Hi Andreas
MEAD cannot create maps from a raw pdb-file. It requires a pqr-file, which is a pdb file that has the Van der Waals radii in the B-factor column, and the atom charges in the occupancy column. Gromacs can assign partial charges and VdW-radii to a pdb-file and write out a pqr-file. If you already did this, rename the Gromacs-written pdb-file to 1UBQ.pqr - otherwise MEAD will not recognize it. Your error message says something about the ogm-file. Make sure you have a 1UBQ.ogm file that contains this line: ON_GEOM_CENT 65 1.0 Hope this works! Cheers, Esben ----Original Message----- From: Andreas Förster To: EPF (Esben Peter Friis) Cc: 'pymol-users@lists.sourceforge.net' Sent: 10-07-03 21:25 Subject: Re: [PyMOL] Electrostatic potential maps in PyMOL Hi Esben, I tried to follow your instructions to create and display an electrostatic surface potential. I used 1UBQ.pdb as input. In Mead, I encountered the following error when running potential -epsin 2 -CoarseFieldOut 1UBQ 1UBQ Starting potential for molecule named 1UBQ with interior dielectric constant = 2 using the following physical conditions: Exterior dielectric constant, espext = 80 Solvent probe radius, solrad = 1.4 Ion exclusion layer thickness, sterln = 2 Temperature, T = 300 Ionic strength, ionicstr = 0 Hueckel factor (epsext*kappasq) = 0 ln(10) * kBolt * T = 0.00413391 kBolt = 5.98444e-06 conconv = 0.000602214 econv = 331.842 Bohr radius = 0.529177 Proton Charge = 1 No blab level set (so no blabbing) INPUT FAILURE in FinDiffMethodRep::read from file1UBQ.ogmbad Coord-type entry No fld file is created. Any suggestion? The calculation was run on a PIII Xeon linux box. Thanks Andreas On Wed, 2003-07-09 at 08:48, EPF (Esben Peter Friis) wrote: > Hi PyMOL users, > > MEAD's potential maps can be used in PyMOL, but it requires a little more > than a bit of tweaking, as the maps are in the AVS .fld format, which can > not be read by PyMOL. (These maps can be read by Dino, as Paulo just > mentioned). Also, PyMOL reads (as far as I can see) only big-endian > phi-maps. > > I have written a small program, which does the conversion from .fld to > big-endian-.phi, so the maps can be read by PyMOL. It just finished it > today, and it has only been tested on Linux (i386), so beware ;-) > > To create a nice electrostatic surface, you need: > > > * Gromacs (not strictly necessary, but makes life easier) Download from > http://www.gromacs.org > * MEAD. Download from http://www.scripps.edu/bashford/ > * fld2phi, source code quoted below (sorry, but I don't have access to our > external web server, and it's only about 4kb). > * PyMOL, of course (v0.88 or newer). > > > Here is an example how to create everything from scratch for 4PTI.pdb > > > Gromacs steps > ------------- > 1) use pdb2gmx to create .gro and .top files: > pdb2gmx -f 4PTI.pdb -o 4PTI.gro -p 4PTI.top > > 2) use grompp to create .tpr file: > grompp -f 4PTI.mdp -p 4PTI.top -o 4PTI.tpr -c 4PTI.gro > > The file 4PTI.mdp contains the parameters for the Gromacs simulation. But as > we are not going to do any simulation this time, an empty file is ok. It can > be created with touch 4PTI.mdp. > > 3) use editconf to create a MEAD-readable pdb file: > editconf -f 4PTI.tpr -mead -o 4PTI.pqr.pdb > > The output pdb file must then be renamed to be recognized by MEAD: > mv 4PTI.pqr.pdb 4PTI.pqr > > > MEAD steps > ---------- > > 1) create a .ogm file which specifies the grid size. Notice that PyMOL can > only handle grids which are 65x65x65 points, so your only option is to > change the spacing between points. You can specify focussing options in the > .ogm file, but only the coarsest grid is written anyway, so you only need > one line in the 4PTI.ogm file: > > ON_GEOM_CENT 65 1.0 > > See documentation for other centering options (first parameter). Next number > is the number of grid points on each side (must be 65 to be readable by > PyMOL). The last number is a real specifying the distance between grid > points. > > 2) Run 'potential' to create the grid: > potential -epsin 2 -CoarseFieldOut 4PTI 4PTI > > The epsin option is mandatory and specifies the internal (in the protein) > dielectric constant. The program will say something like: > > WARINING from potential main program: > Could not open field point file, 4PTI.fpt, for reading. Exiting without > giving any potentials. > > This can be ignored. The program still writes out a 4PTI.fld file with the > grid. Notice that this file in not overwritten, so you must delete it > manually if it already exists. > > Convert to PyMOL readable grid > ------------------------------ > > 1) Use the fld2phi to convert the .fld file to a big-endian .phi grid file: > fld2phi 4PTI.fld 4PTI.phi > > This sould create a 4PTI.phi file which is readable by PyMOL. > > > PyMOL steps > ----------- > > 1) Load the structure including the hydrogens built by Gromacs: > load 4PTI.pqr, 4PTI > > 2) Create a selection of the water: > select water, 4PTI and resn SOL > > 3) Remove the water atoms: > remove water > > 4) Show the surface of the 4PTI object: > show surface, 4PTI > > 5) Load the electrostatic grid: > load 4PTI.phi, map > > You can show the extent of the grid box by clicking on the object called > "map" in the object list to the right. > > 6) Create a color ramp object: > ramp_new e_lvl, map, [-0.02,0.00,0.02] > > 7) Color the surface according to the grid and map: > set surface_color, e_lvl, 4PTI > > Thats it. You can change the color scale on the fly by issuing another > ramp_new command with other numbers. The 3 numbers are red-point, > white-point and blue-point, respectively. The scale can also be changed by > ctrl+mid-click while you drag the color scale. > > It is also possible to create one or more contour surfaces: > isosurface contour1, map, -0.05 > > where contour1 is the object name of the surface (choose whatever you want), > "map" is the object name of the electrostatic potential map and the number > is the contour level. The commands isomesh and isodot have the same syntax > and do exactly what you think. > > > > Best regards (and please forgive me for quoting source code here :) > > Esben > > > ************************************************************** > * Source code for fld2phi * > * save as: fld2phi.c * > * compile with: gcc -o fld2phi fld2phi.c * > ************************************************************** > -- Andreas Förster Dept of Biochem, Univ of Utah, 20N 1900E, #2460 Eccles Bldg. Salt Lake City, UT 84132, phone: 001.801.585.3919 home: 1736 Kensington, SLC, UT 84108, 001.801.463.3607 http://www.biochem.utah.edu/~andreas
