From owner-chemistry@ccl.net Sun Jul 20 00:53:01 2008 From: "gnli gnli*_*dicp.ac.cn" To: CCL Subject: CCL: free program for conformation searching Message-Id: <-37370-080720005136-20949-bAxbLDssIDRZca5nF5VRVA!A!server.ccl.net> X-Original-From: "gnli" Content-Type: multipart/alternative; boundary="----=_NextPart_000_0008_01C8EA67.7A316E10" Date: Sun, 20 Jul 2008 12:52:29 +0800 MIME-Version: 1.0 Sent to CCL by: "gnli" [gnli(0)dicp.ac.cn] This is a multi-part message in MIME format. ------=_NextPart_000_0008_01C8EA67.7A316E10 Content-Type: text/plain; charset="us-ascii" Content-Transfer-Encoding: 7bit Dear CCLer, Can anyone recommend me some free charge program doing monte carlo conformation searching, i.e. giving a initial structure, it can find those energy lowest conformations under the absolute configuration. Easier to be learned is better. Any advice is appreciated. best wishes Guanna Li gnli/a\dicp.ac.cn ------=_NextPart_000_0008_01C8EA67.7A316E10 Content-Type: text/html; charset="us-ascii" Content-Transfer-Encoding: quoted-printable

Dear = CCLer,

Can anyone recommend me some = free charge program doing monte carlo conformation searching, i.e. =  giving a initial structure, it can find those energy lowest conformations under = the absolute configuration.

Easier to be learned is = better.

Any advice is = appreciated.

 

best wishes
Guanna Li
gnli/a\dicp.ac.cn



 

