RE: [PyMOL] Electrostatic potential maps in PyMOL

[EPF (E. P. Friis) <ep...@no...>]

=20

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 F=F6rster
To: EPF (Esben Peter Friis)
Cc: 'pym...@li...'
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 =3D 2
using the following physical conditions:
Exterior dielectric constant, espext =3D 80
Solvent probe radius, solrad =3D 1.4
Ion exclusion layer thickness, sterln =3D 2
Temperature, T =3D 300
Ionic strength, ionicstr =3D 0
Hueckel factor (epsext*kappasq) =3D 0
ln(10) * kBolt * T =3D 0.00413391
kBolt =3D 5.98444e-06
conconv =3D 0.000602214
econv =3D 331.842
Bohr radius =3D 0.529177
Proton Charge =3D 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,
>=20
> 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.=20
>=20
> 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 ;-)
>=20
> To create a nice electrostatic surface, you need:
>=20
>=20
> * 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).=20
> * PyMOL, of course (v0.88 or newer).
>=20
>=20
> Here is an example how to create everything from scratch for 4PTI.pdb
>=20
>=20
> Gromacs steps
> -------------
> 1) use pdb2gmx to create .gro and .top files:
> pdb2gmx -f 4PTI.pdb -o 4PTI.gro -p 4PTI.top=20
>=20
> 2) use grompp to create .tpr file:
> grompp -f 4PTI.mdp -p 4PTI.top -o 4PTI.tpr -c 4PTI.gro
>=20
> 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.=20
>=20
> 3) use editconf to create a MEAD-readable pdb file:=20
> editconf -f 4PTI.tpr -mead -o 4PTI.pqr.pdb
>=20
> The output pdb file must then be renamed to be recognized by MEAD:=20
> mv 4PTI.pqr.pdb 4PTI.pqr=20
>=20
>=20
> MEAD steps
> ----------
>=20
> 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:
>=20
> ON_GEOM_CENT 65 1.0
>=20
> 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.=20
>=20
> 2) Run 'potential' to create the grid:
> potential -epsin 2 -CoarseFieldOut 4PTI 4PTI
>=20
> The epsin option is mandatory and specifies the internal (in the
protein)
> dielectric constant. The program will say something like:
>=20
> WARINING from potential main program:
> Could not open field point file, 4PTI.fpt, for reading. Exiting
without
> giving any potentials.
>=20
> 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.=20
>=20
> Convert to PyMOL readable grid
> ------------------------------
>=20
> 1) Use the fld2phi to convert the .fld file to a big-endian .phi grid
file:
> fld2phi 4PTI.fld 4PTI.phi
>=20
> This sould create a 4PTI.phi file which is readable by PyMOL.=20
>=20
>=20
> PyMOL steps
> -----------
>=20
> 1) Load the structure including the hydrogens built by Gromacs:
> load 4PTI.pqr, 4PTI=20
>=20
> 2) Create a selection of the water:
> select water, 4PTI and resn SOL=20
>=20
> 3) Remove the water atoms:
> remove water=20
>=20
> 4) Show the surface of the 4PTI object:
> show surface, 4PTI=20
>=20
> 5) Load the electrostatic grid:
> load 4PTI.phi, map
>=20
> You can show the extent of the grid box by clicking on the object
called
> "map" in the object list to the right.=20
>=20
> 6) Create a color ramp object:
> ramp_new e_lvl, map, [-0.02,0.00,0.02]=20
>=20
> 7) Color the surface according to the grid and map:
> set surface_color, e_lvl, 4PTI=20
>=20
> 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.
>=20
> It is also possible to create one or more contour surfaces:=20
> isosurface contour1, map, -0.05
>=20
> 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.
>=20
>=20
>=20
> Best regards (and please forgive me for quoting source code here :)
>=20
> Esben
>=20
>=20
> **************************************************************
> *  Source code for fld2phi                                   *
> *  save as: fld2phi.c                                        *
> *  compile with: gcc -o fld2phi fld2phi.c                    *
> **************************************************************
>=20

--=20
                    Andreas F=F6rster
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