Auxiliary programs used by MM-PBSA

The MSMS program

The MSMS program is not distributed with this script and may be downloaded from the site:

http://www.scripps.edu/pub/olson-web/people/sanner/home.html

The GB program

The GB program is distributed with this script as a courtesy of Drs. D. L. Beveridge and B. Jayaram. (Note that this is a slightly different implementation of the generalized Born model than is provided in the sander program.) You need to provide the amber94_GB.crg and amber94_GB.siz files for my program pdb_for_GB, which prepares *.pdb.GB file for GB program, which contains along with PDB format also charges and vdW radii.

Example files are distributed with this script:

amber94_GB.crg -- parm94 charges (four significant digits after decimal point)
amber94_GB.siz -- van der Waals parameters from parm94 scaled accordingly
see B. Jayaram, D. Sprous, D. L. Beveridge, JPC, 102 (1998) 9571

The pdb_for_GB program

GB_CRG=file_name_for_charges
GB_SIZ=file_name_for_vdW_Radii
optional words and parameters:
DEFAULT <-- the conversion factor=1/(2.)**(1./6.) will be used,
see Jayaram et. al.JPC, 102 (1998) 9571
CONV=some_number <-- conversion factor
otherwise conversion factor=1/(2.)**(1./6.) will be used

The Delphi program

http://honiglab.cpmc.columbia.edu/

You need to provide the amber94_delphi.crg charges file for DelPhi and my_delphi.siz -- file with van der Waals Radii for DelPhi Example files are distributed with this script in PARAMETERS directory:

amber94_delphi.crg -- parm94 charges (three significant digits after
decimal point no nucleic acids parameters)
amber94_delphi.crg_4 -- parm94 charges (four significant digits after
decimal point)
my_delphi.siz -- van der Waals parameters (OPLS-like)

etc... see PARAMETERS/0README for details

NOTE 1: that my_delphi.siz, a file with van der Waals radii for DelPhi, does not have a definition for phosphorous. It contains entries only for C, O, N, H, and S.

NOTE 2: Also the change should be made to the beginning of the amber94_delphi.crg file to fit your protein. If this is a DNA or other biomolecule of non-protein origin then this file should be totally replaced with the charges corresponding to your molecule. Do not forget to add charges for your ligand if you have one.

NOTE 3: For proteins you can use my file amber94_delphi.crg or amber94_delphi.crg_4. Do not forget to rename it as amber94_delphi.crg. Also you have to provide the N- and C-termini charges. In my case, this is Glu-1 and Val-88. You can find the C-terminus atomic charges in file: $AMBERHOME/dat/all_aminoct94.in and N-terminal atomic charges in file: $AMBERHOME/dat/all_aminont94.in

DO NOT FORGET TO REMOVE MY LINES FOR THE C- AND N-terminal groups from amber94_delphi.crg and add yours, otherwise Val-88 would have C-terminus charges if you coincidentally have one!!!

Here is an amber94_delphi.crg EXAMPLE:

!Amber parm94 charges
atom__resnumbc_charge_
N GLU 1 0.002
H1 GLU 1 0.239
H2 GLU 1 0.239
H3 GLU 1 0.239
CA GLU 1 0.059
HA GLU 1 0.120
CB GLU 1 0.092
HB2 GLU 1 -0.023
HB3 GLU 1 -0.023
2HB GLU 1 -0.023
3HB GLU 1 -0.023
CG GLU 1 -0.024
HG2 GLU 1 -0.032
HG3 GLU 1 -0.032
2HG GLU 1 -0.032
3HG GLU 1 -0.032
CD GLU 1 0.809
OE1 GLU 1 -0.819
OE2 GLU 1 -0.819
C GLU 1 0.562
O GLU 1 -0.589
N VAL 88 -0.382
H VAL 88 0.268
CA VAL 88 -0.345
HA VAL 88 0.143
CB VAL 88 0.193
HB VAL 88 0.030
CG1 VAL 88 -0.306
HG11 VAL 88 0.084
HG12 VAL 88 0.084
HG13 VAL 88 0.084
1HG1 VAL 88 0.084
2HG1 VAL 88 0.084
3HG1 VAL 88 0.084
CG2 VAL 88 -0.306
HG21 VAL 88 0.084
HG22 VAL 88 0.084
HG23 VAL 88 0.084
1HG2 VAL 88 0.084
2HG2 VAL 88 0.084
3HG2 VAL 88 0.084
C VAL 88 0.835
O VAL 88 -0.817
OXT VAL 88 -0.817
N ALA -0.416
H ALA 0.272
and etc...