From chemistry-request &$at$& server.ccl.net Wed Feb 26 15:17:59 2003 Received: from ns1.scripps.edu ([192.42.82.59]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h1QKHwa27111 for ; Wed, 26 Feb 2003 15:17:58 -0500 Received: from antigen.scripps.edu (antigen.scripps.edu [137.131.200.100]) by ns1.scripps.edu (8.11.6/TSRI-4.1rx) with SMTP id h1QKHvV06774 for ; Wed, 26 Feb 2003 12:17:58 -0800 (PST) Received: from relay2.scripps.edu(137.131.200.30) by antigen.scripps.edu via csmap id 19799; Wed, 26 Feb 2003 12:10:12 -0800 (PST) Received: from gage.scripps.edu (gage.scripps.edu [137.131.252.115]) by relay2.scripps.edu (8.11.6/TSRI-4.2rAV) with ESMTP id h1QKHqC25491; Wed, 26 Feb 2003 12:17:52 -0800 (PST) Received: from gage (localhost [127.0.0.1]) by gage.scripps.edu (8.9.2/TSRI-3.0.1) with ESMTP id LAA24668; Wed, 26 Feb 2003 11:50:29 -0800 (PST) Message-Id: <200302261950.LAA24668 "at@at" gage.scripps.edu> To: chemistry' at \`ccl.net Cc: Vlad Cojocaru , bashford -AatT- scripps.edu Subject: Re: MEAD help In-Reply-To: Your message of "Thu, 16 Jan 2003 12:27:53 +0100." <3E269739.8000103 $#at#$ mpi-bpc.mpg.de> Date: Wed, 26 Feb 2003 11:50:28 -0800 From: Don Bashford >>>>> "Vlad" == Vlad Cojocaru writes: Vlad> Dear CCLers, I am trying to use MEAD for the first Vlad> time. Since the documentation is very scarce I would like to Vlad> ask somebody that has already calculated electrostatic Vlad> potentials on macromocules using "potential" from MEAD suite Vlad> to give me some hints. I am refering here to a simple basic Vlad> calculation. I tried to look at the examples in the Vlad> distribution but there is no examples for how to take a Vlad> structure from the pdb and calculate the potential and Vlad> visualizing it. All the examples deal with more advanced Vlad> stuff. I tried "potential -epsin 1.0 -CoarseFieldOut file Vlad> molname" on a pqr file created with ambpdb (AMBER) and a ogm Vlad> file that looks like below: Vlad> Vlad> ON_GEOM_CENT 41 1.0 Vlad> ON_GEOM_CENT 41 0.25 Vlad> I got some warnings and errors that look like this: Vlad> Vlad> WARNING: AtomChargeSet::get_cuberep: 162charges fall outside of the lattice, Vlad> WARNING: SAVanal_calc: vertex found with count = 2 Vlad> WARNING: SAVanal_calc: vertex found with count = 2 Vlad> WARNING: SAVanal_calc: vertex found with count = 1 Vlad> WARNING: AtomChargeSet::get_cuberep: 2410charges fall outside of the Vlad> WARINING from potential main program: Vlad> Could not open field point file, comp_test.fpt, for reading. Exiting without giving any potentials. First the easy ones. The warnings from SAVanal_calc are harmless, and have to do with numerical degeneracies in the calculation of the molecular surface. If you really want to delve into it, see You and Bashford (1995) JCC 16:743. The complaint from main about the lack of an .fpt file is a bug, but also essentially harmless. Given that you specified a course field file for output, the program should not really require you to supply an .fpt file too, and in fact it doesn't really, the course field file that you requested was generated. (At least, it is when I try it!) It's just the warning that's the bug, and it's on my TO DO list. The "charges fall outside of the lattice" is potentially more serious. Taking the coord file you sent me, I see that it's x-coordinates span about 54 Ang (spans in y and z are less). The coarse grid that you specified, 41 points at 1.0 Ang spacing can only span 40 Ang, so some atoms are bound to fall outside, and that's the source of the first of the two warnings you get. In principle, charges outside the box can be taken care of through the box boundary conditions, but this requires (in principle) solving already the Poisson eqn for those charges! In practice MEAD sets the coarsest-grid boundary conditions using a simple analytical assumption about the potential on that boundary due to all charges (inside or outside). but its validity depends on that boundary being entirely in the exterior (solvent) region and relatively far (say, 10 to 15 Ang) from any dielectric discontinuities. Bottom line: expand your coarse grid so it spans, say 80 Ang, either be increasing the number of points or the spacing between them. The second "charges fall outside of the lattice" warning is from the fine grid calculation. This is harmless if the coarse grid calculation is good, since the fine-grid boundary conditions are set up by interpolation from the coarse grid, and therefore include a reasonable Poisson solution for the influence of the out-of-fine-box charges on the within-fine-box potential. However, in your case, there are two problems: first the coarse-grid calculation is in doubt; second, because you take the coarse grid as your final program output, you're not getting any information from the fine grid calculations. The multiple grids of the .ogm file just represent nesting or "focusing" as Gilson et al have called it, the fine grid does not feed information back to the coarse grid as it would in a "multigrid" calculation. -Don