From owner-chemistry@ccl.net Thu Apr 13 07:25:01 2017 From: "Robert William Molt r.molt.chemical.physics .. gmail.com" To: CCL Subject: CCL:G: Units in Transition Dipole Matrix of Gaussian Anharmonic Calculation Message-Id: <-52739-170413072427-14230-1UidyRA/sBPQoQmJHSzGeA{=}server.ccl.net> X-Original-From: "Robert William Molt" Date: Thu, 13 Apr 2017 07:24:25 -0400 Sent to CCL by: "Robert William Molt" [r.molt.chemical.physics|,|gmail.com] I have a question pertaining to the units in the output of a Gaussian09 revision E calculation. I have tried contacting the folks at Gaussian, but they elected not to respond. I am hoping someone has experience to know the unit choice. In an anharmonic calculation (i.e., specified by #p B971/gen freq= (anharmonic,readanharm)), in the output, one can find the anharmonic transition moments. What are the units? Are they in Bohr radii or in Angstroms? Unless the table is referring to the derivative of the electric dipole moment with respect to the normal mode and thus unitless? The table in question is printed below, as a example. I certainly hope the answer isn't obvious and I am just missing it! ================================================== Anharmonic Transition Moments ================================================== Electric dipole : Fundamental Bands ------------------------------------------------------------------------ Mode(Quanta) X Y Z 1(1) -0.229363E-02 0.216347E-04 -0.165372E-04 2(1) -0.378456E-05 -0.757900E-02 0.495758E-02 3(1) -0.174538E-03 -0.292937E-01 -0.108572E-01 4(1) 0.640748E-02 -0.147416E-03 -0.387546E-04 5(1) -0.331733E-03 -0.412749E-02 0.217199E-01 6(1) -0.322556E-01 0.140901E-03 -0.301806E-03 7(1) -0.135410E-04 0.157547E-01 -0.349931E-01 8(1) 0.339716E-01 -0.840677E-04 -0.669247E-04 9(1) 0.106962E-03 0.291647E-01 -0.150517E-01 10(1) 0.835677E-04 0.188475E-01 0.131796E-01 11(1) 0.623295E-02 -0.124958E-03 -0.688922E-04 12(1) 0.250309E-05 0.635861E-03 0.153666E-01 13(1) -0.165867E-01 0.545289E-04 0.397994E-05 14(1) 0.363989E-04 0.402722E-02 -0.120758E-01 15(1) -0.410448E-02 0.317111E-04 -0.106966E-04 16(1) 0.116963E-01 -0.440165E-04 0.532907E-05 17(1) 0.118271E-05 0.652388E-03 -0.173159E-02 18(1) 0.351650E-04 0.977472E-02 -0.934390E-02 19(1) -0.234592E-01 0.717347E-04 -0.519995E-05 20(1) 0.836829E-04 0.252747E-01 0.380139E-01 21(1) -0.806775E-02 0.324950E-04 0.131289E-04 22(1) 0.279633E-01 -0.109396E-03 0.593255E-05 23(1) 0.203583E-04 0.792405E-02 0.338931E-01 24(1) 0.481287E-04 0.162253E-01 -0.243383E-01 25(1) 0.612414E-04 0.203126E-01 0.409559E-01 26(1) -0.101900E-01 0.478852E-04 0.820998E-05 27(1) -0.303762E-04 -0.882881E-02 -0.330163E-01 28(1) -0.442498E-04 -0.440780E-03 -0.292694E-02 29(1) 0.157015E-01 -0.644128E-04 -0.351860E-05 30(1) 0.154980 -0.536615E-03 0.152241E-04 From owner-chemistry@ccl.net Thu Apr 13 13:33:00 2017 From: "Partha Sengupta anapspsmo]*[gmail.com" To: CCL Subject: CCL: Conversion of Protein data bank data say 5i71 into cartesian (XYZ) format in Gaussview 5. Message-Id: <-52740-170413132950-6499-Zv9rANGh3iGFFqKRrWpOxQ[-]server.ccl.net> X-Original-From: Partha Sengupta Content-Type: multipart/alternative; boundary=001a114b3ebcc13a9f054d0fab8d Date: Thu, 13 Apr 2017 22:59:44 +0530 MIME-Version: 1.0 Sent to CCL by: Partha Sengupta [anapspsmo^^gmail.com] --001a114b3ebcc13a9f054d0fab8d Content-Type: text/plain; charset=UTF-8 Friends, How can I convert protein data bank of pdb 5i71 into Cartesian (XYZ) format in Gaussview 5. ? -- *Dr. Partha Sarathi SenguptaAssociate ProfessorVivekananda Mahavidyalaya, Burdwan* --001a114b3ebcc13a9f054d0fab8d Content-Type: text/html; charset=UTF-8 Content-Transfer-Encoding: quoted-printable
Friends, How can I =C2=A0convert protein data bank of pdb = 5i71 into Cartesian (XYZ) format in Gaussview 5. ?
=C2=A0


