From owner-chemistry@ccl.net Fri May 25 04:57:00 2012 From: "Daniel Fernando Coimbra danielfcoimbra#%#gmail.com" To: CCL Subject: CCL: Assistance in EDA results using WB97XD functional Message-Id: <-46981-120525034321-27243-/skAWjy8bnoM1S8PLeKpsw[A]server.ccl.net> X-Original-From: Daniel Fernando Coimbra Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Fri, 25 May 2012 04:40:55 -0300 MIME-Version: 1.0 Sent to CCL by: Daniel Fernando Coimbra [danielfcoimbra-x-gmail.com] At first look it would seem that at least one of your SCF calculations did not converge. You should make sure that monomers and supermolecule achieved a proper convergence, searching for "CONVERGED" in the output file will quickly lead you to those results. On 05/24/2012 11:21 PM, Rosana Amorim amorimrm:superig.com.br wrote: > Sent to CCL by: "Rosana Amorim" [amorimrm++superig.com.br] > Greetings all, > > I'm using Energy Decomposition Analysis methodology in my research. I always used the B3LYP functional without having any problem with the results of energy decomposition. However, recently I started using the WB97X-D functional, which incorporates a dispersion correction, and to my surprise the results of EDA using this functional were nonsense, with huge absolute energy decomposition values in kcal. > For exemple of what I try to explain, I present the results of the decomposed energies, for the same input, only changing the functional. > > With B3LYP: > ------------- > OWN BASIS SET KCAL/MOL > ------------- > ELECTROSTATIC ENERGY ES=-47.76 > EXCHANGE ENERGY EX=-50.69 > REPULSION ENERGY REP=166.67 > POLARIZATION ENERGY POL=-58.64 > DFT DISPERSION ENERGY DISP=-12.07 > TOTAL INTERACTION ENERGY HF OR DFT E=-2.49 > > With WB97X-D: > ------------- > OWN BASIS SET KCAL/MOL > ------------- > ELECTROSTATIC ENERGY ES=5895.85 > EXCHANGE ENERGY EX=-52.81 > REPULSION ENERGY REP=166.76 > POLARIZATION ENERGY POL=-6001.96 > DFT DISPERSION ENERGY DISP=-13.96 > TOTAL INTERACTION ENERGY HF OR DFT E=-6.12 > > Would anyone know why this difference? and Why such high values for polarization and electrostatic energies using the WB97XD functional? > > Sincerely, > > Rosana Amorim > amorimrm^^superig.com.br > -- Daniel Fernando Coimbra Grupo de Estrutura Eletrônica Molecular Departamento de Química Universidade Federal de Santa Catarina From owner-chemistry@ccl.net Fri May 25 05:32:01 2012 From: "sobia ahsan halim sobia_halim{=}yahoo.com" To: CCL Subject: CCL: ligbuilder error Message-Id: <-46982-120525051150-18283-tXCeYPT0Kimb7pujJM06SA_._server.ccl.net> X-Original-From: "sobia ahsan halim" Date: Fri, 25 May 2012 05:11:48 -0400 Sent to CCL by: "sobia ahsan halim" [sobia_halim|,|yahoo.com] Hi I am running cavity input in Ligbuilder but it is giving the following error. Anyone please let me know how to fix this error Cavity search begining ... Now reading parameters from 'cavity.input' ... Search Rule : Depth-Volume Limit ... Number of atoms = 0 Search Mode : Whole Protein Mode ... Now reading the protein from 