Custom Search
-- Ray Luo, Ph.D. Professor of Structural Biology/Biochemistry/Biophysics, Chemical Physics, Biomedical Engineering, and Chemical Engineering Department of Molecular Biology and Biochemistry University of California, Irvine, CA 92697-3900 On Fri, Feb 24, 2017 at 1:32 AM, Paulo Costa <pjfmcosta.gmail.com> wrote: > Dear AMBER users > > I'm sorry for the long post ... > > I'm performing some test calculations with the pbsa solver (AmberTools16) > to get the solvation free energies of small molecules. These small > molecules are built with antechamber using GAFF atom types. > > I started with a simple single point calculation using the example from the > manual > > Sample single point PB calculation > &cntrl > / > inp=2 > &pb > npbverb=1, istrng=150, fillratio=1.5, saopt=1, radiopt=1 > / > > I got the non-polar contribution modeled by 2 terms, cavity + dispersion > (inp=2) and I since GAFF atom types are employed, radii from the prmtop > file will be used according to the manual (radipot=1). This calculation > yielded > > EPB = -12.3409 | ECAVITY= 16.4597 | EDISPER = -15.1553 > > So, let's imagine I want to optimize the radii of the elements of my > molecule. The manual states that one should change the RADII section of the > topology and read those radii via RADIOPT=0. But if I use the exact same > topology as before, the radii should be the same. Therefore, I repeated the > calculation with > > Sample single point PB calculation > &cntrl > / > inp=2 > &pb > npbverb=1, istrng=150, fillratio=1.5, saopt=1, radiopt=0 > / > > and I got > > EPB = -12.3409, ECAVITY= 16.4597, EDISPER = -17.0143 > > the value for EDISPER is completely different. Using the verbose option in > both runs, I confirmed in the output that all radii (PB and NP) are exactly > the same for both runs. > > Besides EDISPER, the outputs differ in the following > > < Use Tan, Yang, and Luo optimized cavity radii definition > --- >> Use cavity radii in the prmtop file > > Indeed, if one changes the RADII section in the topology for one or more > atoms, this only affects the EPB values as these are used for for the > electrostatic contribution calculation. Apparently the NP radii are always > the Rmin values of the FF. If so, it makes sense that the ECAVITY term is > equal regardless if we use radiopt = 0 or 1 since, in both cases, Rmin > values are used. On the other hand, why are EDISPER values different? > > If we optimize a radii for an element (via the topology), we should run a > radiopt = 0 but how to compare it with the non-optimized raddii? The > default calculations are performed with radiopt = 1 but that will change te > contribution from EDISPER as well ... > > If one wishes to optimize the NP radii, used for the calculation of the > non-polar contributions, we have to "hack" the source code? Or is there any > other way to do it (e.g. via topology)? > > Again, sorry for the long post and thanks in advance for your help! > > Paulo Costa > _______________________________________________ > 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 Fri Feb 24 2017 - 09:00:03 PST