From owner-chemistry@ccl.net Tue Oct 20 03:01:00 2009 From: "John Simmie john.simmie|nuigalway.ie" To: CCL Subject: CCL:G: Surviving two optimisations Message-Id: <-40500-091020025833-20014-UeiMiEo8EMuEkxIrnAwoQA _ server.ccl.net> X-Original-From: "John Simmie" Date: Tue, 20 Oct 2009 02:58:30 -0400 Sent to CCL by: "John Simmie" [john.simmie[]nuigalway.ie] Is it possible to freeze a single geometrical parameter (say bond distance) thru the two optimisations steps in a composite method such as G3 ? The first optimisation can be circumvented via an IOP (1/7=1000000) but this is overwritten in the second optimisation. [Gaussian 09 or 03] John Simmie::NUIG::Ireland From owner-chemistry@ccl.net Tue Oct 20 10:12:01 2009 From: "Morad M El-Hendawy M80elhendawy{:}yahoo.com" To: CCL Subject: CCL:G: AMBER 94 Atom Type in MOE and Gaussian 03/09 Message-Id: <-40501-091020100724-4244-ht2YLDZtwYnV0ZNRf/feIA**server.ccl.net> X-Original-From: "Morad M El-Hendawy" Date: Tue, 20 Oct 2009 10:07:20 -0400 Sent to CCL by: "Morad M El-Hendawy" [M80elhendawy=yahoo.com] Hello CCLers! I prepared an input file of the active site of certain protein to do QM/MM; MM=AMBER94 using ONIOM Gaussian 03. When compare the atom types in both cases I found there some differences, for example, a hydrogen atom has atom type= HP in MOE and that of Gaussian03 is H1. So, am confused for that. I wonder if there is Any expertise body can give a clear cut for this confusion. Best regards, Morad M EL-Hendawy IRELAND From owner-chemistry@ccl.net Tue Oct 20 11:55:00 2009 From: "Kalju Kahn kalju^chem.ucsb.edu" To: CCL Subject: CCL: Conformational Analysis of Toxogonine, TMB-4 and HI-6 using PM6!! Message-Id: <-40502-091018001306-15342-PrnEnkXTJfOUWY3Jd7m4iA,server.ccl.net> X-Original-From: "Kalju Kahn" Content-Transfer-Encoding: 8bit Content-Type: text/plain;charset=iso-8859-1 Date: Sat, 17 Oct 2009 21:12:54 -0700 MIME-Version: 1.0 Sent to CCL by: "Kalju Kahn" [kalju^chem.ucsb.edu] Fabio, Before getting too exited please note that the DFT methods used in the validation do not describe London dispersion ... this may introduce significant errors for larger flexible molecules where pi-stacking is possible ... like the oximes in this study. Kalju > Sent to CCL by: "Fabio P. Costa" [fabioparanho=gmail.com] > I'd like to performed a conformational analysis in order to investigate a > chemical reaction when I've found this interesting paper: Conformational > Analysis of Toxogonine, TMB-4 and HI-6 using PM6 and RM1 Methods! > > http://jbcs.sbq.org.br/online/fpapers/09036SR.pdf > Supplementary Material: :http://jbcs.sbq.org.br/online/fpapers/09036SI.pdf > > It shows that new semi-empirical methods are able to correctly reproduce > DFT ones. It is really sound nice, I mean to able to obtain good results > with a semi-empirical approach. What do you think about it? > > > Best regards. > > Fabio Costa> > > ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Dr. Kalju Kahn Department of Chemistry and Biochemistry UC Santa Barbara, CA 93106 From owner-chemistry@ccl.net Tue Oct 20 13:07:01 2009 From: "Erdem Kamil YILDIRIM ekyildirim(a)gmail.com" To: CCL Subject: CCL:G: Gaussian03 atomic radius Message-Id: <-40503-091019135817-7055-7roQBTiN/qsjs2fl/pDAYw[]server.ccl.net> X-Original-From: "Erdem Kamil YILDIRIM" Content-Language: tr Content-Type: multipart/alternative; boundary="----=_NextPart_000_001C_01CA50FD.E9A2A9A0" Date: Mon, 19 Oct 2009 20:51:19 +0300 MIME-Version: 1.0 Sent to CCL by: "Erdem Kamil YILDIRIM" [ekyildirim|gmail.com] Bu, MIME bigiminde bir gok pargal} iletidir. ------=_NextPart_000_001C_01CA50FD.E9A2A9A0 Content-Type: text/plain; charset="us-ascii" Content-Transfer-Encoding: 7bit Hello Dear All I am trying to optimize and calculate the molecular orbitals for small boron clusters. For molecular orbital Calculations I use pop keyword with the fallowing options (FULL,MK). However I get the error message given below Merz-Kollman atomic radii used. Read replacement radii for each type of atom: Atom Element Radius 1 22 0.00 GetVDW: no radius for atom 1 atomic number 22. Error termination via Lnk1e in /usr/local/g03/l602.exe at Mon Oct 19 20:06:53 2009. Job cpu time: 0 days 0 hours 0 minutes 17.9 seconds. File lengths (MBytes): RWF= 12 Int= 0 D2E= 0 Chk= 10 Scr= 1 Can anyone help me please to solve this problem. Thank you very much Erdem YILDIRIM ------=_NextPart_000_001C_01CA50FD.E9A2A9A0 Content-Type: text/html; charset="us-ascii" Content-Transfer-Encoding: quoted-printable

