g_mmpbsa energy2bfac

This tool maps the binding energy contribution of each residue on the structure. The energy will be written in the B-factor field of the output PDB file/s. These PDB files can be used with any molecular visualizer and residues can be colored according to their energetic contribution. The molecular visualizer should support method to color residues by the B-factor values.

Warning

tpr/tpx file should not contain PBC broken molecule. One may check by generating a PDB file with following command: editconf -f topol.tpr -o check.pdb. Check check.pdb file through visualization.

Execute following command to get full help

g_mmpbsa energy2bfac -h

Command summary

g_mmpbsa energy2bfac [-s [<.tpr/.gro/...>]] [-i [<.dat>]] [-n [<.ndx>]]
                     [-c [<.pdb>]] [-s1 [<.pdb>]] [-s2 [<.pdb>]] [-b <time>]
                     [-e <time>] [-dt <time>] [-tu <enum>] [-[no]w]

Options summary

Options to specify input files:

-s      [<.tpr/.gro/...>]  (topol.tpr)
        Structure+mass(db): tpr gro g96 pdb brk ent
-i      [<.dat>]           (decomp_energy.dat)
        Generic data file
-n      [<.ndx>]           (index.ndx)      (Opt.)
        Index file

Options to specify output files:

-c      [<.pdb>]           (complex.pdb)    (Opt.)
        Protein data bank file
-s1     [<.pdb>]           (subunit_1.pdb)  (Opt.)
        Protein data bank file
-s2     [<.pdb>]           (subunit_2.pdb)  (Opt.)
        Protein data bank file

Other options:

-b      <time>             (0)
        Time of first frame to read from trajectory (default unit ps)
-e      <time>             (0)
        Time of last frame to read from trajectory (default unit ps)
-dt     <time>             (0)
        Only use frame when t MOD dt = first time (default unit ps)
-tu     <enum>             (ps)
        Unit for time values: fs, ps, ns, us, ms, s
-[no]w                     (no)
        View output .xvg, .xpm, .eps and .pdb files

Description

-s topol.tpr

Input tpr/tpx file of molecule

-n index.ndx

Input atomic index file. User will get choice to select atomic groups

-i decomp_energy.dat

File containing energy contribution of each residue obtained from g_mmpbsa decompose. One can use -i energyMapIn.dat directly for the input.

-c complex.pdb

Output PDB file of molecular complex taken for the calculation, e.g. protein-ligand, protein-DNA or protein-protein.

-s1 subunit_1.pdb

Output PDB file of first sub-unit in accordance with first atomic group chosen through index file.

-s2 subunit_2.pdb

Output PDB file of second sub-unit in accordance with second atomic group chosen through index file.