'receptor/1m48.pdb' ... Detecting chain : single chain of a monomer Protein checking: Pass Center of protein is 9.2 12.2 6.1 Now defining the box by protein ... Now analyzing the protein ... SelfHB = 91.015823 HB num = 100 Check 26 Now detecting cavity in the box ... Whole protein search need more time, please wait ... Segmentation fault Thanks in advance Sobia From owner-chemistry@ccl.net Fri May 25 16:32:00 2012 From: "Eliac Brown Eliacbrown*yahoo.com" To: CCL Subject: CCL: 2D Electrostatic Potential map Message-Id: <-46983-120525163004-6902-rJnw5xQZ62aCGTzZRo5Q4g{=}server.ccl.net> X-Original-From: "Eliac Brown" Date: Fri, 25 May 2012 16:29:50 -0400 Sent to CCL by: "Eliac Brown" [Eliacbrown#%#yahoo.com] Dear All In a part of my project, we need to generate the electrostatic potential map for some molecules using pre-calculated charges. The conventional way to draw the electrostatic maps is to generate the density and potential cubes and load them in a visualization program. While, here we want to generate the electrostatic map using a new set of charges. Do you know any software that can be used to perform this job? I was also wondering if you could tell me which program can be used to draw 2D electrostatic map (not 3D grid). Any kind of help would be appreciated Cheers E. Brown From owner-chemistry@ccl.net Fri May 25 17:08:01 2012 From: "Abhik Seal abhik1368++gmail.com" To: CCL Subject: CCL: 2D Electrostatic Potential map Message-Id: <-46984-120525170715-17275-zAf661SsH3X55gS09N0HhQ() server.ccl.net> X-Original-From: Abhik Seal Content-Type: multipart/alternative; boundary=f46d044288bc411c4204c0e2c023 Date: Fri, 25 May 2012 17:06:47 -0400 MIME-Version: 1.0 Sent to CCL by: Abhik Seal [abhik1368**gmail.com] --f46d044288bc411c4204c0e2c023 Content-Type: text/plain; charset=ISO-8859-1 Hi You can use this http://www.scl.ameslab.gov/MacMolPlt/ The documentation is here. http://www.scl.ameslab.gov/MacMolPlt/Manual_pages/MacMolPlt_Surfaces.html Abhik Seal Indiana University Bloomington Department of Chemical Informatics abseal]-[indiana.edu *OSDD CHEMINFORMATICS* +18123699097 http://mypage.iu.edu/~abseal/index.htm On Fri, May 25, 2012 at 4:29 PM, Eliac Brown Eliacbrown*yahoo.com < owner-chemistry]-[ccl.net> wrote: > > Sent to CCL by: "Eliac Brown" [Eliacbrown#%#yahoo.com] > Dear All > In a part of my project, we need to generate the electrostatic potential > map > for some molecules using pre-calculated charges. The conventional way to > draw > the electrostatic maps is to generate the density and potential cubes and > load > them in a visualization program. While, here we want to generate the > electrostatic map using a new set of charges. Do you know any software > that can > be used to perform this job? > I was also wondering if you could tell me which program can be used to > draw 2D > electrostatic map (not 3D grid). > Any kind of help would be appreciated > Cheers > E. Brown> > > --f46d044288bc411c4204c0e2c023 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Hi=A0