Hello Dear = All

 

I am trying to optimize and = calculate the molecular orbitals for small boron clusters. For molecular orbital = Calculations I use pop keyword with the fallowing options (FULL,MK). However I get = the error message given below

 

Merz-Kollman atomic radii = used.

 Read replacement radii for = each type of atom:

 Atom Element = Radius

    = 1    22    0.00

 GetVDW:  no radius = for atom   1 atomic number  22.

 Error termination via = Lnk1e in /usr/local/g03/l602.exe at Mon Oct 19 20:06:53 = 2009.

 Job cpu time:  0 = days  0 hours  0 minutes 17.9 seconds.

 File lengths = (MBytes):  RWF=3D     12 Int=3D      0 = D2E=3D      0 Chk=3D     10 = Scr=3D      1

 

 

Can anyone help me please to = solve this problem. Thank you very much

 

Erdem = YILDIRIM

 

 

------=_NextPart_000_001C_01CA50FD.E9A2A9A0-- From owner-chemistry@ccl.net Tue Oct 20 14:24:00 2009 From: "David Gallagher gallagher.da{:}gmail.com" To: CCL Subject: CCL: Increased ligand-protein docking accuracy Message-Id: <-40504-091020135814-2041-8OAaa+dQT0difPikYxssVg,server.ccl.net> X-Original-From: David Gallagher Content-Type: multipart/alternative; boundary="=====================_982515==.ALT" Date: Tue, 20 Oct 2009 10:28:20 -0700 Mime-Version: 1.0 Sent to CCL by: David Gallagher [gallagher.da*gmail.com] --=====================_982515==.ALT Content-Type: text/plain; charset="us-ascii"; format=flowed Subject: Increased ligand-protein docking accuracy A recent study (1) has concluded that: "...the docking accuracy in regard to complex geometry......significantly increased when partial charges of the ligands and proteins were calculated with the semi-empirical PM6 method." This new methodology using MOPAC2009 PM6 partial charges in AutoDock for both ligand and protein, is now implemented in "DockingServer" which is available on-line at http://www.dockingserver.com/web? (1) Journal of Cheminformatics 2009, 1:15, doi:10.1186/1758-2946-1-15 http://www.jcheminf.com/content/1/1/15 David Gallagher CACheResearch.com --=====================_982515==.ALT Content-Type: text/html; charset="us-ascii" Subject:  Increased ligand-protein docking accuracy

A recent study (1) has concluded that: "...the docking accuracy in regard to complex geometry......significantly increased when partial charges of the ligands and proteins were calculated with the semi-empirical PM6 method."

This new methodology using MOPAC2009 PM6 partial charges in AutoDock for both ligand and protein, is now implemented in "DockingServer" which is available on-line at http://www.dockingserver.com/web?