------=_NextPart_000_0008_01C8EA67.7A316E10-- From owner-chemistry@ccl.net Sun Jul 20 03:05:01 2008 From: "naser E Eltayeb nasertaha90-#-yahoo.co.uk" To: CCL Subject: CCL:G: Molecular Orbital Energy in G03 Message-Id: <-37371-080720030307-22364-9rscSkxz7i3d9f5U91N/Aw:+:server.ccl.net> X-Original-From: "naser E Eltayeb" Date: Sun, 20 Jul 2008 03:03:04 -0400 Sent to CCL by: "naser E Eltayeb" [nasertaha90|yahoo.co.uk] Dear All I am interesting in calculation of molecular orbitals to get the band gap, I run DFT calculation in Gaussian03, I copy part of the log file below, I know that the first column is the energy of the orbital, what about the rest column? I compare the result from the log file and the energy obtained using M.O in gaussview I found some differences in determination which is HOMO and which is LUMO. I am looking for your answer. Thank you Naser E. Eltayeb Universiti Sains Malaysia nasertaha90!A!yahoo.co.uk The electronic state is 1-A. Alpha occ. eigenvalues -- -9.83283 -9.83283 -9.83252 -9.83251 -9.82399 Alpha occ. eigenvalues -- -9.82399 -9.82340 -9.82340 -9.82337 -9.82337 Alpha occ. eigenvalues -- -9.82254 -9.82254 -9.82226 -9.82225 -0.82730 Alpha occ. eigenvalues -- -0.79666 -0.75041 -0.73140 -0.70059 -0.69030 Alpha occ. eigenvalues -- -0.65516 -0.60402 -0.57725 -0.56673 -0.55353 Alpha occ. eigenvalues -- -0.50171 -0.49584 -0.47726 -0.43812 -0.42999 Alpha occ. eigenvalues -- -0.42536 -0.42256 -0.39896 -0.39314 -0.38818 Alpha occ. eigenvalues -- -0.38529 -0.36591 -0.35770 -0.35423 -0.32569 Alpha occ. eigenvalues -- -0.31572 -0.30999 -0.30549 -0.29902 -0.26232 Alpha occ. eigenvalues -- -0.25244 -0.20837 Alpha virt. eigenvalues -- -0.12164 -0.07563 -0.06479 -0.04497 -0.02358 Alpha virt. eigenvalues -- -0.01807 -0.01629 -0.00887 0.00309 0.00454 Alpha virt. eigenvalues -- 0.01559 0.02333 0.02338 0.03142 0.03367 Alpha virt. eigenvalues -- 0.04149 0.04249 0.04310 0.04584 0.06347 Alpha virt. eigenvalues -- 0.07502 0.07662 0.08473 0.08590 0.08835 Alpha virt. eigenvalues -- 0.08996 0.10309 0.10417 0.10962 0.11315 From owner-chemistry@ccl.net Sun Jul 20 09:17:00 2008 From: "Hemant Kumar Srivastava hemantkrsri _ gmail.com" To: CCL Subject: CCL:G: Graphical Representation of Transition Dipole Moment Message-Id: <-37372-080720091622-18142-UBH7XGzTCl+f5jSnjyxM3Q%%server.ccl.net> X-Original-From: "Hemant Kumar Srivastava" Date: Sun, 20 Jul 2008 09:16:18 -0400 Sent to CCL by: "Hemant Kumar Srivastava" [hemantkrsri^gmail.com] Hello all. Does anyone know of a viewing package to have graphical representation of a transition dipole moment? The transition dipole moment was calculated using G03 Thanks a lot in advance Best reagrds, Hemant ================== Dr. Hemant Kumar Srivastava, Department of Medicinal Chemistry and Natural Products, School of Pharmacy, Faculty of Medicine, Ein Kerem Campus, The Hebrew University of Jerusalem, Jerusalem - 91120, ISRAEL, ======================================================== From owner-chemistry@ccl.net Sun Jul 20 10:51:01 2008 From: "Utpal Sarkar utpalchemiitkgp#gmail.com" To: CCL Subject: CCL:G: Molecular Orbital Energy in G03 Message-Id: <-37373-080720104854-16281-ubKBCpHyTvdU1vpIxYHHBA-.-server.ccl.net> X-Original-From: "Utpal Sarkar" Content-Disposition: inline Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1 Date: Sun, 20 Jul 2008 16:48:35 +0200 MIME-Version: 1.0 Sent to CCL by: "Utpal Sarkar" [utpalchemiitkgp=-=gmail.com] dear naser, your HOMO energy is -0.20837 HOMO-1 energy is -0.25244 HOMO-2 energy is -0.26232 and so on and LUMO energy is -0.12164 LUMO+1 energy is -0.07563 LUMO+2 energy is -0.06479 and so on reagrds utpal On 7/20/08, naser E Eltayeb nasertaha90-#-yahoo.co.uk wrote: > > Sent to CCL by: "naser E Eltayeb" [nasertaha90|yahoo.co.uk] > Dear All > > I am interesting in calculation of molecular orbitals to get the band gap, I run DFT calculation in Gaussian03, I copy part of the log