The documentation is here. http://www.scl.ameslab.gov/MacMolPlt/Manual_pages/MacMolPlt_Surf= aces.html=A0
=A0
=A0
Abhik Seal
Indiana University Bloomington
Department of Chemical Informatics



On Fri, May 25, 2012 at 4:29 PM, Eliac B= rown Eliacbrown*yahoo.com <owner-ch= emistry]-[ccl.net> wrote:

Sent to CCL by: "Eliac =A0Brown" [Eliacbrown#%#yahoo.com]
Dear All
In a part of my project, we need to generate the electrostatic potential ma= p
for some molecules using pre-calculated charges. The conventional way to dr= aw
the electrostatic maps is to generate the density and potential cubes and l= oad
them in a visualization program. While, here we want to generate the
electrostatic map using a new set of charges. Do you know any software that= can
be used to perform this job?
I was also wondering if you could tell me which program can be used to draw= 2D
electrostatic map (not 3D grid).
Any kind of help would be appreciated
Cheers
E. Brown



-=3D This is automatically added to each message by the mailing script =3D-=
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--f46d044288bc411c4204c0e2c023-- From owner-chemistry@ccl.net Fri May 25 17:46:00 2012 From: "Giuseppe Mallia g.mallia_._imperial.ac.uk" To: CCL Subject: CCL: MSSC2012 - Ab initio Modelling in Solid State Chemistry Message-Id: <-46985-120525174254-21479-lmFL5J4FVq7Ustaglu+7aQ[-]server.ccl.net> X-Original-From: "Giuseppe Mallia" Date: Fri, 25 May 2012 17:42:50 -0400 Sent to CCL by: "Giuseppe Mallia" [g.mallia{}imperial.ac.uk] MSSC2012 - Ab initio Modelling in Solid State Chemistry Discovering quantum-mechanical simulations with CRYSTAL http://www.cse.scitech.ac.uk/events/MSSC2012 London (UK), September 17-21, 2012 Directors: N.M. Harrison - G. Mallia The week long school is designed for CRYSTAL users, PhD students, Post-Docs and researchers with interests in solid state chemistry, physics, materials science, surface science, catalysis, magnetism and nano-science. It will provide both an introduction to the capabilities of quantum mechanical simulation and to the practical use of CRYSTAL09 (http://www.crystal.unito.it/) and CRYSCOR (http://www.cryscor.unito.it). Please note that the deadline for bursary applications is on the 1st of June. The programme will be available soon. From owner-chemistry@ccl.net Fri May 25 18:21:00 2012 From: "Giuseppe Mallia g.mallia]=[imperial.ac.uk" To: CCL Subject: CCL: MSSC^-^Brazil - Announcement Message-Id: <-46986-120525174420-22906-k3+WSptwuVJkeLT9rOkTpw^-^server.ccl.net> X-Original-From: "Giuseppe Mallia" Date: Fri, 25 May 2012 17:44:19 -0400 Sent to CCL by: "Giuseppe Mallia" [g.mallia{}imperial.ac.uk] The Universidade Federal do Rio Grande do Norte and the Theoretical Chemistry Group of the Torino University, in collaboration with the Universidade Estatual Paulista is organizing a new edition of the Summer School in Brazil: Ab initio Modelling in Solid State Chemistry MSSC],[Brazil http://www.crystal.unito.it/mssc-brazil December 7-12, 2012 - Natal (RN), Brazil Directors: J.R. Sambrano, E. Longo, R. Dovesi, C.M. Zicovich-Wilson The School is addressed to PhD students, Post-Docs and researchers with interests in solid state chemistry, physics, materials science, surface science and catalysis. It provides an overview of the possibilities offered by ab initio quantum mechanical techniques when applied to the characterization of crystalline materials. The capabilities of CRYSTAL09 (http://www.crystal.unito.it/) and CRYSCOR (http://www.cryscor.unito.it) will be illustrated, with hands-on tutorials organized in the afternoon sessions. For further details and updated information visit the School web site: http://www.crystal.unito.it/mssc-brazil From owner-chemistry@ccl.net Fri May 25 18:56:00 2012 From: "Nancy nancy5villa\a/gmail.com" To: CCL Subject: CCL: PubChem Online Compound Search and Download Message-Id: <-46987-120525185233-16473-UNz+KR17sMLIntVQnihedw{:}server.ccl.net> X-Original-From: Nancy Content-Type: multipart/alternative; boundary=20cf30667c0def438004c0e438b0 Date: Fri, 25 May 2012 15:52:27 -0700 MIME-Version: 1.0 Sent to CCL by: Nancy [nancy5villa===gmail.com] --20cf30667c0def438004c0e438b0 Content-Type: text/plain; charset=ISO-8859-1 Hi All, I have been using the PubChem database to search for uncharged small molecules. However, even after specifying zero charge, PubChem still outputs compounds containing amino groups (-NH2) and carboxylic acids (-COOH); since I am interested in physiological pH, these compounds would actually be charged. Is there some way to exclude molecules containing these functional groups? I've noticed that there is an option on PubChem to include only certain atoms, but the search times out at 2 minutes if I try this. I'd like to exclude halogens and aldehydes as well, can this be specified? Finally, after searching for numerous compounds, how could all of them be downloaded into an organized compound library? If there is another online compound database besides PubChem that can be easily searched and has the same or better functionality, I'd greatly appreciate any info about it. Thanks, Nancy --20cf30667c0def438004c0e438b0 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Hi All,

I have been using the PubChem database to search for uncharg= ed small molecules.=A0 However, even after specifying zero charge, PubChem = still outputs compounds containing amino groups (-NH2) and carboxylic acids= (-COOH); since I am interested in physiological pH, these compounds would = actually be charged.

