From owner-chemistry@ccl.net Fri Jul 21 08:27:01 2006 From: "Felipe Fleming ffleming|a|globo.com" To: CCL Subject: CCL: How to visualize a lone pair Message-Id: <-32211-060720081714-14996-zFSMSXi5lueLT8kpUE89Cw^^server.ccl.net> X-Original-From: "Felipe Fleming" Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset="iso-8859-1" Date: Thu, 20 Jul 2006 08:35:33 -0300 MIME-Version: 1.0 Sent to CCL by: "Felipe Fleming" [ffleming[-]globo.com] Hello, lone pairs, chemical bonds and chemical structure are all models derived > from valence bond theory... NBO, AIM, ELF and related calculations all try to recover a VB poit of view from a MO wave function. Why not do a Modern Valence Bond calculation? Best regards, Fleming ----- Original Message ----- > From: "Mateusz Witkowski big_mateo-#-inbox.com" To: "Fleming, Felipe " Sent: Wednesday, July 19, 2006 10:27 AM Subject: CCL: How to visualize a lone pair > Sent to CCL by: Mateusz Witkowski [big_mateo++inbox.com] > > Hi, > I'm interested in the directionality of O,N,S lone pairs in creation of hydrogen bonds. > Is it possible to visualize a lone pair from QM results? If so, what should be done, which software should be used? > What is your general impression about hydrogen bonds with XH-A angle ~100-120deg? Is there any border between HB and purely electrostatic interaction? > > TIA > Mateo> > From owner-chemistry@ccl.net Fri Jul 21 09:18:00 2006 From: "Joe Harriman j.harriman]-[unb.ca" To: CCL Subject: CCL: Calculation of protein's active site surface buried by a ligand Message-Id: <-32212-060718125201-29580-tQ+YArHvL76JMLXOyokjUg%%server.ccl.net> X-Original-From: Joe Harriman Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=US-ASCII; delsp=yes; format=flowed Date: Tue, 18 Jul 2006 12:56:04 -0300 Mime-Version: 1.0 (Apple Message framework v752.2) Sent to CCL by: Joe Harriman [j.harriman- -unb.ca] The site finder in MOE will do this. It is very easy to use and is pretty accurate. -Joe On 18-Jul-06, at 11:56 AM, Gerard Pujadas gerard.pujadas- -urv.cat wrote: > Sent to CCL by: "Gerard Pujadas" [gerard.pujadas**urv.cat] > Dear CCL list members, > > I wonder if there is a program that takes a PDB file of a protein- > ligand complex and calculates the area of the protein's active site > surface that it is buried by the contact with all or part of the > ligand. > > With many thanks in advances for your help > > Yours sincerely > > Gerard > > > > -= 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)> > -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+- > +-+-+ > > > From owner-chemistry@ccl.net Fri Jul 21 10:10:00 2006 From: "alex\.msilva alex.msilva~~uol.com.br" To: CCL Subject: CCL:G: Gaussian and memory Message-Id: <-32213-060721092258-1477-vJiL/gGK9oFU/oCQHQ6T6Q],[server.ccl.net> X-Original-From: "alex\.msilva" Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=iso-8859-1 Date: Fri, 21 Jul 2006 09:29:16 -0300 MIME-Version: 1.0 Sent to CCL by: "alex\.msilva" [alex.msilva%%uol.com.br] Hello, I woud like to known if it is possible to get gaussian executable files that can support up to 4GB of memory. Someone could explain what to do? Thanks in advance, Alexander. From owner-chemistry@ccl.net Fri Jul 21 11:26:01 2006 From: "Paul Hawkins phawkins+/-eyesopen.com" To: CCL Subject: CCL: Calculation of protein's active site surface buried by a ligand Message-Id: <-32214-060721111915-10605-zYvsLASn9misyiBgm1YzRw[A]server.ccl.net> X-Original-From: Paul Hawkins Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Fri, 21 Jul 2006 08:37:00 -0600 MIME-Version: 1.0 Sent to CCL by: Paul Hawkins [phawkins__eyesopen.com] There is also a routine in FlexX from BioSolveIT to do this. Paul. Joe Harriman j.harriman]-[unb.ca wrote: >Sent to CCL by: Joe Harriman [j.harriman- -unb.ca] > > >The site finder in MOE will do this. It is very easy to use and is >pretty accurate. > >-Joe > >On 18-Jul-06, at 11:56 AM, Gerard Pujadas gerard.pujadas- -urv.cat >wrote: > > > >>Sent to CCL by: "Gerard Pujadas" [gerard.pujadas**urv.cat] >>Dear CCL list members, >> >>I wonder if there is a program that takes a PDB file of a protein- >>ligand complex and calculates the area of the protein's active site >>surface that it is buried by the contact with all or part of the >>ligand. >> >>With many thanks in advances for your help >> >>Yours sincerely >> >>Gerard >> >> >> >>-= 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)> >>-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+- >>+-+-+> > > > From owner-chemistry@ccl.net Fri