Re: [Apbs-users] Comparing APBS PB Grid with Congen Grid?
Biomolecular electrostatics software
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From: Nathan B. <ba...@cc...> - 2007-04-12 11:58:12
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Hi David -- > Hopefully this will be a detailed enough description to help you > understand the problem. It looks like a detailed description! :) > As part of the electrostatics calculation in a simulation, we > currently use a pre-calculated PBE grid around a protein. This grid > is currently calculated using the PBE solver in Congen with Amber > parameters for radius, charge and hydrogen locations. The simulation > expects the grid to have the same spacing in the X, Y and Z > dimensions. It does not require the same number of spacings in each > dimension. OK; APBS can certainly do that as well. > While Congen is technically free, it is no longer developed or > supported and we feel it is time to attempt to replace it. The > obvious replacement to us was APBS because of the active development > and support community. Great! > We have developed a converter that allows us to use the APBS grid as a > drop in replacement for the Congen grid in the simulation. However, > due to Congen being considered the gold standard for us for so long, > we felt it was necessary to try to quantify the differences in the two > grids before trusting the final simulation results. Does your converter account for possible differences in the electrostatic potential units between the two grids? This was a big problem when we initially attempted to compare APBS results to UHBD (for example). > The method that is failing for us at the moment is a direct comparison > of the grid point values in the two grids. We have been able to set > the origins the same and have the same grid size. We are using AMBER > parameters in both Congen and APBS (via PDB2PQR). On average, the > points near the edge of the grid differ by 10-15% This is surprising. Can you describe the boundary conditions used by CONGEN? > and the points > inside of the protein and near the surface can differ by 300-500% > (worst case is a value difference of 680 (not percent)). Please keep in mind that values close to charge locations will be arbitrarily bad because both numerical solvers are attempting to approximate a function that should tend to infinity near point charges (e.g., as Coulomb's law). The most stable comparisons should be outside the biomolecular surface. One possibility is to "mask" your comparison code with the dielectric value: this would give you a simple way to compare potentials outside the biomolecular interiors. If you truly are interested in potential values inside the proteins, then a much more stable way to evaluate these is to calculate reaction field potentials (e.g., the potential due to polarization of the solvent) with APBS through 2 calculations using homogeneous and inhomogeneous dielectric and ion accessibility coefficients. This reaction field potential can then be added to an appropriately-scaled Coulombic potential to give the total electrostatic potential at any point. > We have > determined this by randomly picking and comparing values and also by > visualizing the entire 3D grids and then visualizing the differences > between the two. I do not expect the values to match exactly due to > differences in the solver and some minor differences in the AMBER > parameters (I have a question for the PDB2PQR mailing list regarding > this) but we thought we should be able to find a consistent difference > (10-15% would be acceptable for us). Yes, but I think this will depend on where you look... Outside the biomolecule, I would expect this level of agreement or better (assuming all is well with the CONGEN solver...). > As a note, the field outside > the protein and at the surface is the most important to us, it appears > that outside the protein we get results that are within our tolerance > but the surface values are not acceptable without at least a better > idea of why they could be so different. The surface values are going to be extremely dependent on the surface definition -- this is one reason why we're advocates of smoother biomolecular surface definitions (e.g., splines or Gaussians). We also use a different smoothing routine than UHBD (and presumably CONGEN) for Connolly-type molecular surfaces. You might try comparing surface values without smoothing and see if these give better agreement. > We have tried the comparison with 0mM ionic strength and this is how > we are able to get the closest agreement of the two grids. I was > concerned about the ION parameter so we were only going to test that > once everything else came close to agreeing. That's good. > I can forward APBS input files shortly. They need to be cleaned up at > the moment to the version the provided us what we are considering our > best results so far. > > Thanks again for any help. OK, thanks for switching (or trying to switch) to APBS! -- Nathan > David > > On 4/8/07, Nathan Baker <ba...@cc...> wrote: >> Hi David -- >> >> > I have a program that currently depends on the PBE grid >> generated by >> > Congen (http://www.congenomics.com/congen/congen_toc.html). While >> > Congen is technically free, I would much rather use a system >> that is >> > actively developed and supported. I have tried every >> combination of >> > APBS parameters and have even modified the Congen parameters we >> have >> > used for years to try to get the two grids to converge and this has >> > proved almost futile. I am looking for any help or suggestions >> as to >> > what to try >> >> Can you describe what quantities you're trying to get agree (e.g., >> solvation energy vs. pointwise error in potential vs. mean-squared >> error in potential, etc.)? >> >> > First, has anyone possibly gone thru this or similar transition >> before >> > and can you make any recommendations? >> >> There have been lots of comparisons of APBS with other PB solvers but >> this is the first time I've seen a comparison with Congen. >> >> > 1. The ION parameter in APBS: In Congen, we set an IONSTR >> parameter >> > to a concentration of 0.15 M. There is no ability to specify a >> charge >> > or radius, so I do not know how to translate this into the APBS >> > parameter because the ION parameter requires a charge, >> concentration >> > and radius. >> >> I'd just use >> >> ion 1.0 0.150 2.0 >> ion -1.0 0.150 2.0 >> >> since the 2.0 A radius is fairly standard. This will give you 150 mM >> ionic strength conditions. >> >> However, have you tried the comparison with Congen with 0 mM ionic >> strength? >> >> > 2. The fine grid to course grid relationship: Due to the >> nature of >> > our legacy software, I need the grid to be the same spacing in each >> > direction (0.8A but I am willing to change the size if that will >> help >> > me). I have tried using fg_manual and using a single gird. >> >> The mg-manual should give you the best control. Note that grid >> spacing (h) is related to the number of grid points (n) and the grid >> length (L) by the relationship >> >> h/L = n - 1 >> >> > I have >> > tried fg_auto and forcing the size of the fine grid to be (# grid >> > points * 0.8A) both with some success but nothing great. I have >> > noticed that changing the course grid even slightly can impact the >> > values in the PBE grid by orders of magnitude. >> >> Really? What are the sizes of your coarse and fine grids? This is >> very strange behavior. >> >> > Is there an optimal >> > ratio of fine grid to course grid? >> >> Yes, but mg-auto changes the number of focusing steps to take care of >> this for you. >> >> > Or is there a better way to get a >> > fixed width grid? >> >> Some more specifics about your problem (desired grid lengths, example >> APBS input files, etc.) would help with this. >> >> Thanks, >> >> Nathan >> >> > Thanks. >> > David >> > >> > >> > Below are the parameters we use with Congen in case it helps >> anyone: >> > >> > pbe setup solvent 78.000000 interior 4.000000 all end - >> > boundary adebye ionstr 0.15 - >> > grid 0.800000 temp 300.0 water 1.4 stern 2.0 - >> > margin 1 xdim 85 ydim 66 zdim 57 - >> > epsave harm molsurf subdivision 5 spill uniform - >> > smooth type grid points 15 weight constant offgrid solvent >> end - >> > all >> > >> > >> --------------------------------------------------------------------- >> - >> > --- >> > Take Surveys. Earn Cash. 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