From chemistry-request@server.ccl.net Sat Dec 7 14:43:07 2002 Received: from hermes.csd.unb.ca ([131.202.3.20]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id gB7Jh7i10349 for ; Sat, 7 Dec 2002 14:43:07 -0500 Received: from mailserv2 (mailserv.unb.ca [131.202.3.23]) by hermes.csd.unb.ca (8.12.3/8.12.3) with SMTP id gB7Jh4AV019880 for ; Sat, 7 Dec 2002 15:43:04 -0400 (AST) Received: FROM pop.unb.ca BY mailserv2 ; Sat Dec 07 15:43:04 2002 -0400 Received: from webmail1 (webmail1.unb.ca [131.202.130.26]) by pop.unb.ca (8.11.6+Sun/8.11.6) with ESMTP id gB7Jh4K07039 for ; Sat, 7 Dec 2002 15:43:04 -0400 (AST) X-WebMail-UserID: l72k6 Date: Sat, 7 Dec 2002 15:43:03 -0400 Sender: Robert Flight From: Robert Flight To: Computational Chemistry List X-EXP32-SerialNo: 00003025, 00003442 Subject: Internal Ligand Energy in Autodock Message-ID: <3DF67AC8@webmail1> Mime-Version: 1.0 Content-Type: text/plain; charset="US-ASCII" Content-Transfer-Encoding: 7bit X-Mailer: WebMail (Hydra) SMTP v3.61.08 Hi All, I am trying to determine how Autodock calculates the internal energies of the docked poses generated from a docking run. There is plenty of documentation on how the intermolecular energies are calculated (main references from the Autodock site) but I was not able to find anything in the literature on how Autodock calculates the internal energies except for a brief mention that it happens (J. Comp. Chem. 1998 and J. Mol. Rec. 1996). > From what I can understand, pairwise interactions between all the ligand atoms are calculated and summed for internal energy, vs the interactions between the ligand and receptor atoms for intermolecular energy. Is this right? And does the calculation take into account any out of plane distortions and non-ideal bond angles and distances? Any information on this subject would be appreciated, or even a reference that I could look at. Responses will be summarized and posted. Thank you very much for your help, Robert ******************************** Robert Flight Masters Student Department of Chemistry University of New Brunswick Fredericton, NB Canada E3B 6E2 e-mail: L72K6@unb.ca ******************************** "A computer terminal is not some clunky old television with a typewriter in front of it. It is an interface where the mind and body can connect with the universe and move bits of it about." -- Hitch Hikers Guide to the Galaxy From chemistry-request@server.ccl.net Sat Dec 7 09:40:10 2002 Received: from GWIA.HSC.WVU.EDU ([157.182.105.18]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id gB7EeAA05212 for ; Sat, 7 Dec 2002 09:40:10 -0500 Received: from HSC-DOM5-MTA by GWIA.HSC.WVU.EDU with Novell_GroupWise; Sat, 07 Dec 2002 09:40:06 -0500 Message-Id: X-Mailer: Novell GroupWise Internet Agent 6.0.2 Date: Sat, 07 Dec 2002 09:39:42 -0500 From: "Peter Gannett" To: , Subject: Re: CCL:ion concentration in protein simulation Mime-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Disposition: inline Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id gB7EeAA05213 Ioana: We had a similar question with Amber. The general consensus was to do exactly as you suggest. The only thing to watch for is if you need to have a system with overall neutrality in which case add counter ions to neutralize you molecule and then salt to bring it to the desired concentration. This worked just fine for us under Amber/Sander Pete Gannett >>> Ioana Cozmuta 12/06/02 09:30PM >>> Hi, I have a more general question and I've tried to look it up in the archive but I could not really get something similar. So here it is: My question relates to adding ions when simulating a large protein system. The experiments were performed using an ionic solution with a 1M concentration and with an applied electric field. I was wondering what is the usual approach in this kind of simulations: to bring the ion concentration close to the physiological number, for example? Also the solution is one of KCl so when adding ions would it be required to add in equal amounts both K+ and Cl-? I would appreciate your advice. Thank you in advance, Ioana **************************************************************************** * Ioana Cozmuta, PhD * * * NASA-AMES Research Center * "Gravitation can not be held responsible* * Mail Stop 230-3 * for people falling in love" * * Moffet Field * * * phone: (650) 604-0993 * Albert Einstein* * fax: (650) 604-0350 * (1879-1955) * **************************************************************************** -= This is automatically added to each message by mailing script =- CHEMISTRY@ccl.net -- To Everybody | CHEMISTRY-REQUEST@ccl.net -- To Admins Ftp: ftp.ccl.net | WWW: http://www.ccl.net/chemistry/ | Jan: jkl@ccl.net From chemistry-request@server.ccl.net Sat Dec 7 00:19:47 2002 Received: from kafka.net.nih.gov ([165.112.130.10]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id gB75JlA12186 for ; Sat, 7 Dec 2002 00:19:47 -0500 Received: from gandalf.cber.nih.gov (gandalf.cber.nih.gov [128.231.52.5]) by kafka.net.nih.gov (/8.10.1) with ESMTP id gB75JiWZ014076; Sat, 7 Dec 2002 00:19:44 -0500 (EST) Date: Fri, 6 Dec 2002 23:18:53 -0500 From: Rick Venable To: Ioana Cozmuta cc: CHEMISTRY@ccl.net Subject: Re: CCL:ion concentration in protein simulation In-Reply-To: Message-ID: ReplyTo: Rick_Venable@nih.gov MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII The ion concentration question has a couple nuances. It's typically too costly (CPU time) to simulate a system with enough water to match the experimental protein concentration, i.e. [protein]sim > [protein]expt Instead, it might be better to match the salt/protein mole ratio, rather than the concentration based on the simulation cell volume. Depending on the density of charged residues on the surface of the protein, this may be an underestimate. There may be considerable ion condensation around the protein, so that the ion distribution in the solution would be non-uniform and higher near the protein. For Ewald electrostatic methods, a system with a net zero charge is recommended. In addition to adding an equal number of K+ and Cl- ions to at least match expt salt/protein, one should also add enough of one type of ion to neutralize the net charge of the protein. =+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+= Rick Venable 29/500 FDA/CBER/OVRR Biophysics Lab 1401 Rockville Pike HFM-419 Rockville, MD 20852-1448 U.S.A. (301) 496-1905 Rick_Venable@nih.gov ALT email: rvenable@speakeasy.org =+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+= On Fri, 6 Dec 2002, Ioana Cozmuta wrote: > My question relates to adding ions when simulating a large protein > system. The experiments were performed using an ionic solution with > a 1M concentration and with an applied electric field. I was > wondering what is the usual approach in this kind of simulations: to > bring the ion concentration close to the physiological number, for > example? Also the solution is one of KCl so when adding ions would > it be required to add in equal amounts both K+ and Cl-? > > **************************************************************************** > * Ioana Cozmuta, PhD * * > * NASA-AMES Research Center * "Gravitation can not be held responsible* > * Mail Stop 230-3 * for people falling in love" * > * Moffet Field * * > * phone: (650) 604-0993 * Albert Einstein* > * fax: (650) 604-0350 * (1879-1955) * > ****************************************************************************