Jul 21 12:04:00 2006 From: "Wai-To Chan chan=curl.gkcl.yorku.ca" To: CCL Subject: CCL: How to visualize a lone pair Message-Id: <-32215-060721120101-824-4bq8sMYZpU6nG36WVJ1dqw(0)server.ccl.net> X-Original-From: Wai-To Chan Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=us-ascii Date: Fri, 21 Jul 2006 12:02:22 -0400 (EDT) MIME-Version: 1.0 Sent to CCL by: Wai-To Chan [chan:+:curl.gkcl.yorku.ca] <<<<<<<<<<<<<<<<<< one pairs, chemical bonds and chemical structure are all models derived from valence bond theory... NBO, AIM, ELF and related calculations all try to recover a VB poit of view from a MO wave function. Why not do a Modern Valence Bond calculation? >>>>>>>>>>>>>>>>>>... AIM recover lone pairs from rho. Whether rho is derived from MO wavefunction (usually it is) is not relevant in the sense that you can apply AIM to rho obtained from experiments. I seemingly remember ELF in its original formulation by Axel Becke is orbital dependent. Not sure if this was changed in its later implementations. Having said that I don't see any of these different definitions of lone pair as necessarily better than the others. Wai-To Chan From owner-chemistry@ccl.net Fri Jul 21 12:38:00 2006 From: "ALBERT POATER TEIXIDOR albert.poater[A]udg.es" To: CCL Subject: CCL:G: Solvation of organic molecules (with GROMACS) Message-Id: <-32216-060721052803-18848-SjXKadwOWugm3TVqtdhirQ,+,server.ccl.net> X-Original-From: "ALBERT POATER TEIXIDOR" Content-Transfer-Encoding: 8bit Content-Type: text/plain;charset=iso-8859-1 Date: Fri, 21 Jul 2006 10:47:14 +0200 (CEST) MIME-Version: 1.0 Sent to CCL by: "ALBERT POATER TEIXIDOR" [albert.poater-#-udg.es] Dear Gaussian users, I receive this error message in PCM single point calculations of molecules with nearly 100 atoms. There is a H atom, which is in the middle of two other atoms. I have tested the options of PCM to converge it. And the IPCM, which is too computationally expensive. Does anyone any idea to get this type of calculation? Any help will be appreciated. Best regards, Albert United Atom Topological Model (UA0 parameters set). UA0: Hydrogen 55 is unbound. Keep it explicit at all point on the UA0: potential energy surface to get meaningful results. Error termination via Lnk1e in /estufa/soft/g03pedro/g03/l301.exe at Fri Jul 21 03:17:13 2006. Job cpu time: 0 days 0 hours 0 minutes 4.4 seconds. File lengths (MBytes): RWF= 11 Int= 0 D2E= 0 Chk= 1 Scr= 1 Dr. Albert Poater Teixidor c/Campus de Montilivi s/n 972418358 From owner-chemistry@ccl.net Fri Jul 21 14:26:00 2006 From: "luis Simon Rubio luissimonrubio,hotmail.com" To: CCL Subject: CCL:G: Solvation of organic molecules (with GROMACS) Message-Id: <-32217-060721142114-23845-LTWGvo9v0EpuGEdDzMOg9g|a|server.ccl.net> X-Original-From: "luis Simon Rubio" Content-Type: text/plain; charset=iso-8859-1; format=flowed Date: Fri, 21 Jul 2006 17:08:47 +0000 Mime-Version: 1.0 Sent to CCL by: "luis Simon Rubio" [luissimonrubio]*[hotmail.com] try to change the topological model: at the end of the input, let a blank line and after that write "radii=UAKS" (for instance, there are other ways of constructing the cavity that are specified in the manual). It works for me Good luck: L. Sim'on >From: "ALBERT POATER TEIXIDOR albert.poater[A]udg.es" > >Reply-To: "CCL Subscribers" >To: "Simón, Luis Manuel " >Subject: CCL:G: Solvation of organic molecules (with GROMACS) >Date: Fri, 21 Jul 2006 12:43:46 -0400 > >Sent to CCL by: "ALBERT POATER TEIXIDOR" [albert.poater-#-udg.es] > >Dear Gaussian users, >I receive this error message in PCM single point calculations of molecules >with nearly 100 atoms. There is a H atom, which is in the middle of two >other atoms. I have tested the options of PCM to converge it. And the >IPCM, which is too computationally expensive. Does anyone any idea to get >this type of calculation? Any help will be appreciated. >Best regards, >Albert > > > United Atom Topological Model (UA0 parameters set). > UA0: Hydrogen 55 is unbound. Keep it explicit at all point on the > UA0: potential energy surface to get meaningful results. > Error termination via Lnk1e in /estufa/soft/g03pedro/g03/l301.exe at Fri >Jul 21 03:17:13 2006. > Job cpu time: 0 days 0 hours 0 minutes 4.4 seconds. > File lengths (MBytes): RWF= 11 Int= 0 D2E= 0 Chk= 1 >Scr= 1 > > >Dr. Albert Poater Teixidor >c/Campus de Montilivi s/n >972418358> > > _________________________________________________________________ Horóscopo, tarot, numerología... Escucha lo que te dicen los astros. http://astrocentro.msn.es/