From owner-chemistry@ccl.net Mon Nov 12 02:56:00 2007 From: "Stan van Gisbergen vangisbergen(-)scm.com" To: CCL Subject: CCL: Looking for Casimir-Polder type calculation program package Message-Id: <-35584-071112025434-24367-JFyKs65igYhOLBw3p6ydlQ-$-server.ccl.net> X-Original-From: Stan van Gisbergen Content-Type: multipart/alternative; boundary=Apple-Mail-54--349028874 Date: Mon, 12 Nov 2007 08:53:39 +0100 Mime-Version: 1.0 (Apple Message framework v752.3) Sent to CCL by: Stan van Gisbergen [vangisbergen[-]scm.com] --Apple-Mail-54--349028874 Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=US-ASCII; delsp=yes; format=flowed Dear Cong Wang, The DISPER program that comes with the ADF density functional package does what you need for C6 up to C10 van der Waals coefficients, both isotropic and anisotropic. It uses ADF's multipole-multipole polarizabillities at imaginary frequencies. These are read from file, so you could also use input > from other codes. Source code for DISPER and ADF is available, so it's possible to make the modifications you need. For input / output description, see: http://www.scm.com/Doc/ Doc2007.01/ADF/Properties/page49.html For ADF + DISPER input file, see: http://www.scm.com/Doc/Doc2007.01/ ADF/Examples/page69.html Free ADF trial to see how everything works: http://www.scm.com/ SCMForms/TrialRequest.jsp If you have further questions, feel free to contact me directly. Best regards, Stan van Gisbergen On Nov 9, 2007, at 4:18 PM, Cong Wang wc0546[a]gmail.com wrote: > > Sent to CCL by: "Cong Wang" [wc0546^_^gmail.com] > Hello everyone, > > I am looking for some program package can perform Casimir-Polder > type calculation for dispersion interaction. It is better to have > some flexibility that is possible to modify the formula of > polarizability. I am grateful for any suggestions, thank you very much > > Best regards > Cong Wang > > > > -= 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/ > > Search Messages: http://www.ccl.net/htdig (login: ccl, Password: > search)> > -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+- > +-+-+ > > > Dr. S.J.A. van Gisbergen Scientific Computing & Modelling NV Theoretical Chemistry, Vrije Universiteit De Boelelaan 1083 1081 HV Amsterdam The Netherlands vangisbergen-*-scm.com http://www.scm.com T: +31-20-5987626 F: +31-20-5987629 --Apple-Mail-54--349028874 Content-Transfer-Encoding: quoted-printable Content-Type: text/html; charset=ISO-8859-1 Dear Cong Wang,=A0

The DISPER program that = comes with the ADF density functional package does what you need for C6 = up to C10 van der Waals coefficients, both isotropic and = anisotropic.
It uses ADF's multipole-multipole = polarizabillities at imaginary frequencies. These are read from file, so = you could also use input from other codes.=A0
Source code for = DISPER and ADF is available, so it's possible to make the modifications = you need.=A0

For input / output = description, see:=A0http= ://www.scm.com/Doc/Doc2007.01/ADF/Properties/page49.html
For= ADF + DISPER input file, see:=A0http:/= /www.scm.com/Doc/Doc2007.01/ADF/Examples/page69.html
Free = ADF trial to see how everything works: http://www.scm.com/S= CMForms/TrialRequest.jsp

If you have further = questions, feel free to contact me directly.=A0

Best = regards,
Stan van Gisbergen

On Nov 9, = 2007, at 4:18 PM, Cong Wang wc0546[a]gmail.com wrote:


Sent to = CCL by: "Cong=A0 Wang" = [wc0546^_^gmail.com]
Hello everyone,

=A0 I am looking for some program = package can perform Casimir-Polder type calculation for dispersion = interaction. It is better to have some flexibility that is possible to = modify the formula of polarizability. I am grateful for any suggestions, = thank you very much
Best regards
Cong Wang



