Color molecule using electrostatic potential

1: install apbs:
download the source code.
./configure --prefix=/use/local
make all
sudo make install

2: install pdb2pqr:(http://pdb2pqr.sourceforge.net/userguide.html#introduction)
(wasn't able to find numpy, so pdb2pka is disabled)
./configure --disable-pdb2pka --prefix=/usr/local
make
sudo make install

3: following the instructions on the tutorial
http://137.189.50.96/kbwong/teaching/pymol/pymol_tutorial.html

a. Use PDB2PQR to convert the PDB format to PQR format
> pdb2pqr.py --ff=amber --apbs-in 1w2i_nowat.pdb pymol.pqr
The PQR file will be output to pymol.pqr.

b. Use psize.py to determine the grid dimensions for APBS calculation
> psize.py pymol.pqr
You should be able to see the following results:

Center = 37.468 x 31.798 x 12.177 A
:
:
Coarse grid dims = 53.011 x 58.568 x 65.807 A
Fine grid dims = 51.183 x 54.452 x 58.710 A
Num. fine grid pts. = 97 x 97 x 97

Take a note on these parameters.

c. Edit the apbs.in
You need to enter the following parameters:

cgcent 37.468 31.798 12.177 # Grid Center
fgcent 37.468 31.798 12.177 # Grid Center

cglen 53.011 58.568 65.807 # coarse mesh lengths (A)
fglen 51.183 54.452 58.710 # fine mesh lengths (A)

dime 97 97 97 # Grid Points

d. Run APBS
> apbs apbs.in
After a while, it will create an electrostatics map called "pymol.dx".

just use vmd to import both .pdb and .dx file. Then choose drawing method to be surf, and coloring method to be volume. Then change the color scale data range in Trajectory bar to be like -8.00 to 8.00.

Beautiful plot appeared.!

blue surface : positively charged
red surface : negatively charged
white surface : neutral