(1) Journal of Cheminformatics 2009, 1:15,  
     doi:10.1186/1758-2946-1-15
     http://www.jcheminf.com/content/1/1/15

David Gallagher
CACheResearch.com --=====================_982515==.ALT-- From owner-chemistry@ccl.net Tue Oct 20 17:56:00 2009 From: "Daniel Glossman-Mitnik dglossman%a%gmail.com" To: CCL Subject: CCL: solvation energy in mopac Message-Id: <-40505-091020175156-22500-soeyZvYaGV439UAMqSy5PQ..server.ccl.net> X-Original-From: Daniel Glossman-Mitnik Content-Type: multipart/alternative; boundary=000325559f563898ec047664de12 Date: Tue, 20 Oct 2009 15:51:43 -0600 MIME-Version: 1.0 Sent to CCL by: Daniel Glossman-Mitnik [dglossman]*[gmail.com] --000325559f563898ec047664de12 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: quoted-printable Dear netters: How should one calculate the solvation energy of a given molecule using MOPAC 2009? It is enough with doing one calculation in gas phase and another in solvent and then substracting both heats of formation? Any example input related to these questions will be appreciated. Best regards, Daniel ***************************************************************************= ********************************** Dr. Daniel Glossman-Mitnik: Centro de Investigaci=C3=B3n en Materiales Avanzados, SC Grupo NANOCOSMOS - Nanotecnolog=C3=ADa Computacional, Simulaci=C3=B3n y M= odelado Molecular Miguel de Cervantes 120 - Complejo Industrial Chihuahua - Chihuahua, Chih 31109, Mexico Phone: +52 614 4391151 Secretary/FAX: +52 614 4394852 Lab: +52 614 4394805 E-mail: daniel.glossman*cimav.edu.mx dglossman*gmail.com WWW: http://www.cimav.edu.mx/cv/daniel.glossman http://blogs.cimav.edu.mx/daniel.glossman ***************************************************************************= ********************************** --000325559f563898ec047664de12 Content-Type: text/html; charset=UTF-8 Content-Transfer-Encoding: quoted-printable Dear netters:

How should one calculate the solvation energy of a giv= en molecule using MOPAC 2009?
It is enough with doing one calculation in= gas phase and another in solvent and then
substracting both heats of fo= rmation?
Any example input related to these questions will be appreciated.

Be= st regards,

Daniel

****************************= ***************************************************************************= ******
Dr. Daniel Glossman-Mitnik:
Centro de Investigaci=C3=B3n en Materiales A= vanzados, SC
Grupo NANOCOSMOS =C2=A0- =C2=A0Nanotecnolog=C3=ADa Computac= ional, Simulaci=C3=B3n y Modelado Molecular
Miguel de Cervantes 120 - Co= mplejo Industrial Chihuahua - Chihuahua, Chih 31109, Mexico
Phone: +52 614 4391151 =C2=A0 =C2=A0 Secretary/FAX: +52 614 4394852 =C2=A0 = =C2=A0 Lab: +52 614 4394805
E-mail: =C2=A0daniel.glossman*cimav.edu.mx =C2=A0 =C2=A0 =C2=A0 =C2= =A0 =C2=A0dglossman*gmail.com WWW: =C2=A0http://ww= w.cimav.edu.mx/cv/daniel.glossman
=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2= =A0 =C2=A0 =C2=A0http= ://blogs.cimav.edu.mx/daniel.glossman
***************************************************************************= **********************************
--000325559f563898ec047664de12-- From owner-chemistry@ccl.net Tue Oct 20 22:17:00 2009 From: "David Gallagher gallagher.da**gmail.com" To: CCL Subject: CCL: solvation energy in mopac Message-Id: <-40506-091020221414-24222-o0CEAy2tFhwOp781szC+gw*server.ccl.net> X-Original-From: David Gallagher Content-Type: multipart/alternative; boundary="=====================_8827718==.ALT" Date: Tue, 20 Oct 2009 19:08:48 -0700 Mime-Version: 1.0 Sent to CCL by: David Gallagher [gallagher.da**gmail.com] --=====================_8827718==.ALT Content-Type: text/plain; charset="iso-8859-1"; format=flowed Content-Transfer-Encoding: quoted-printable Hi Daniel, To get the free energy of solvation of the=20 gaseous compound, you would, indeed, optimize and=20 calculate the Delta-G of the single molecule in=20 the gas phase, and then optimize and calculate=20 Delta-G of the molecule in a solvent using the=20 appropriate COSMO settings, and calculate the=20 difference. Using a cluster of solvent molecules=20 (instead of the COSMO solvent field) can be more=20 error prone, as you have to optimize the solvent=20 molecules with and without the solute, and their=20 energy may vary slightly depending on their=20 specific interactions and orientations relative=20 to each other after each optimization. A more accurate approach for energy of solvation=20 and solubility prediction is to use a quantum=20 method in conjunction with statistical=20 thermodynamics, such as COSMOtherm. Which ever approach you use, you may also need to=20 consider specific solute-solvent interactions,=20 ionization, tautomerization, zwitter-ion formation, etc. Regards, David Gallagher CACheResearch.com At 02:51 PM 10/20/2009, Daniel Glossman-Mitnik dglossman%a%gmail.com wrote: >Dear netters: > >How should one calculate the solvation energy of=20 >a given molecule using MOPAC 2009? >It is enough with doing one calculation in gas=20 >phase and another in solvent and then >substracting both heats of formation? >Any example input related to these questions will be appreciated. > >Best regards, > >Daniel > >***************************************************************************= ********************************** >Dr. Daniel Glossman-Mitnik: >Centro de Investigaci=C3=B3n en Materiales Avanzados, SC >Grupo NANOCOSMOS =C2 - =C2 Nanotecnolog=C3=ADa=20 >Computacional, Simulaci=C3=B3n y Modelado Molecular >Miguel de Cervantes 120 - Complejo Industrial=20 >Chihuahua - Chihuahua, Chih 31109, Mexico >Phone: +52 614 4391151 =C2 =C2 Secretary/FAX: +52=20 >614 4394852 =C2 =C2 Lab: +52 614 4394805 >E-mail: =C2=20 >daniel.glossman[A]cimav.edu.mx=20 >=C2 =C2 =C2 =C2 =C2 dglossman[A]gmail.com >WWW: =C2=20 >http://www.cimav.edu.mx/cv/dani= el.glossman >=C2 =C2 =C2 =C2 =C2 =C2 =C2 http://blogs.cimav.edu.mx/daniel.glossman >***************************************************************************= ********************************** --=====================_8827718==.ALT Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Hi Daniel,