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=



Dr. S.J.A. van Gisbergen
Scientific Computing & Modelling NV
Theoretical Chemistry, Vrije Universiteit
De Boelelaan 1083
1081 HV = Amsterdam
The Netherlands=A0=A0 =A0 =A0 =A0 = =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0

 =

= --Apple-Mail-54--349028874-- From owner-chemistry@ccl.net Mon Nov 12 05:39:00 2007 From: "etamar:-:fh.huji.ac.il" To: CCL Subject: CCL:G: NBO Natural Bond Orbital Deletion Gaussian 98 Message-Id: <-35585-071112024658-24001-yTEsPAc3GHU4n7TgQSqFwA|,|server.ccl.net> X-Original-From: etamar\a/fh.huji.ac.il Content-Disposition: inline Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset=UTF-8; DelSp="Yes"; format="flowed" Date: Mon, 12 Nov 2007 09:48:54 +0200 MIME-Version: 1.0 Sent to CCL by: etamar---fh.huji.ac.il Hi Randall I dont know what kind of deletion you are interested at, but you can try this one. good luck Tamar #hf/6-31+g* pop=3D(full,nbodel) 5d test -1 1 cl 0.000000 0.000000 0.000000 c 0.000000 0.000000 2.383179 h -1.061228 0.000000 2.383179 h 0.530614 0.919051 2.383179 h 0.530614 -0.919051 2.383179 cl 0.000000 0.000000 4.766359 $NBO archive file=3Dtest $end $del zero 2 deloc from 1 to 2 from 2 to 1 $END Quoting "Randall H Goldsmith r-goldsmith _ northwestern.edu" =20 : > > Sent to CCL by: "Randall H Goldsmith" [r-goldsmith^^northwestern.edu] > Hello all, > > I'm looking to perform NBO deletion analysis using the NBO 3.1 =20 > package that comes with Gaussian 98. Following instructions for NBO =20 > 3.0 implementation in Gaussian 88 (the only ones i can find), i =20 > attempted to use nonstandard input to tell Gaussian to do the =20 > analysis, but the job always died prematurely. Does anybody know =20 > how to perform this analysis in Gaussian 98? Obviously, an example =20 > job file would be most valuable. > > Thank you very much for your time! > > randall. > > > > -=3D This is automatically added to each message by the mailing script =3D= -> > > ---------------------------------------------------------------- This message was sent using IMP, the Internet Messaging Program. From owner-chemistry@ccl.net Mon Nov 12 06:14:01 2007 From: "may abdelghani may01dz_-_yahoo.fr" To: CCL Subject: CCL: RE : CCL: Looking for Point Group Symmetrizing Program Message-Id: <-35586-071112054245-17066-qqHXYKBQ6c4gMdSaXqlvww]*[server.ccl.net> X-Original-From: may abdelghani Content-Transfer-Encoding: 8bit Content-Type: multipart/alternative; boundary="0-930613282-1194860874=:22225" Date: Mon, 12 Nov 2007 10:47:54 +0100 (CET) MIME-Version: 1.0 Sent to CCL by: may abdelghani [may01dz]_[yahoo.fr] --0-930613282-1194860874=:22225 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit you can use "chemcraft" "Yangsoo Kim vsmember..gmail.com" a écrit : Dear CCL Members, I'm looking for a program that can change into molecular coordinates having higher-order point group. The purpose of that program is the fine tuning of input coordinates. Then I found the symmetrize tool (Enable Point Group Symmetry) in Gaussview3. But I want to execute in command mode, not GUI... I would appreciate if you could give me some suggestions. Thank you very much. Yangsoo Kim --------------------------------- Ne gardez plus qu'une seule adresse mail ! Copiez vos mails vers Yahoo! Mail --0-930613282-1194860874=:22225 Content-Type: text/html; charset=iso-8859-1 Content-Transfer-Encoding: 8bit you can use "chemcraft"

"Yangsoo Kim vsmember..gmail.com" <owner-chemistry#ccl.net> a écrit :
Dear CCL Members,
I'm looking for a program that can change into molecular coordinates having higher-order point group.
The purpose of that program is the fine tuning of input coordinates.
Then I found the symmetrize tool (Enable Point Group Symmetry) in Gaussview3.
But I want to execute in command mode, not GUI...
I would appreciate if you could give me some suggestions.
Thank you very much.