file below, I know that the first column is the energy of the orbital, what about the rest column? I compare the result from the log file and the energy obtained using M.O in gaussview I found some differences in determination which is HOMO and which is LUMO. > I am looking for your answer. > > Thank you > > Naser E. Eltayeb > Universiti Sains Malaysia > nasertaha90 a yahoo.co.uk > > > The electronic state is 1-A. > Alpha occ. eigenvalues -- -9.83283 -9.83283 -9.83252 -9.83251 -9.82399 > Alpha occ. eigenvalues -- -9.82399 -9.82340 -9.82340 -9.82337 -9.82337 > Alpha occ. eigenvalues -- -9.82254 -9.82254 -9.82226 -9.82225 -0.82730 > Alpha occ. eigenvalues -- -0.79666 -0.75041 -0.73140 -0.70059 -0.69030 > Alpha occ. eigenvalues -- -0.65516 -0.60402 -0.57725 -0.56673 -0.55353 > Alpha occ. eigenvalues -- -0.50171 -0.49584 -0.47726 -0.43812 -0.42999 > Alpha occ. eigenvalues -- -0.42536 -0.42256 -0.39896 -0.39314 -0.38818 > Alpha occ. eigenvalues -- -0.38529 -0.36591 -0.35770 -0.35423 -0.32569 > Alpha occ. eigenvalues -- -0.31572 -0.30999 -0.30549 -0.29902 -0.26232 > Alpha occ. eigenvalues -- -0.25244 -0.20837 > Alpha virt. eigenvalues -- -0.12164 -0.07563 -0.06479 -0.04497 -0.02358 > Alpha virt. eigenvalues -- -0.01807 -0.01629 -0.00887 0.00309 0.00454 > Alpha virt. eigenvalues -- 0.01559 0.02333 0.02338 0.03142 0.03367 > Alpha virt. eigenvalues -- 0.04149 0.04249 0.04310 0.04584 0.06347 > Alpha virt. eigenvalues -- 0.07502 0.07662 0.08473 0.08590 0.08835 > Alpha virt. eigenvalues -- 0.08996 0.10309 0.10417 0.10962 0.11315> > > From owner-chemistry@ccl.net Sun Jul 20 12:56:01 2008 From: "Khaled El-Sayed El-Kelany elkelanystar2008. a .yahoo.com" To: CCL Subject: CCL: Negative frequency Message-Id: <-37374-080720090517-17381-KUvnffpA4+78ZdwjpQR9TQ a server.ccl.net> X-Original-From: "Khaled El-Sayed El-Kelany" Date: Sun, 20 Jul 2008 09:05:13 -0400 Sent to CCL by: "Khaled El-Sayed El-Kelany" [elkelanystar2008---yahoo.com] Dears,,,,, I want to ask what can i do? In carrying a frequency analysis "Hessian run" for a transition state, or for more correct for an optimized transition state, by GAMESS program, i have more than value for negative frequency, two some times three..., I copy part of the file below. I am looking for your answer. Thank you Khaled El-Kelany Minia University Egypt FREQUENCIES IN CM**-1, IR INTENSITIES IN DEBYE**2/AMU-ANGSTROM**2 1 2 3 4 5 FREQUENCY: 451.05 I 72.13 I 42.19 20.29 17.26 IR INTENSITY: 5.39515 0.01022 0.01270 0.00125 0.00336 From owner-chemistry@ccl.net Sun Jul 20 13:31:01 2008 From: "Khaled El-Sayed El-Kelany elkelanystar2008 * yahoo.com" To: CCL Subject: CCL: "CCL" Negative Frequency Message-Id: <-37375-080720091507-18044-YlfefUi4nXjYUSk3HrxCxQ=-=server.ccl.net> X-Original-From: "Khaled El-Sayed El-Kelany" Date: Sun, 20 Jul 2008 09:15:03 -0400 Sent to CCL by: "Khaled El-Sayed El-Kelany" [elkelanystar2008|,|yahoo.com] Dears,,,,, I want to ask what can i do? In carrying a frequency analysis "Hessian run" for a transition state, or for more correct for an optimized transition state, by GAMESS program, i have more than value for negative frequency, two some times three..., I copy part of the file below. I am looking for your answer. Thank you Khaled El-Kelany Minia University Egypt FREQUENCIES IN CM**-1, IR INTENSITIES IN DEBYE**2/AMU-ANGSTROM**2 1 2 3 4 5 FREQUENCY: 451.05 I 72.13 I 42.19 20.29 17.26 IR INTENSITY: 5.39515 0.01022 0.01270 0.00125 0.00336 From owner-chemistry@ccl.net Sun Jul 20 16:33:01 2008 From: "spitaleri.andrea__hsr.it" To: CCL Subject: CCL: free program for conformation searching Message-Id: <-37376-080720072030-30045-gccLWVHxExQ0RrOUIeEBBw(!)server.ccl.net> X-Original-From: Content-Language: en Content-Type: multipart/mixed; boundary="--14c060161d996b71" Date: Sun, 20 Jul 2008 12:08:48 +0200 MIME-Version: 1.0 Sent to CCL by: [spitaleri.andrea=hsr.it] This is a multi-part message in MIME format. ----14c060161d996b71 