From owner-chemistry@ccl.net Sat Mar 8 13:33:01 2008 From: "errol lewars elewars-#-trentu.ca" To: CCL Subject: CCL:G: A question to the GAUSSIAN group Message-Id: <-36460-080307120923-27034-WoMYcoEwn/qIriXhAHGkhg|a|server.ccl.net> X-Original-From: errol lewars Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Fri, 07 Mar 2008 11:14:13 -0500 MIME-Version: 1.0 Sent to CCL by: errol lewars [elewars---trentu.ca] 2008 March 07 hello, For a list of which functionals are hardcoded in various programs, see S F Sousa, P A Fernandes, M J Ramos, JPCA, 2007, 111(42), 10439 [able 2]; this paper also has plenty info' on the popularity of the functionals, etc. E. Lewars ===== Alcides Simao alsimao~~gmail.com wrote: > Dear Dr Clemente, > > I have some ideas/suggestions to make to you, and also some doubts. > > First, what are the kind of DFT functionals hardcoded in GAUSSIAN? > > In my present research, in hydrogen-bonding, I've been interested in > using some rather 'exotic' functionals, such as MPWPW91, by Barone, > which seems to be implemented in GAUSSIAN. However, I would very much > to know which functionals are implemented in GAUSSIAN, and which ones > are more recomendable for computing intermolecular H-bonding. > > As a spectroscopist, I am sometimes baffled with overtones, fermi > ressonances, and anharmonic vibrations. while the latter is > implemented in GAUSSIAN (although I am not sure of its scope), > overtones and Fermi ressonances procedures seems not to be available. > For me, they are of great interest! > > Another feature that I would like to see is the way that electron > density changes during a specific vibrational mode. This is > particulary useful for some times of docking that involve just on kind > of molecular motion. > > My very best regards, > > Alcides From owner-chemistry@ccl.net Sat Mar 8 23:53:01 2008 From: "kalpana kalpuk---gmail.com" To: CCL Subject: CCL: calculating and displaying surface residues Message-Id: <-36461-080308122221-20366-2NbaQmdzjXHCm+8GjNpz2w/./server.ccl.net> X-Original-From: kalpana Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Sat, 08 Mar 2008 21:49:14 +0530 MIME-Version: 1.0 Sent to CCL by: kalpana [kalpuk!=!gmail.com] Hi Elaine: Thanks for the detailed instructions, I have managed to display the surface, I will take you up on the offer to help as I proceed with the analysis, Chimera is a pretty powerful tool! Cheers Kalpana Elaine Meng meng()cgl.ucsf.edu wrote: > Sent to CCL by: "Elaine Meng" [meng]=[cgl.ucsf.edu] > On Mar 6, 2008, at 7:51 PM, Kalpana Krishnaswami kalpuk*_*gmail.com wrote: > Hi > We would like to calculate and display exposed hydrophobic surfaces on a protein. We would also like to list the residues on the surface. Are there freeware/ scripts/plugins to pymol/rasmol that would do this? > Thanks >