Yangsoo Kim

Ne gardez plus qu'une seule adresse mail ! Copiez vos mails vers Yahoo! Mail --0-930613282-1194860874=:22225-- From owner-chemistry@ccl.net Mon Nov 12 08:41:00 2007 From: "Tamas Gunda tgunda2%%puma.unideb.hu" To: CCL Subject: CCL: UV and IR spectographs Message-Id: <-35587-071112083843-20353-Ovk+MVqsl0l6ZmSugkDIhw=-=server.ccl.net> X-Original-From: "Tamas Gunda" Content-Transfer-Encoding: 7bit Content-Type: text/plain; format=flowed; charset="iso-8859-1"; reply-type=original Date: Mon, 12 Nov 2007 14:40:56 +0100 MIME-Version: 1.0 Sent to CCL by: "Tamas Gunda" [tgunda2^_^puma.unideb.hu] Sorry for wasting the bandwidth with a partly off question: We would like to buy IR and UV spectrographs for our student lab. What models could you suggest? We need simple but reliable models without bells-and-whistles, used by students when checking or analyzing their own preparations or commercial products. Thanks Dr. Tamas E. Gunda University of Debrecen Department of Pharmaceutical Chemistry tgunda2 {-at-} puma.unideb.hu From owner-chemistry@ccl.net Mon Nov 12 09:16:00 2007 From: "Eddy Thiriot Eddy.Thiriot]_[cbt.uhp-nancy.fr" To: CCL Subject: CCL:G: Restart CCSD(T) job Message-Id: <-35588-071109115017-9994-vHw37uiVNlpHiuGnaViDIA]~[server.ccl.net> X-Original-From: "Eddy Thiriot" Date: Fri, 9 Nov 2007 11:50:13 -0500 Sent to CCL by: "Eddy Thiriot" [Eddy.Thiriot.:.cbt.uhp-nancy.fr] Good afternoon, I'm currently using Gaussian03 in order to get the CCSD(T) energy of a molecular structure of 16 atoms (7 heavy atoms) with the 6-311++g(2df,2p) basis set. Because of the time limitation of the computation center I'd submitted this job, it stopped before the end of CC convergence. A checkpoint file was created and is available. I'd like to know if the RESTART option is available in CCSD keywords or, at least, if it's possible to restart this job from the chk. In this case, could you give me the procedure ? Thanks for your help. Eddy Thiriot From owner-chemistry@ccl.net Mon Nov 12 10:35:00 2007 From: "Jeff Hammond jeff.science]![gmail.com" To: CCL Subject: CCL:G: Restart CCSD(T) job Message-Id: <-35589-071112103158-21531-B6iIRa4vPvLxYAGv1Hxl9Q[*]server.ccl.net> X-Original-From: "Jeff Hammond" Content-Disposition: inline Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1 Date: Mon, 12 Nov 2007 09:31:43 -0600 MIME-Version: 1.0 Sent to CCL by: "Jeff Hammond" [jeff.science^^gmail.com] Eddy, A better solution would be to the parallel CCSD(T) codes in NWChem or MolPro, and increase the number of processors such that the job runs in the 12, 24, 48, etc. hours you are limited to. You will find that when the number of processors is sufficient to run fully in-core, the wall time goes down tremendously. An example of the size of CCSD(T) calculation that is possible with NWChem on a large parallel machine (1468 basis functions) is described here: J. Phys. Chem. A 2005, 109, 6934-6938. I suspect MolPro and NWChem are already installed at your facility, but if not, NWChem is free and well-supported, particularly regarding installation. If you provide information on the hardware and your job (only the number of electrons, orbitals, and symmetry) I can give you a decent estimate of what number of processors and approximate time for your job. Jeff On Nov 9, 2007 10:50 AM, Eddy Thiriot Eddy.Thiriot]_[cbt.uhp-nancy.fr wrote: > > Sent to CCL by: "Eddy Thiriot" [Eddy.Thiriot.:.cbt.uhp-nancy.fr] > > Good