From owner-chemistry@ccl.net Sat May 13 11:19:01 2006 From: "Santosh Khedkar santykhedkar]*[rediffmail.com" To: CCL Subject: CCL: P2 statistics in QSAR Message-Id: <-31756-060513023354-2817-BSR++Wa/+7eV7eFw60mIPg]*[server.ccl.net> X-Original-From: "Santosh Khedkar" Content-type: multipart/alternative; boundary="Next_1147498363---0-202.54.124.203-13927" Date: 13 May 2006 05:32:43 -0000 MIME-Version: 1.0 Sent to CCL by: "Santosh Khedkar" [santykhedkar__rediffmail.com] This is a multipart mime message --Next_1147498363---0-202.54.124.203-13927 Content-type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable Content-Disposition: inline Dear All, =0ADo you have any references where p2 value is quoted instead of= r2 in QSAR. I came across this terminology first time in Quasar manual (Ve= dani, et al.). =0AI would appreciate your help in calculating (any formula,= please!) and its significance in QSAR over r2.=0AAlso I would appreciate = some QSAR refernces, where p2 is reported and discussed.=0AThank you very m= uch in advance.=0Aregards,=0ASantosh Khedkar =0A=0A=0ASANTOSH AMBADAS KHEDK= AR=0D=0A=0D=0AComputer-Aided Molecular Design Lab=0D=0ADepartment of Pharma= ceutical Chemistry=0D=0ABombay College of Pharmacy=0D=0AKalina, Santacruz (= E), Mumbai-400 098=0D=0AMobile: 09324329337. Home:02447-244064.=0D=0A------= ---------------------------------------------------------------------------= ---------------------------------------=0D=0A"When one door of happiness cl= oses, another opens; but often we look so long at the=0D=0Aclosed door that= we do not see the one which has opened for us" --Helen Keller=0D=0A*******= ***************************************************************************= *************** --Next_1147498363---0-202.54.124.203-13927 Content-type: text/html; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable Content-Disposition: inline

=0ADear All,
=0ADo you have any references where p2 value is quoted = instead of r2 in QSAR. I came across this terminology first time in Quasar = manual (Vedani, et al.).
=0AI would appreciate your help in calculating= (any formula, please!)  and its significance in QSAR over r2.
=0AA= lso I would appreciate some QSAR refernces, where p2 is reported and discus= sed.
=0AThank you very much in advance.
=0Aregards,
=0ASantosh Khe= dkar
=0A=0A

=0A=0A=0ASANTOSH AMBADAS KHEDKAR=0D
=0A=0D
= =0AComputer-Aided Molecular Design Lab=0D
=0ADepartment of Pha= rmaceutical Chemistry=0D
=0ABombay College of Pharmacy=0D
=0AKal= ina, Santacruz (E), Mumbai-400 098=0D
=0AMobile: 09324329337.&= nbsp;Home:02447-244064.=0D
=0A------------------------------------------= ---------------------------------------------------------------------------= ---=0D
=0A"When one door of happiness closes, another ope= ns; but often we look so long at the=0D
=0Aclosed do= or that we do not see the one which has opened&nbs= p;for us" --Helen Keller=0D
=0A************************************= *************************************************************

=0A=0A --Next_1147498363---0-202.54.124.203-13927-- From owner-chemistry@ccl.net Sat May 13 11:53:01 2006 From: "David A. Case case a scripps.edu" To: CCL Subject: CCL: energy convergence in Tinker? Message-Id: <-31757-060512221021-20673-nIjecOVyu92Qw9gYdighwg[-]server.ccl.net> X-Original-From: "David A. Case" Content-Disposition: inline Content-Type: text/plain; charset=us-ascii Date: Fri, 12 May 2006 18:29:15 -0700 Mime-Version: 1.0 Sent to CCL by: "David A. Case" [case]=[scripps.edu] On Fri, May 12, 2006, Samuel Flores samuel.flores]_[yale.edu wrote: > > I've been using energy to monitor how well my structure is equilibrated in > Tinker. However, it occurs to me that a lot of the fluctuation may be > thermal. Is it safe to assume that if my system has, say, 1000 DOF at 300K, > then I should expect energy fluctuations of 600 kcal/mol, which will never > go away until I lower the temperature? Remember that the energy fluctuations in the individual modes are not correlated with each other (to a first approximation) so that the fluctuation in total energy of an individual molecule will be much smaller (say by the sqare root of 1000) that the number cited above. But you are correct in surmising that they never "go away" at a given temperature. The "classical" discussion of this is in Chapter XII of "Statistical Physics" by Landau and Lifshitz. A nice, short (2-page) discussion of energy fluctuations with applications to proteins is available here: %A A. Cooper %T Thermodynamic fluctuations in protein molecules %J Proc. Natl. Acad. Sci. USA %V 73 %P 2740-2741 %D 1976 The energy fluctuations can seem quite large (e.g. larger than the unfolding free energy of a protein.) Cooper discusses what all this means. You don't say what sort of simulation you are running. An explicit solvent simulation might have zero fluctuation in the total energy (if you are using Newton's equations of motion). But some (necessarily approximate) division of this energy into a "protein" part and a "solvent" part would then show fluctuations in the protein energy that would be roughly in accord with the formulas given in the above paper. Or, if you are running an implicit solvent (or vacuum) simulation with a thermostat that gives canonical behavior, the energy fluctuations in the whose system (which would just be one protein molecule) would follow these rules. ...hope this helps....dave case