To get the free energy of solvation of the gaseous compound, you would, indeed, optimize and calculate the Delta-G of the single molecule in the gas phase, and then optimize and calculate Delta-G of the molecule in a solvent using the appropriate COSMO settings, and calculate the difference.  Using a cluster of solvent molecules (instead of the COSMO solvent field) can be more error prone, as you have to optimize the solvent molecules with and without the solute, and their energy may vary slightly depending on their specific interactions and orientations relative to each other after each optimization.

A more accurate approach for energy of solvation and solubility prediction is to use a quantum method in conjunction with statistical thermodynamics, such as COSMOtherm.

Which ever approach you use, you may also need to consider specific solute-solvent interactions, ionization, tautomerization, zwitter-ion formation, etc.

Regards,
David Gallagher
CACheResearch.com


At 02:51 PM 10/20/2009, Daniel Glossman-Mitnik dglossman%a%gmail.com wrote:
Dear netters:

How should one calculate the solvation energy of a given molecule using MOPAC 2009?
It is enough with doing one calculation in gas phase and another in solvent and then
substracting both heats of formation?
Any example input related to these questions will be appreciated.

Best regards,

Daniel

****************************************************************************= *********************************
Dr. Daniel Glossman-Mitnik:
Centro de Investigaci=C3=B3n en Materiales Avanzados, SC
Grupo NANOCOSMOS =C2 - =C2 Nanotecnolog=C3=ADa Computacional, Simulaci=C3=B3= n y Modelado Molecular
Miguel de Cervantes 120 - Complejo Industrial Chihuahua - Chihuahua, Chih 31109, Mexico
Phone: +52 614 4391151 =C2  =C2  Secretary/FAX: +52 614 4394852 =C2  =C2  Lab: +52 614 4394805
E-mail: =C2 daniel.glossman[A]cimav.edu.mx =C2  =C2  =C2  =C2  = =C2 dglossman[A]gmail.com
WWW: =C2 http://www.cimav.edu.mx/cv/daniel.glossman
=C2  =C2  =C2  =C2  =C2  =C2  =C2 http://blogs.cimav.edu.mx/daniel.glossman
****************************************************************************= *********************************
--=====================_8827718==.ALT--