afternoon, > > I'm currently using Gaussian03 in order to get the CCSD(T) energy of a molecular structure of 16 atoms (7 heavy atoms) with the 6-311++g(2df,2p) basis set. Because of the time limitation of the computation center I'd submitted this job, it stopped before the end of CC convergence. A checkpoint file was created and is available. > I'd like to know if the RESTART option is available in CCSD keywords or, at least, if it's possible to restart this job from the chk. In this case, could you give me the procedure ? > > Thanks for your help. > > Eddy Thiriot> > > > -- Jeff Hammond The University of Chicago From owner-chemistry@ccl.net Mon Nov 12 11:10:00 2007 From: "Nuno A. G. Bandeira nuno.bandeira(~)ist.utl.pt" To: CCL Subject: CCL: RE : CCL: Looking for Point Group Symmetrizing Program Message-Id: <-35590-071112084739-23243-a2vd3BQpptQssR72VVXXWg{:}server.ccl.net> X-Original-From: "Nuno A. G. Bandeira" Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Mon, 12 Nov 2007 13:09:22 +0000 MIME-Version: 1.0 Sent to CCL by: "Nuno A. G. Bandeira" [nuno.bandeira:_:ist.utl.pt] You have both Chemcraft and CACAO98. -- Nuno A. G. Bandeira, AMRSC Graduate researcher and molecular sculptor Inorganic and Theoretical Chemistry Group, Faculty of Science University of Lisbon - C8 building, Campo Grande, 1749-016 Lisbon,Portugal http://cqb.fc.ul.pt/intheochem/nuno.html Doctoral student % IST,Lisbon -- From owner-chemistry@ccl.net Mon Nov 12 11:44:01 2007 From: "errol lewars elewars::trentu.ca" To: CCL Subject: CCL: UV and IR spectographs Message-Id: <-35591-071112103918-23462-so8TpQrysyKA77EkGtNVMA{}server.ccl.net> X-Original-From: errol lewars Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Mon, 12 Nov 2007 10:39:14 -0500 MIME-Version: 1.0 Sent to CCL by: errol lewars [elewars]~[trentu.ca] 2007 Nov 12 Hello, Regarding a choice of spectrometers: For IR we bought ca. 18 months ago: company, Thermo Electric Corporation model, Nicolet 380 FT-IR price, $25000 The computer is extra For UV we bought ca. 7 years ago: company, Varian model, Cary 50 price, ca. $14000 The computer is extra I'm told that both instruments are very satisfactory. E. Lewars ==== Tamas Gunda tgunda2%%puma.unideb.hu wrote: > > Sent to CCL by: "Tamas Gunda" [tgunda2^_^puma.unideb.hu] > Sorry for wasting the bandwidth with a partly off question: > > We would like to buy IR and UV spectrographs for our student lab. What > models could you suggest? We need simple but reliable models without > bells-and-whistles, used by students when checking or analyzing their > own preparations or commercial products. > > Thanks > > Dr. Tamas E. Gunda > University of Debrecen > Department of Pharmaceutical Chemistry > tgunda2 {-at-} puma.unideb.huhttp://www.ccl.net/chemistry/sub_unsub.shtmlConferences: > http://server.ccl.net/chemistry/announcements/conferences/> > > From owner-chemistry@ccl.net Mon Nov 12 12:19:01 2007 From: "Vishal Koparde koparde.vishal_-_gmail.com" To: CCL Subject: CCL: Using CNS solve Message-Id: <-35592-071112114345-29732-zgh25tqwrZSEExbjTO2RLw**server.ccl.net> X-Original-From: "Vishal Koparde" Content-Disposition: inline Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1 Date: Mon, 12 Nov 2007 09:54:24 -0500 MIME-Version: 1.0 Sent to CCL by: "Vishal Koparde" [koparde.vishal||gmail.com] Hello All, Can anyone suggest me a tutorial for using CNS solve (other than the one on the cns