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-- (2) But if we construct a "dummy" atom in H2 and don't remove the angle, bond, and dihedral terms involving in the dummy atom in H2, which is adopted by the tutorial, all the bond, angle and dihedral terms in H(lambda) will be independent to lambda. In this case, these terms will not contribute to the free energy calculation in either model system or protein system. In this case, the contribution of these terms are not directly included into the DeltaG of either model or protein system, but would effect the DeltaG value during the sampling process. When DeltaDeltaG is calculated btw model and protein system, these contributions can be cancelled under the hypothesis that the average sampling behaviors contributed by these terms in model and protein are identical. Thus, the cancellation of these terms in DeltaDeltaG is not the same as in (1). Maybe the AMBER adopts the second scheme for convenience. But I don't think these terms in theorectical H(lambda) (as in (1)) should be independent to Lambda. I am not sure whether I understand this question correctly or not in this way and thus request further elucidation. Many thanks. Jeffrey Yang --- 10年5月8日，周六, Jason Swails <jason.swails.gmail.com> 写道： 发件人: Jason Swails <jason.swails.gmail.com> 主题: Re: [AMBER] How to disable the VDW interaction? 收件人: "AMBER Mailing List" <amber.ambermd.org> 日期: 2010年5月8日,周六,下午9:17 Hello, On Sat, May 8, 2010 at 8:44 AM, Jeffrey <jeffry20072008.yahoo.cn> wrote: > Thanks for your clarification. I have two other relating questions: > 1. If I make a new residue file with a different atom > type, which parameters for bond, angle, and dihedral involving the new atom > type should be used? Can these parameters be copied to the new atom type by > tleap when construting the prmtop file? > You will need to create an frcmod file for this. You can put the same parameters in the frcmod as were loaded by tleap for the old atom type. parmchk should show you all the parameters that you need to incorporate, and you can compare with $AMBERHOME/dat/leap/parm/parm99.dat (or whatever force field you're using) to get the proper parameters. > 2. In fact, I am not very clear about the statement "We don't need to worry > about removing the bonds, angles and dihedral terms as these are all > internal to the residue and so the average properties of these terms should > be identical in the model and protein systems. There is also no > contribution from these terms to the derivative of the potential with > respect to lambda." in the tutorial for pka calculation by TI method as in > http://ambermd.org/tutorials/advanced/tutorial6/section1.htm > When you're doing TI, the free energy change between two hamiltonians is calculated via the differential (dH/dL) where L is lambda. If you break the hamiltonian into its component parts, you get H = bond + angle + dihedral + eel + vdw + 1-4 interactions. Because the differential operator is linear, you can separately take the derivative of each term with respect to lambda. The bond, angle, and dihedral parameters are not changing as a function of Lambda, so those derivatives should be zero, since, with respect to Lambda, they're constant (and you're differentiating with respect to Lambda). The tutorial is saying this is a valid approach (i.e. it is not needed as a further refinement to change bond/angle/dihedral parameters) because they are only dependent on the local conformations adopted by the residue in question, and those local conformations should be distributed approximately equivalently between the model residue and the residue in the protein matrix. Thus, when you take DELTA DELTA G, they cancel out anyway (since TI requires sampling, which averages over all properties). All the best, Jason > > Suppose the following Hamiltonian is used, > H(lambda) = lambda * H1 + (1-lambda) * H2, which H1 and H2 correspond to > the protonated and unprotonated states, respectively. > > If the bond, angle and dihedral/torsion interactions involving > the disappeared hydrogen atom is not removed from the unprotonated state > (prmtop), the derivative of the H(lambda) with respect to lambda (H1-H2) > will also include the contribution from these terms. Why the tutorial says > that "There is also no contribution from these terms to the derivative of > the potential with respect to lambda." Do I understand it correctly? > > Any suggestion is appreciated. > Many thanks. > > Mingjun > --- 10年5月8日，周六, Carlos Simmerling <carlos.simmerling.gmail.com> 写道： > > > 发件人: Carlos Simmerling <carlos.simmerling.gmail.com> > 主题: Re: [AMBER] How to disable the VDW interaction? > 收件人: "AMBER Mailing List" <amber.ambermd.org> > 日期: 2010年5月8日,周六,下午6:01 > > > 1) the RADII section is for the intrinsic radius for the implicit > solvation calculations. it is not vdw radius. > 2) the prmtop does not contain per-atom vdw parameters, only pointers > into the atom type arrays that hold the parameters. so, you can't > change 1 atom's parameters there, because you would have to change > them for all hydrogens of the same atom type. > 3) it seems to me that you need to go back to the actual residue > library file and determine the atom type- some of the hydrogen atoms > in Amber's force fields already have zero for the vdw well depth (you > want that, not zero for radius). you need to check and see what it is, > and if it isn't zero then you will need to make a new residue file > with a different atom type that has zero for vdw interaction. it's nI ot > as simple as modifying the prmtop. > > On Sat, May 8, 2010 at 2:51 AM, Jeffrey <jeffry20072008.yahoo.cn> wrote: > > Dear AMBER users, > > > > We are going to calculate the pka of a protonation of residue in a > protein model, following the tutorial at > http://ambermd.org/tutorials/advanced/tutorial6/. I disabled the vdw > interaction by setting the vdw radii of the hydrogen atom to 0.0 in the > prmtop file (the term under %FLAG RADII). But it is strange that the vdw > interaction didn't change w/o modification of the radii. > > > > I am not sure whether I did it correctly or not and so request your > suggestions. > > > > Many thanks. > > > > Jeffrey Yang > > > > > > > > _______________________________________________ > > AMBER mailing list > > AMBER.ambermd.org > > http://lists.ambermd.org/mailman/listinfo/amber > > > > _______________________________________________ > AMBER mailing list > AMBER.ambermd.org > http://lists.ambermd.org/mailman/listinfo/amber > > > > > _______________________________________________ > AMBER mailing list > AMBER.ambermd.org > http://lists.ambermd.org/mailman/listinfo/amber > -- Jason M. Swails Quantum Theory Project, University of Florida Ph.D. Graduate Student 352-392-4032 _______________________________________________ AMBER mailing list AMBER.ambermd.org http://lists.ambermd.org/mailman/listinfo/amber _______________________________________________ AMBER mailing list AMBER.ambermd.org http://lists.ambermd.org/mailman/listinfo/amberReceived on Sat May 08 2010 - 09:00:03 PDT