From owner-chemistry@ccl.net Sun Nov 13 12:07:01 2005 From: "ccl mekelleche ccl_mekelleche[#]yahoo.fr" To: CCL Subject: CCL: Charge-transfer Energy Message-Id: <-29955-051113085913-2172-HTvq3ZcMnh1jKJmpIghU0Q{=}server.ccl.net> X-Original-From: ccl mekelleche Content-Transfer-Encoding: 8bit Content-Type: multipart/alternative; boundary="0-225489696-1131890348=:51023" Date: Sun, 13 Nov 2005 14:59:08 +0100 (CET) MIME-Version: 1.0 Sent to CCL by: ccl mekelleche [ccl_mekelleche!^!yahoo.fr] --0-225489696-1131890348=:51023 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit Dear CCLers I am studing the carbon acidity of some cyclic and acyclic compounds. My question is: How to calculate the charge-transfer energy using NBO analysis for the deprototonation process? Sincerely --------------------------------- Appel audio GRATUIT partout dans le monde avec le nouveau Yahoo! Messenger Téléchargez le ici ! --0-225489696-1131890348=:51023 Content-Type: text/html; charset=iso-8859-1 Content-Transfer-Encoding: 8bit
Dear CCLers
I am studing the carbon acidity of some cyclic and acyclic compounds. My question is:
How to calculate the charge-transfer energy using NBO analysis for the deprototonation process?
Sincerely

Appel audio GRATUIT partout dans le monde avec le nouveau Yahoo! Messenger
Téléchargez le ici ! --0-225489696-1131890348=:51023-- From owner-chemistry@ccl.net Sun Nov 13 12:42:01 2005 From: "yang zhen na yangzn553%a%nenu.edu.cn" To: CCL Subject: CCL: excited state optimization Message-Id: <-29956-051113085634-2003-cAKo4cL0exNZdJx2Vyy2nQ###server.ccl.net> X-Original-From: "yang zhen na" Sent to CCL by: "yang zhen na" [yangzn553##nenu.edu.cn] First,I don't know how to use cis-mp2 method to optimize the molecule, what keywords should I input? Second, how to use UHF method to optimize the molecule in neutral form in the excited state? Is the charge and multiplicity zero and one respectively? Third, how to search the energy of the molecule in the excited state in the output file of optimization using cis method. That is to say which keywords should I search, scf done or E(cis). please help me, I need your help. thank you very much. From owner-chemistry@ccl.net Sun Nov 13 13:17:01 2005 From: "Dr. Csaba Hetenyi csaba:-:ovrisc.mdche.u-szeged.hu" To: CCL Subject: CCL: AutoDock3 and shuffled peptide sequences Message-Id: <-29957-051113084511-32037-FZTTgN0XTxTZiNiJgQRmpg++server.ccl.net> X-Original-From: "Dr. Csaba Hetenyi" Content-Type: TEXT/PLAIN; charset=US-ASCII Date: Sun, 13 Nov 2005 14:00:59 +0100 (CET) MIME-Version: 1.0 Sent to CCL by: "Dr. Csaba Hetenyi" [csaba[#]ovrisc.mdche.u-szeged.hu] Hi, For larger peptides larger number of energy evaluations and population size may be necessary. For validation of the parameters of LGA it is necessary to measure RMSD between the X-ray position and the docked peptide. Grid spacing of .3 A helps in some cases. You may trust your results and actual LGA (grid) parameter setup after validation. Best, Csaba On Sat, 12 Nov 2005, Starr Hazard hazards+*+musc.edu wrote: > Sent to CCL by: Starr Hazard [hazards|-|musc.edu] > Folks, > > I am examining the docking of a hexapeptide to a protein with AutoDock3. I > generated some initial results and sought to examine specificity. I > shuffled the sequence (ie left amino acid content constant and altered the > sequence order) and tried to AutoDock3 again. In many cases the shuffled > sequences show better scores than the original sequences. > > The shuffled and "wildtype" sequences were docked under similar ie mostly > default conditions. Have I shown that the binding is none specific or have > just got a sampling error? > > Starr > > > Starr> > > > ------ Csaba Hetenyi, MSc, PhD Dept. of Medical Chemistry, University of Szeged, 8 Dom ter, Szeged 6720, Hungary From owner-chemistry@ccl.net Sun Nov 13 18:28:00 2005 From: "Jim Kress ccl_nospam:-:kressworks.com" To: CCL Subject: CCL: excited state optimization Message-Id: <-29958-051113180436-28916-V3d4n1TmY2r55b/z+h+w1g||server.ccl.net> X-Original-From: "Jim Kress" Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset="us-ascii" Date: Sun, 13 Nov 2005 18:04:13 -0500 MIME-Version: 1.0 Sent to CCL by: "Jim Kress" [ccl_nospam:kressworks.com] Did you read the manual that came with the software? Or did you just get an executable version with no documentation? Also, there are usually help files. Did you search those for keywords such as cis or mp2? Jim > -----Original Message----- > From: yang zhen na yangzn553%a%nenu.edu.cn > [mailto:owner-chemistry/./ccl.net] > Sent: Sunday, November 13, 2005 1:01 PM > To: Kress, Jim > Subject: CCL: excited state optimization > > Sent to CCL by: "yang zhen na" [yangzn553##nenu.edu.cn] > First,I don't know how to use cis-mp2 method to optimize the > molecule, what keywords should I input? > Second, how to use UHF method to optimize the molecule in > neutral form in the excited state? Is the charge and > multiplicity zero and one respectively? > Third, how to search the energy of the molecule in the > excited state in the output file of optimization using cis > method. That is to say which keywords should I search, scf > done or E(cis). > please help me, I need your help. thank you very much. > > > > -= This is automatically added to each message by the mailing > script =- To recover the email address of the author of the > message, please change the strange characters on the top line > to the /./ sign. You can also look up the X-Original-From: line > in the mail header.> > -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+ > -+-+-+-+-+ > > > > > >