website)? Also, has anyone tried to modified the FORTRAN 77 code or use CNS as a tool in some other software/code? I am new to the area of X-ray crystallography. Therefore, any comments/suggestions are greatly appreciated. Vishal Koparde, PhD. koparde.vishal],[gmail.com From owner-chemistry@ccl.net Mon Nov 12 12:55:00 2007 From: "akef afaneh akef_afnh . yahoo.com" To: CCL Subject: CCL:G: NBO Natural Bond Orbital Deletion Gaussian 98 Message-Id: <-35593-071112123232-3531-jnlS4A+kGAABFwyLtFuLwg+*+server.ccl.net> X-Original-From: akef afaneh Content-Transfer-Encoding: 8bit Content-Type: multipart/alternative; boundary="0-2076472354-1194888739=:25522" Date: Mon, 12 Nov 2007 09:32:19 -0800 (PST) MIME-Version: 1.0 Sent to CCL by: akef afaneh [akef_afnh{=}yahoo.com] --0-2076472354-1194888739=:25522 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit Hi; I do not know what the purpose of your deletion ($DEL) is, but there are many ways for deletion in Gaussian. First, you must know that this analysis is performed by (1) deleting specified elements (or blocks of elements) from the NBO Fock matrix, (2) diagonalizing this new Fock matrix to obtain a new density matrix, and (3) passing this density matrix to the SCF routines for a single pass through the SCF energy evaluator. The difference between this 'deletion' energy and the original SCF energy provides a useful measure of the energy contribution of the deleted terms. Now, I can summarize the deletion procedure as follows: The deletions keylist begins with the "$DEL" keyword. After the last deletion, the word "$END" signals the end of the keylist. (1) Deletion of entire orbitals. This is called for by typing "DELETE", then the number of orbitals to be deleted, then the keyword "ORBITAL" (or "ORBITALS"), then the list of the orbitals to be deleted. Example: #P RHF/6-31G* Nosymm pop=nbodel opt H2O 0 1 8 0. 0. 0.11469 1 0. 0.75408 -0.45874 1 0. -0.75408 -0.45874 $NBO file=dfe_c $end $del Delete 2 orbitals 6 9 $end (2) Deletion of specific Fock matrix elements. This is called for by typing "DELETE", then the number of elements to be deleted, then the keyword "ELEMENT" (or "ELEMENTS"), then the list of the elements to be deleted (each as a pair of integers). Example: #P RHF/6-31G* Nosymm pop=nbodel opt CH4 0 1 6 0. 0. 0. 1 0.62565 0.62565 0.62565 1 -0.62565 -0.62565 0.62565 1 -0.62565 0.62565 -0.62565 1 0.62565 -0.62565 -0.62565 $NBO file=dfe_c $end $del DELETE 3 ELEMENTS 5 16 5 17 5 18 $end (3) Deletion of off-diagonal blocks of the Fock matrix. Each block is specified by two sets of orbitals, and all Fock matrix elements in common between these two sets are set to zero. This is called for by typing "ZERO", then the number of off-diagonal blocks to be zeroed, and then, for each block, the following: (1) the dimensions of the block, separated by the word "BY" (e.g., "6 BY 3" if the first set has 6 orbitals and the second set has 3 orbitals); (2) the list of orbitals in the first set; (3) the list of orbitals in the second set. An example is shown below: $NBO file=dfe_c $end $del ZERO 2 BLOCKS 2 BY 5 3 4 9 10 11 14 19 3 BY 2 1 2 7 20 24 $end This will set the following Fock matrix elements to zero: (3,9), (3,10), (3,11), (3,14), (3,19), (9,3), (10,3), (11,3), (14,3), (19,3), (4,9), (4,10), (4,11), (4,14), (4,19), (9,4), (10,4), (11,4), (14,4), (19,4), (1,20), (1,24), (2,20), (2,24), (7,20), (7,24) (20,1), (24,1), (20,2), (24,2), (20,7), (24,7) (4) Deletion