RISM-VMol



Program for visualizing the most probable positions of binding molecules


 * Download:**

0) download 1) Unpack tar -xzf rism-vmol_2012_05_31.tar.gz
 * How to Install:**

2) go to the created folder   cd rism-vmol_2012_05_31

3) compile FFTW library

./makeFFTW

4) compile the source code

./makeAll

5) (optionally) setup paths    export PATH=$PATH:$(pwd)     echo export 'PATH=$PATH:'$(pwd) >> ~/.bashrc

To use the code you will need 1) *.3d distributions calculated with RISM-MOL-3D 2) *.grd grid files for these distributions' 3) solvent.xyz (solvent.pdb) - file in xyz or pdb format with solvent coordinates 4) distributions.txt - file wich defines, which atom in solvent.xyz corresponds to which *.3d distribution 5) solute.xyz (solute.pdb) - file in xyz or pdb format with solute coordinated
 * How to use**

With the code is provided example: cyclodextrine in water distributions Files: CD_in_water_g0.3d - water oxygen distribution around the alpha-cyclodextrine CD_in_water_g1.3d - water hydrogen distribution around the alpha-cyclodextrine CD_in_water_X.grd, CD_in_water_Y.grd, CD_in_water_Z.grd - grid files for distributions CD.xyz - coordinates of cyclodextrine water.xyz - coordinates of water distributions.txt - file which contain three lines: CD_in_water_g0.3d CD_in_water_g1.3d CD_in_water_g1.3d
 * EXAMPLE:**

This means, that in water.xyz file the first atom (oxygen) corresponds to the CD_in_water_g0.3d distibution, and two other atoms (hydrogens) correspond to the CD_in_water_g1.3d distribution

//**STEP1**//: we need to calculate the most probable rotations of the molecules at each point To do this: ./getBestRotationsFast water.xyz distributions.txt CD_in_water CD_in_water 2

Here water.xyz is a solvent file distributions.txt is a distribution correspondance file CD_in_water (first) is the grid prefix (by convention the grid files are prefix_X.grd, prefix_Y.grd, prefix_Z.grd) CD_in_water (second) is the output files prefix 2 is the threshold. The point where all the input distributions are less then the threshold are not considered.

Four files will be created:

CD_in_water_Gmax.3d - maximal water relative density at each point CD_in_water_PhiMax.3d, CD_in_water_PsiMax.3d, CD_in_water_ThetaMax.3d - euler angles at each point which give the maximal water density

To do this: ./createBindingMoleculesXYZ water.xyz CD_in_water CD_in_water 2  > binding.xyz
 * //STEP2://** convert the Gmax and Euler angles to the binding molecules in xyz format.

Here  water.xyz is a solvent file CD_in_water (first) is a grid prefix CD_in_water (second) is a prefix for Gmax and Euler angle files 2 is the threshold. The points where Gmax is less than threshold will not be visualized binding.xyz is the output xyz

//**STEP3:**// convert Gmax to the dx format (readable by vmd) To do this: ./3DtoDX CD_in_water CD_in_water_Gmax.3d CD_in_water_Gmax.dx

Here CD_in_water is the grid prefix CD_in_water_Gmax.3d is the input *.3d file CD_in_water_Gmax.dx is the output *.dx file //**STEP4:**// visualization

Run vmd 1) Open the molecule CD.xyz ( MainMenu-> New Molecule, in the field "filename" type CD.xyz, press load, close the window ) 2) load the 3D distribution ( Main manu, right click on  CD.xyz, select "Load Data into Molecule", at the new window type "CD_in_water_Gmax.dx" in the field "Filename", press load, close the window) 3) load the binding molecules ( MainMenu-> New Molecule, in the field "filename" type binding.xyz, press load, close the window )

Now, you have everything in VMD. To visualize Gmax, go to "Main Menu -> Graphics->representations and create new representation "Isosurface" for CD.xyz )

To make the picture looking good i used the following parameters for the visualizing:

binding.xyz - VDW, sphere size 0.6 CD.xyz - surf, silver color isosurface ( new representation for CD.xyz) - isovalue 2.5, solid color, blue

the result is below: