kind of bonding. So, this is only multiple phenomenological observations on that spatial domains
bounded by zero-flux surfaces properties that gives you some sure that QTAIM may give you a GUESS about preferential interactions in your molecule.
Remember, that to obtain an "evidence" you should use another approaches (NBO, vibrational spectroscopy etc) along with AIM. Perhaps, "multi-method" approach
is the only way that may give you enough data to make yourself sure to claim that there is some bonding in the molecule.

Regards,
Tymofii Nikolaienko
Taras Shevchenko National University of Kyiv,
Faculty of Physics, Molecular Physics Department
http://timn.ho.ua/ccs

�
23.03.2012 20:19, ili jordak ilijordak*yahoo.fr wrote:

Sent to CCL by: "ili  jordak" [ilijordak%%yahoo.fr]
I would like to make a calculation by the theory of Bader (with the AIM2000 software) to obtain direct evidence of interaction between two atoms. 
Could you help me to create a file (*.aim or *.wfn) or tell me how I can do to make this calculation ?.E-mail to subscribers: CHEMISTRY(_)ccl.net or use:
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