of all Rydberg and antibond orbitals. The Rydberg and antibond orbitals are the non-Lewis NBO orbitals that have stars in their labels (RY*, BD*) in the NBO analysis output. To delete all these orbitals, simply enter "NOSTAR". The result of this deletion is the energy of the idealized NBO natural Lewis structure, with all Lewis NBOs doubly occupied. (Unlike other deletions, in which there is a slight loss of variational self-consistency due to the redistributed occupancy of the deleted orbitals, the result of a "NOSTAR" deletion corresponds rigorously to the variational expectation value of the determinant of doubly occupied Lewis NBOs). $NBO file=dfe_c $end $del NOSTAR $end AND SO ON J "etamar:-:fh.huji.ac.il" wrote: Sent to CCL by: etamar---fh.huji.ac.il Hi Randall I dont know what kind of deletion you are interested at, but you can try this one. good luck Tamar #hf/6-31+g* pop=(full,nbodel) 5d test -1 1 cl 0.000000 0.000000 0.000000 c 0.000000 0.000000 2.383179 h -1.061228 0.000000 2.383179 h 0.530614 0.919051 2.383179 h 0.530614 -0.919051 2.383179 cl 0.000000 0.000000 4.766359 $NBO archive file=test $end $del zero 2 deloc from 1 to 2 from 2 to 1 $END Quoting "Randall H Goldsmith r-goldsmith _ northwestern.edu" : > > Sent to CCL by: "Randall H Goldsmith" [r-goldsmith^^northwestern.edu] > Hello all, > > I'm looking to perform NBO deletion analysis using the NBO 3.1 > package that comes with Gaussian 98. Following instructions for NBO > 3.0 implementation in Gaussian 88 (the only ones i can find), i > attempted to use nonstandard input to tell Gaussian to do the > analysis, but the job always died prematurely. Does anybody know > how to perform this analysis in Gaussian 98? Obviously, an example > job file would be most valuable. > > Thank you very much for your time! > > randall.> > > ---------------------------------------------------------------- This message was sent using IMP, the Internet Messaging Program.http://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt__________________________________________________ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com --0-2076472354-1194888739=:25522 Content-Type: text/html; charset=iso-8859-1 Content-Transfer-Encoding: 8bit
Hi;
I do not know what the purpose of your deletion ($DEL) is, but there are many ways for deletion in Gaussian. First, you must know that this analysis is performed by (1) deleting specified elements (or blocks of elements) from the NBO Fock matrix, (2) diagonalizing this new Fock matrix to obtain a new density matrix, and (3) passing this density matrix to the SCF routines for a single pass through the SCF energy evaluator. The difference between this 'deletion' energy and the original SCF energy provides a useful measure of the energy contribution of the deleted terms.  Now, I can summarize the deletion procedure as follows:
The deletions keylist begins with the "$DEL" keyword. After the last deletion, the word "$END" signals the end of the keylist.
(1) Deletion of entire orbitals.
This is called for by typing "DELETE", then the number of orbitals to be deleted, then the keyword "ORBITAL" (or "ORBITALS"), then the list of the orbitals to be deleted.
Example:
#P RHF/6-31G* Nosymm pop=nbodel opt
H2O
0 1
 8                     0.        0.        0.11469
 1                     0.        0.75408  -0.45874
 1                     0.       -0.75408  -0.45874
 