--
Dr. Partha Sarathi Sengupta
Associate Professor
Vi= vekananda Mahavidyalaya, Burdwan
--001a114b3ebcc13a9f054d0fab8d-- From owner-chemistry@ccl.net Thu Apr 13 15:17:01 2017 From: "Robert W Molt r.molt.chemical.physics-#-gmail.com" To: CCL Subject: CCL:G: Units in Transition Dipole Matrix of Gaussian Anharmonic Calculation Message-Id: <-52741-170413151624-11260-cbLXTd1yHGWmheX/nmW3rA.@.server.ccl.net> X-Original-From: "Robert W Molt" Date: Thu, 13 Apr 2017 15:16:23 -0400 Sent to CCL by: "Robert W Molt" [r.molt.chemical.physics!^!gmail.com] I recognize there is an implicit charge unit in there, too; I would assume that this would be in Debye, thus, but I'm not sure one wouldn't stick to atomic units strictly (i.e., is it eA or ea sub zero)? > "Robert William Molt r.molt.chemical.physics .. gmail.com" wrote: > > Sent to CCL by: "Robert William Molt" [r.molt.chemical.physics|,|gmail.com] > I have a question pertaining to the units in the output of a Gaussian09 revision E > calculation. I have tried contacting the folks at Gaussian, but they elected not to > respond. I am hoping someone has experience to know the unit choice. > > In an anharmonic calculation (i.e., specified by #p B971/gen freq= > (anharmonic,readanharm)), in the output, one can find the anharmonic transition > moments. What are the units? Are they in Bohr radii or in Angstroms? Unless the table is > referring to the derivative of the electric dipole moment with respect to the normal mode > and thus unitless? The table in question is printed below, as a example. I certainly hope > the answer isn't obvious and I am just missing it! > > ================================================== > Anharmonic Transition Moments > ================================================== > > Electric dipole : Fundamental Bands > ------------------------------------------------------------------------ > Mode(Quanta) X Y Z > 1(1) -0.229363E-02 0.216347E-04 -0.165372E-04 > 2(1) -0.378456E-05 -0.757900E-02 0.495758E-02 > 3(1) -0.174538E-03 -0.292937E-01 -0.108572E-01 > 4(1) 0.640748E-02 -0.147416E-03 -0.387546E-04 > 5(1) -0.331733E-03 -0.412749E-02 0.217199E-01 > 6(1) -0.322556E-01 0.140901E-03 -0.301806E-03 > 7(1) -0.135410E-04 0.157547E-01 -0.349931E-01 > 8(1) 0.339716E-01 -0.840677E-04 -0.669247E-04 > 9(1) 0.106962E-03 0.291647E-01 -0.150517E-01 > 10(1) 0.835677E-04 0.188475E-01 0.131796E-01 > 11(1) 0.623295E-02 -0.124958E-03 -0.688922E-04 > 12(1) 0.250309E-05 0.635861E-03 0.153666E-01 > 13(1) -0.165867E-01 0.545289E-04 0.397994E-05 > 14(1) 0.363989E-04 0.402722E-02 -0.120758E-01 > 15(1) -0.410448E-02 