Is there some way to exclude molecules containing these functional grou= ps?=A0 I've noticed that there is an option on PubChem to include only = certain atoms, but the search times out at 2 minutes if I try this.=A0 I= 9;d like to exclude halogens and aldehydes as well, can this be specified?= =A0 Finally, after searching for numerous compounds, how could all of them = be downloaded into an organized compound library?

If there is another online compound database besides PubChem that can b= e easily searched and has the same or better functionality, I'd greatly= appreciate any info about it.

Thanks,
Nancy



--20cf30667c0def438004c0e438b0-- From owner-chemistry@ccl.net Fri May 25 19:39:01 2012 From: "Giovanni Finoto Caramori giovanni.caramori~!~ufsc.br" To: CCL Subject: CCL: Assistance in EDA results using WB97XD functional Message-Id: <-46988-120525103136-2940-XXJr8XNFCHXpQh5eyXZ+wg(0)server.ccl.net> X-Original-From: Giovanni Finoto Caramori Content-Type: multipart/alternative; boundary="=_398b52846b7d260934ef0364e32abb6b" Date: Fri, 25 May 2012 10:38:53 -0300 MIME-Version: 1.0 Sent to CCL by: Giovanni Finoto Caramori [giovanni.caramori::ufsc.br] --=_398b52846b7d260934ef0364e32abb6b Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=UTF-8 Dear Rosana, Fisrt of all, please check the convergence of the SCF for fragments and for the whole molecule. Values of this magnitude are common to appear when the SCF does not converge in any of the steps of the EDA. Best wishes from Florianópolis, Giovanni On Thu, 24 May 2012 22:21:07 -0400, Rosana Amorim amorimrm:superig.com.br wrote: > Sent to CCL by: "Rosana Amorim" [amorimrm++superig.com.br] > Greetings all, > > I'm using Energy Decomposition Analysis methodology in my research. I always used the B3LYP functional without having any problem with the results of energy decomposition. However, recently I started using the WB97X-D functional, which incorporates a dispersion correction, and to my surprise the results of EDA using this functional were nonsense, with huge absolute energy decomposition values in kcal. > For exemple of what I try to explain, I present the results of the decomposed energies, for the same input, only changing the functional. > > With B3LYP: > ------------- > OWN BASIS SET KCAL/MOL > ------------- > ELECTROSTATIC ENERGY ES=-47.76 > EXCHANGE ENERGY EX=-50.69 > REPULSION ENERGY REP=166.67 > POLARIZATION ENERGY POL=-58.64 > DFT DISPERSION ENERGY DISP=-12.07 > TOTAL INTERACTION ENERGY HF OR DFT E=-2.49 > > With WB97X-D: > ------------- > OWN BASIS SET KCAL/MOL > ------------- > ELECTROSTATIC ENERGY ES=5895.85 > EXCHANGE ENERGY EX=-52.81 > REPULSION ENERGY REP=166.76 > POLARIZATION ENERGY POL=-6001.96 > DFT DISPERSION ENERGY DISP=-13.96 > TOTAL INTERACTION ENERGY HF OR DFT E=-6.12 > > Would anyone know why this difference? and Why such high values for polarization and electrostatic energies using the WB97XD functional? > > Sincerely, > > Rosana Amorim > amorimrm^^superig.com.br> > E-mail to subscribers: CHEMISTRY,,ccl.net [1] or use:[2] > > E-mail to administrators: CHEMISTRY-REQUEST,,ccl.net [3] or use[4][5][6][7][8][9][10][11] -- Giovanni Finoto Caramori PhD Departamento de Química - CFM-UFSC Campus Universitário Trindade - C.P. 476 88040-900 Florianópolis/SC http://www.qmc.ufsc.br/~caramori[1] Phone: ++55(48)3721-6844/6845/6846 Fax: ++55(48)3721-6852 Ramal 239 Mobile: ++55(48)9926-8342 Links: ------ [1] mailto:CHEMISTRY,,ccl.net [2][3] mailto:CHEMISTRY-REQUEST,,ccl.net [4][5][6] http://www.ccl.net [7] http://www.ccl.net/jobs [8] http://server.ccl.net/chemistry/announcements/conferences/ [9] http://www.ccl.net/chemistry/searchccl/index.shtml [10][11] http://www.ccl.net/chemistry/aboutccl/instructions/ --=_398b52846b7d260934ef0364e32abb6b Content-Transfer-Encoding: quoted-printable Content-Type: text/html; charset=UTF-8