$NBO file=dfe_c $end
$del
Delete 2 orbitals
6 9
$end
 
(2) Deletion of specific Fock matrix elements.
This is called for by typing "DELETE", then the number of elements to be deleted, then the keyword "ELEMENT" (or "ELEMENTS"), then the list of the elements to be deleted (each as a pair of integers).
Example:
#P RHF/6-31G* Nosymm pop=nbodel opt
CH4
0 1
6                     0.        0.        0.
 1                     0.62565   0.62565   0.62565
 1                    -0.62565  -0.62565   0.62565
 1                    -0.62565   0.62565  -0.62565
 1                     0.62565  -0.62565  -0.62565
 
$NBO file=dfe_c $end
$del
DELETE  3  ELEMENTS 5 16 5 17 5 18
$end
 
(3) Deletion of off-diagonal blocks of the Fock matrix.
Each block is specified by two sets of orbitals, and all Fock matrix elements in common between these two sets are set to zero. This is called for by typing "ZERO", then the number of off-diagonal blocks to be zeroed, and then, for each block, the following:
(1) the dimensions of the block, separated by the word "BY" (e.g., "6 BY 3" if the first set has 6 orbitals and the second set has 3 orbitals);
(2) the list of orbitals in the first set;
(3) the list of orbitals in the second set.
An example is shown below:
$NBO file=dfe_c $end
$del
ZERO  2  BLOCKS  2  BY  5
                               3  4
                               9  10  11  14  19
                      3  BY  2
                               1  2  7
                              20  24
$end
 
This will set the following Fock matrix elements to zero:
(3,9), (3,10), (3,11), (3,14), (3,19), (9,3), (10,3), (11,3), (14,3), (19,3), (4,9), (4,10), (4,11), (4,14), (4,19), (9,4), (10,4), (11,4), (14,4), (19,4), (1,20), (1,24), (2,20), (2,24), (7,20), (7,24) (20,1), (24,1), (20,2), (24,2), (20,7), (24,7)
(4) Deletion of all Rydberg and antibond orbitals.
The Rydberg and antibond orbitals are the non-Lewis NBO orbitals that have stars in their labels (RY*, BD*) in the NBO analysis output. To delete all these orbitals, simply enter "NOSTAR". The result of this deletion is the energy of the idealized NBO natural Lewis structure, with all Lewis NBOs doubly occupied. (Unlike other deletions, in which there is a slight loss of variational self-consistency due to the redistributed occupancy of the deleted orbitals, the result of a "NOSTAR" deletion corresponds rigorously to the variational expectation value of the determinant of doubly occupied Lewis NBOs).
$NBO file=dfe_c $end
$del
      NOSTAR
$end
 
AND SO ON J
 

"etamar:-:fh.huji.ac.il" <owner-chemistry#ccl.net> wrote:

Sent to CCL by: etamar---fh.huji.ac.il
Hi Randall
I dont know what kind of deletion you are interested at, but
you can try this one.
good luck
Tamar

#hf/6-31+g* pop=(full,nbodel) 5d

test

-1 1
cl 0.000000 0.000000 0.000000
c 0.000000 0.000000 2.383179
h -1.061228 0.000000 2.383179
h 0.530614 0.919051 2.383179
h 0.530614 -0.919051 2.383179
cl 0.000000 0.000000 4.766359

$NBO archive file=test $end
$del zero 2 deloc from 1 to 2 from 2 to 1 $END




Quoting "Randall H Goldsmith r-goldsmith _ northwestern.edu"
:

>
> Sent to CCL by: "Randall H Goldsmith" [r-goldsmith^^northwestern.edu]
> Hello all,
>
> I'm looking to perform NBO deletion analysis using the NBO 3.1
> package that comes with Gaussian 98. Following instructions for NBO
> 3.0 implementation in Gaussian 88 (the only ones i can find), i
> attempted to use nonstandard input to tell Gaussian to do the
> analysis, but the job always died prematurely. Does anybody know
> how to perform this analysis in Gaussian 98? Obviously, an example
> job file would be most valuable.
>
> Thank you very much for your time!
>
> randall.
>
>
>
>>
>
>



