Pair-wise interaction terms

[Matthew H Bakalar]

Is there any way to output all pairwise interaction terms with non-zero energy? I have tried using --atom_terms, but I am having trouble interpreting the ouput. It appears that that columns 'atomid' and 'el' are both empty:

atomid el pos gauss(o=0,_w=0.8,_c=8) repulsion(o=0,_c=8) hydrophobic(g=0,_b=2.5,_c=8) non_dir_h_bond(g=-0.6,_b=0,_c=8)
<17.493,10.3809,14.0701> -0.0350395 0 -0 -0
<17.7062,9.7887,15.458> -0.000693863 0 -0 -0
<18.7655,10.6829,13.4257> -0.0168031 0 -0 -0
<16.6797,9.40742,13.2145> -0.0307793 0 -0.16949 -0

What I would like is something where each row represents a pair of atoms along with the value of each energy term from the pair.
Thanks for the help

[David Koes]

Hmm.. unfortunately the atoms only have ids and named elements if the input file is a pdb (or something that internally gets converted to a pdb - not an sdf). If you provide pdb formatted inputs do you get reasonable atom term output?

In any case, there's no facility for outputing the individual pairwise interactions.

[Matthew H Bakalar]

No. I am using a PDB input for both the ligand and receptor, and am getting ids. No way to output pairwise interactions is too bad! Thanks for the help.

[David Koes]

What if it is a pdbqt?

[Matthew H Bakalar]

Same output with a pdbqt as ligand input.

[Matthew H Bakalar]

The ligand I am docking is a peptide, and my intention is to group atom terms by residue.

[David Koes]

If I specify the ligand as a pdbqt, I get the expected atom identifiers. Does your file end in pdbqt?

dkoes@jedi:~/tmp$ smina -r rec.pdb -l lig.pdbqt  --score_only --atom_terms atoms
   _______  _______ _________ _        _______ 
  (  ____ \(       )\__   __/( (    /|(  ___  )
  | (    \/| () () |   ) (   |  \  ( || (   ) |
  | (_____ | || || |   | |   |   \ | || (___) |
  (_____  )| |(_)| |   | |   | (\ \) ||  ___  |
        ) || |   | |   | |   | | \   || (   ) |
  /\____) || )   ( |___) (___| )  \  || )   ( |
  \_______)|/     \|\_______/|/    )_)|/     \|

smina is based off AutoDock Vina. Please cite appropriately.

Weights      Terms
-0.035579    gauss(o=0,_w=0.5,_c=8)
-0.005156    gauss(o=3,_w=2,_c=8)
0.840245     repulsion(o=0,_c=8)
-0.035069    hydrophobic(g=0.5,_b=1.5,_c=8)
-0.587439    non_dir_h_bond(g=-0.7,_b=0,_c=8)
1.923        num_tors_div

==============================
*** Open Babel Warning  in PerceiveBondOrders
  Failed to kekulize aromatic bonds in OBMol::PerceiveBondOrders

## Name gauss(o=0,_w=0.5,_c=8) gauss(o=3,_w=2,_c=8) repulsion(o=0,_c=8) hydrophobic(g=0.5,_b=1.5,_c=8) non_dir_h_bond(g=-0.7,_b=0,_c=8) num_tors_div
Affinity: -1.02176 (kcal/mol)
Intramolecular energy: 0.01557
Term values, before weighting:
##  7.52471 190.57049 0.62642 13.60170 0.00000 0.00000
Refine time 0.00055
Loop time 0.00136
dkoes@jedi:~/tmp$ cat atoms
atomid el pos gauss(o=0,_w=0.5,_c=8) gauss(o=3,_w=2,_c=8) repulsion(o=0,_c=8) hydrophobic(g=0.5,_b=1.5,_c=8) non_dir_h_bond(g=-0.7,_b=0,_c=8)
    1  N  <85.893,12.591,2.489> -2.78782e-15 -0.0814956 0 -0 -0
    2  CA <84.852,11.736,1.946> -3.62635e-06 -0.121146 0 -0 -0
    3  C  <83.461,12.228,2.332> -1.1655e-05 -0.0965621 0 -0 -0
    5  CB <85.004,10.282,2.454> -0.00574239 -0.142136 0 -0.0608153 -0
    4  O  <82.579,12.324,1.484> -0.0057333 -0.0937174 0 -0 -0
    7  CG <86.454,9.816,2.304> -0.00325474 -0.123925 0 -0.0629948 -0
    6  CG <84.085,9.361,1.668> -0.0866686 -0.184218 0.389567 -0.0925825 -0
    8  CD <86.697,8.386,2.77> -0.166307 -0.139381 0.136782 -0.260605 -0
END