Dear Rosana,

Fisrt of all, please check the convergence of the SCF for fragments and for the whole molecule. Values of this magnitude <= span class=3D"hps">are common to appear <= span class=3D"hps">when the SCF does not converge in any of the steps of the EDA.

Best wishes from Florianópolis,

Giovanni

On Thu, 24 May 2012 22:21:07 -0400, Rosana Amorim amorimrm:superig.com= =2Ebr wrote:

Sent to CCL by: "Rosana  Amorim" [amorimrm++superig.com.br]
Greetings all,
=20
I'm using Energy Decomposition Analysis methodology in my research. I alway=
s used the B3LYP functional without having any problem with the results of =
energy decomposition. However, recently I started using the WB97X-D functio=
nal, which incorporates a dispersion correction, and to my surprise the res=
ults of EDA using this functional were nonsense, with huge absolute energy =
decomposition values in kcal.
For exemple of what I try to explain, I present the results of the decompos=
ed energies, for the same input, only changing the functional.
=20
With B3LYP:
 -------------
 OWN BASIS SET                           KCAL/MOL
 -------------
 ELECTROSTATIC ENERGY                   ES=3D-47.76
 EXCHANGE ENERGY                        EX=3D-50.69
 REPULSION ENERGY                       REP=3D166.67
 POLARIZATION ENERGY                    POL=3D-58.64
 DFT DISPERSION ENERGY                  DISP=3D-12.07
 TOTAL INTERACTION ENERGY HF OR DFT     E=3D-2.49
=20
With WB97X-D:
 -------------
OWN BASIS SET                           KCAL/MOL
 -------------
 ELECTROSTATIC ENERGY                   ES=3D5895.85
 EXCHANGE ENERGY                        EX=3D-52.81
 REPULSION ENERGY                       REP=3D166.76
 POLARIZATION ENERGY                    POL=3D-6001.96
 DFT DISPERSION ENERGY                  DISP=3D-13.96
 TOTAL INTERACTION ENERGY HF OR DFT     E=3D-6.12
=20
Would anyone know why this difference? and Why such high values for polariz=
ation and electrostatic energies using the WB97XD functional?
=20
Sincerely,
=20
Rosana Amorim
amorimrm^^superig.com.br



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--=20
Giovanni Finoto Caramori PhD
Departamento de Química - CFM-UFSC
Campus Universitário Trindade - C.P. 476
88040-900 Florianópolis/SC
http://www.qmc.ufsc.br/~caramori[1]
Phone: ++55(48)3721-6844/6845/6846
 Fax: ++55(48)3721-6852 Ramal 239
Mobile: ++55(48)9926-8342
--=_398b52846b7d260934ef0364e32abb6b-- From owner-chemistry@ccl.net Fri May 25 21:56:00 2012 From: "Asif Mahmood eminabadi(!)yahoo.com" To: CCL Subject: CCL: Optimization Conformation? Message-Id: <-46989-120525114914-30567-5X2M5ZuBT3nrvCMp8dXGxQ|*|server.ccl.net> X-Original-From: "Asif Mahmood" Date: Fri, 25 May 2012 11:49:13 -0400 Sent to CCL by: "Asif Mahmood" [eminabadi,+,yahoo.com] How I can confirm the successful optimization of a structure after a normal termination of optimization job. Advance thanks Asif Mahmood Pakistan eminabadi..yahoo.com