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http://mail.yahoo.com --0-2076472354-1194888739=:25522-- From owner-chemistry@ccl.net Mon Nov 12 13:30:01 2007 From: "Vishal Koparde koparde.vishal|,|gmail.com" To: CCL Subject: CCL: CNS solve query Message-Id: <-35594-071112115448-8432-xKzbG6KgFel021QMEGNd7A%%server.ccl.net> X-Original-From: "Vishal Koparde" Content-Disposition: inline Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1 Date: Mon, 12 Nov 2007 11:54:08 -0500 MIME-Version: 1.0 Sent to CCL by: "Vishal Koparde" [koparde.vishal^gmail.com] Hello All, Can anyone suggest me a tutorial for using CNS solve (other than the one on the cns website)? Also, has anyone tried to modified the FORTRAN 77 code or use CNS as a tool in some other software/code? I am new to the area of X-ray crystallography. Therefore, any comments/suggestions are greatly appreciated. Vishal Koparde, PhD. koparde.vishal_at_gmail.com From owner-chemistry@ccl.net Mon Nov 12 14:04:00 2007 From: "Isaac Bersuker bersuker]-[mail.cm.utexas.edu" To: CCL Subject: CCL: Hydrogen bond and QSAR Message-Id: <-35595-071112110703-5084-GyuDu+/fWHKSE7wpl7drag~~server.ccl.net> X-Original-From: Isaac Bersuker Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=windows-1251; format=flowed Date: Mon, 12 Nov 2007 09:07:27 -0600 MIME-Version: 1.0 Sent to CCL by: Isaac Bersuker [bersuker^mail.cm.utexas.edu] Dear Praveen Kumar Shrivastava, Bimolecular activity in QSAR type problems was predicted long ago... See I. B. Bersuker et al., New J. Chem.15, N 5, 307-320, 1991. Isaac Praveen Kumar Shrivastava praveenshrivastav[A]gmail.com wrote: > Sent to CCL by: "Praveen Kumar Shrivastava" [praveenshrivastav ~ gmail.com] > > Hello all, > Two different drug molecule joined by hydrogen bond can be analysed for QSAR methodlogy considering as one molecule. > > Thank you very much for your time! > > Praveen> > > -- Dr. Isaac B. Bersuker Institute for Theoretical Chemistry The University of Texas at Austin Chem & Biochem Department 1 University Station A5300 Austin, TX 78712-0165 Phone: (512) 471-4671; Fax: (512) 471-8696 E-mail: bersuker(0)cm.utexas.edu http://www.cm.utexas.edu/directory/isaac_bersuker/ From owner-chemistry@ccl.net Mon Nov 12 15:49:00 2007 From: "=?ISO-8859-1?Q?=D6d=F6n?= Farkas farkas[]chem.elte.hu" To: CCL Subject: CCL:G: question about freezing coordinates in Gaussian Message-Id: <-35596-071112154250-17699-N35B8OrhimRn0HSdvZG5fw===server.ccl.net> X-Original-From: =?ISO-8859-1?Q?=D6d=F6n?= Farkas Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=UTF-8 Date: Mon, 12 Nov 2007 21:41:19 +0100 Mime-Version: 1.0 Sent to CCL by: =?ISO-8859-1?Q?=D6d=F6n?= Farkas [farkas#%#chem.elte.hu] Hi Wang, The following example shows a Hydrogene peroxide input, where all but the X coordinates are frozen. ------------------------------------------------- #P Opt=(Z-Matrix) HF/3-21G Peroxide, frozen Cartesians 0 1 O 0 X1 -1.09999998 0.00000000 H 0 X2 -0.29081242 0.40512263 O 0 X3 -1.09999998 0.00000000 H 0 X4 -1.90918755 0.40512263 X1=-2.18333334 X2=-2.50378793 X3=-0.86333334 X4=-0.54287876 ------------------------------------------------- Best wishes, Ödön On Fri, 2007-11-09 at 15:08 -0500, Wang xie.wang .. gmail.com wrote: > Sent to CCL by: Wang [xie.wang]=[gmail.com] > Dear all, > > Is there a way in gaussian to fix atomic x,y coordinates but allow z > coordinate to relax in geometry optimization? Thanks a lot in advance! > > Wang> > > -- Ödön Farkas Associate professor Deparment of Organic Chemistry and Laboratory of Chemical Informatics, Institute of Chemistry, Eötvös Loránd University, Budapest Address: 1/A Pázmány Péter sétány, H-1117 Budapest, Hungary Phone: +36-1-372-2570 Cell phone: +36-30-255-3111 Fax: +36-1-372-2620 URL: http://organ.elte.hu/farkas