0.317111E-04 -0.106966E-04 > 16(1) 0.116963E-01 -0.440165E-04 0.532907E-05 > 17(1) 0.118271E-05 0.652388E-03 -0.173159E-02 > 18(1) 0.351650E-04 0.977472E-02 -0.934390E-02 > 19(1) -0.234592E-01 0.717347E-04 -0.519995E-05 > 20(1) 0.836829E-04 0.252747E-01 0.380139E-01 > 21(1) -0.806775E-02 0.324950E-04 0.131289E-04 > 22(1) 0.279633E-01 -0.109396E-03 0.593255E-05 > 23(1) 0.203583E-04 0.792405E-02 0.338931E-01 > 24(1) 0.481287E-04 0.162253E-01 -0.243383E-01 > 25(1) 0.612414E-04 0.203126E-01 0.409559E-01 > 26(1) -0.101900E-01 0.478852E-04 0.820998E-05 > 27(1) -0.303762E-04 -0.882881E-02 -0.330163E-01 > 28(1) -0.442498E-04 -0.440780E-03 -0.292694E-02 > 29(1) 0.157015E-01 -0.644128E-04 -0.351860E-05 > 30(1) 0.154980 -0.536615E-03 0.152241E-04 > > From owner-chemistry@ccl.net Thu Apr 13 16:29:01 2017 From: "Chandan Choudhury iitdckc**gmail.com" To: CCL Subject: CCL: Conversion of Protein data bank data say 5i71 into cartesian (XYZ) format in Gaussview 5. Message-Id: <-52742-170413162705-8389-BBkg+rJ+WRfzk1XlkoZxTw a server.ccl.net> X-Original-From: Chandan Choudhury Content-Type: multipart/alternative; boundary="Apple-Mail=_3639B8DD-3ACA-4B8A-AF0C-A5E15DD080F3" Date: Thu, 13 Apr 2017 16:26:57 -0400 Mime-Version: 1.0 (Mac OS X Mail 10.3 \(3273\)) Sent to CCL by: Chandan Choudhury [iitdckc_+_gmail.com] --Apple-Mail=_3639B8DD-3ACA-4B8A-AF0C-A5E15DD080F3 Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset=us-ascii Hi! You can use OpenBabel instead. Its free and very useful. It supports = many formats. You can download it from http://openbabel.org/wiki/Category:Installation = . Thanks > On Apr 13, 2017, at 1:29 PM, Partha Sengupta anapspsmo]*[gmail.com = wrote: >=20 > Friends, How can I convert protein data bank of pdb 5i71 into = Cartesian (XYZ) format in Gaussview 5. ? > =20 >=20 >=20 > --=20 > Dr. Partha Sarathi Sengupta > Associate Professor > Vivekananda Mahavidyalaya, Burdwan --Apple-Mail=_3639B8DD-3ACA-4B8A-AF0C-A5E15DD080F3 Content-Transfer-Encoding: quoted-printable Content-Type: text/html; charset=us-ascii Hi!

You = can use OpenBabel instead. Its free and very useful. It supports many = formats.
You can download it from http://openbabel.org/wiki/Category:Installation.

Thanks
On = Apr 13, 2017, at 1:29 PM, Partha Sengupta anapspsmo]*[gmail.com <owner-chemistry_._ccl.net> wrote:

Friends, How can I  convert protein data bank of pdb = 5i71 into Cartesian (XYZ) format in Gaussview 5. ?
 


--
Dr. Partha = Sarathi Sengupta
Associate Professor
Vivekananda Mahavidyalaya, = Burdwan

= --Apple-Mail=_3639B8DD-3ACA-4B8A-AF0C-A5E15DD080F3--