Content-Type: text/plain; charset=us-ascii Content-Disposition: inline Content-Transfer-Encoding: 7bit Hi there, have look either to tinker or openeye. regards and Andrea Spitaleri PhD Dulbecco Telethon Institute c/o DIBIT Scientific Institute Biomolecular NMR, 1B4 Via Olgettina 58 20132 Milano (Italy) Tel: 0039-0226434348/5622/3497/4922 Fax: 0039-0226434153 ----- Original Message ----- > From: "gnli gnli*_*dicp.ac.cn" Date: Sunday, July 20, 2008 6:52 am Subject: CCL: free program for conformation searching > Dear CCLer, > > Can anyone recommend me some free charge program doing monte carlo > conformation searching, i.e. giving a initial structure, it can > find those > energy lowest conformations under the absolute configuration. > > Easier to be learned is better. > > Any advice is appreciated. > > > > best wishes > Guanna Li > gnli.#%#.dicp.ac.cn > > > > > > > > ******************************************************************** Sostieni la ricerca del San Raffaele con il 5permille! E' SEMPLICE E NON COSTA NULLA. Basta indicare nell'apposito riquadro della dichiarazione dei redditi ("Finanziamento agli enti della ricerca sanitaria") il codice fiscale della Fondazione Centro S. Raffaele del Monte Tabor: 03 06 42 80 153 e ricordarsi di firmare. Se vuoi saperne di piu' scrivi a 5permille#%#hsr.it o vai sul sito www.5xmille.org ----14c060161d996b71 Content-Type: text/x-vcard; name="spitaleri.andrea.vcf"; charset="iso-8859-1" Content-Disposition: attachment; filename="spitaleri.andrea.vcf" Content-Description: Card for Content-Transfer-Encoding: quoted-printable begin=3Avcard n=3ASpitaleri=3BAndrea fn=3AAndrea Spitaleri tel=3Bfax=3A+390226434153 org=3ADibit Scientific Insititute=3BBioMolecular Structure adr=3A=3B=3Bvia Olgettina 58=3BMilan=3B=3B24132=3BItaly version=3A2=2E1 email=3Binternet=3Aspitaleri=2Eandrea=40hsr=2Eit title=3ADr end=3Avcard ----14c060161d996b71-- From owner-chemistry@ccl.net Sun Jul 20 23:52:00 2008 From: "Vivek Sharma vivek.viv.sharma . gmail.com" To: CCL Subject: CCL: free program for conformation searching Message-Id: <-37377-080720085101-16654-6WBRAxGtVDVbvQBq6r8HcA[#]server.ccl.net> X-Original-From: "Vivek Sharma" Content-Type: multipart/alternative; boundary="----=_Part_33075_32081977.1216554333519" Date: Sun, 20 Jul 2008 04:45:33 -0700 MIME-Version: 1.0 Sent to CCL by: "Vivek Sharma" [vivek.viv.sharma~~gmail.com] ------=_Part_33075_32081977.1216554333519 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Content-Disposition: inline Hello, AMMP (by Dr. Robert Harrison) is one I know and it does conformational search. Please check if its doing Monte Carlo searching. http://www.cs.gsu.edu/~cscrwh/ammp/ammp.html regards, Vivek 2008/7/19 gnli gnli*_*dicp.ac.cn : > *Dear CCLer,* > > *Can anyone recommend me some free charge program doing monte carlo > conformation searching, i.e. giving a initial structure, it can find those > energy lowest conformations under the absolute configuration.* > > *Easier to be learned is better.* > > *Any advice is appreciated.* > > * * > > best wishes > Guanna Li > gnli.- -.dicp.ac.cn > > > > > ------=_Part_33075_32081977.1216554333519 Content-Type: text/html; charset=ISO-2022-JP Content-Transfer-Encoding: 7bit Content-Disposition: inline
Hello,

AMMP (by Dr. Robert Harrison) is one I know and it does conformational search. Please check if its doing Monte Carlo searching.

http://www.cs.gsu.edu/~cscrwh/ammp/ammp.html

regards,

Vivek

2008/7/19 gnli gnli*_*dicp.ac.cn <owner-chemistry- -ccl.net>:

Dear CCLer,

Can anyone recommend me some free charge program doing monte carlo conformation searching, i.e.  giving a initial structure, it can find those energy lowest conformations under the absolute configuration.

Easier to be learned is better.

Any advice is appreciated.

 

best wishes
Guanna Li
gnli.- -.dicp.ac.cn



 


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