V.Kairys, M.K. Gilson, V. Lather, C.A. Schiffer, M.X. Fernandes

Programs to create substrate envelope grid,
evaluate volume of ligand outside of substrate envelope,
and to convert the grid into DX format readable by some
molecular graphics programs (such as VMD):

createsubstrenvelope.f
evaluatesubstrenvelope.f
convertsubstrenvelope.f


1. Compilation 

gfortran -o execname -O2 program.f

Each program compiled individually

2. Usage and some notes.

(A) creation of substrate envelope grid

createsubstrenvelope
	and follow  instructions

This will require specially prepared pdb file. See below and also an example: 
1TSNTHF_sub.pdb

In short, the substrate envelope pdb file has the following format, assuming
for example 3 substrates, containing just 3 atoms each, for simplicity:

PART 1
MOL 1  ! Comment: 1RF7
HETATM 1270  N1  DHF   161      32.087  34.145  13.145  1.00 15.16           N
HETATM 1271  C2  DHF   161      32.933  33.113  13.164  1.00 19.10           C
HETATM 1272  NA2 DHF   161      32.685  32.047  13.605  1.00 24.53           N
ENDMOL 1
MOL 2  ! 1RA2
HETATM 1270  N1  FOL   161      32.108  34.347  12.862  1.00 16.64           N
HETATM 1271  C2  FOL   161      32.971  33.364  12.870  1.00 22.42           C
HETATM 1272  NA2 FOL   161      32.685  32.175  13.192  1.00 15.83           N
ENDMOL 2
MOL 3  ! 1RB2
HETATM 1270  N1  FOL A 161      31.811  34.113  12.926  1.00 19.26           N
HETATM 1271  C2  FOL A 161      32.624  33.017  12.975  1.00 50.45           C
HETATM 1272  NA2 FOL A 161      32.228  31.861  13.376  1.00 25.39           N
ENDMOL 3

In the example 1TSNTHF_sub.pdb  there is one substrate, since
for the original article we used one substrate only.

Make sure the substrates are properly superimposed!

HETATM could be replaced by ATOM.


(B) evaluatesubstrenvelope

evaluatesubstrenvelope gridfile.grd ligfile.pdb protfile.pdb

(C) Conversion of substrate envelope grid into a grid DX format

convertsubstrenvelope gridfile.grd

======================================================
NOTES:

If you use this program in your work, please reference:
V.Kairys, M.K. Gilson, V. Lather, C.A. Schiffer, M.X. Fernandes,Chem. Biol. Drug Des. 2009, v. 74, p.234-45.

For bug reports and questions please email to Visvaldas Kairys <kairys!at!uma.pt>