Hi,
I got the individual HADDOCK scores of structures from file.nam_clust4_haddock-score and the energy values for each structure from file.nam_clust4_ener and file.nam_clust4_Edesolv. As I calculate the HADDOCK score manually using the formula, few of them do not match the scores given in the haddock scores list. Please help with this.
Thank you
Well, which formula did you use?
I used the formula
HADDOCK-score itw = 1.0Evdw + 0.2Eelec + 1.0Edesolv + 0.1Eair
Some haddock scores match but some dont.
Following are the haddock scores and Energies
#struc haddock-score
complex_71w.pdb -92.519967
complex_139w.pdb -78.5782
complex_73w.pdb -71.236331875
complex_105w.pdb -65.8885034
complex_70w.pdb -60.32378
complex_106w.pdb -57.583671
complex_83w.pdb -55.47685
complex_113w.pdb -54.8341638
complex_146w.pdb -52.233659
complex_149w.pdb -50.36044
complex_80w.pdb -48.4914
complex_131w.pdb -39.44707
complex_85w.pdb -33.35439
complex_195w.pdb -32.57694
#struc Einter Enb Evdw+0.1Eelec Evdw Eelec Eair Ecdih Ecoup Esani Evean Edani
complex_71w.pdb -167.358 -224.467 -88.3176 -73.1899 -151.277 69.2096 0 0 0 0 0
complex_139w.pdb -98.6412 -209.529 -87.4771 -73.9158 -135.613 110.887 0 0 0 0 0
complex_73w.pdb -91.0107 -168.78 -73.3652 -62.7635 -106.017 88.9109 0 0 0 0 0
complex_105w.pdb -52.6849 -129.457 -69.0203 -62.3051 -67.1522 82.4548 0 0 0 0 0
complex_70w.pdb -16.2516 -128.616 -72.9746 -66.7922 -61.8241 112.365 0 0 0 0 0
complex_106w.pdb -65.6898 -127.36 -51.894 -43.5089 -83.8514 104.49 0 0 0 0 0
complex_83w.pdb -56.795 -130.775 -63.8871 -56.4552 -74.3195 77.0258 0 0 0 0 0
complex_113w.pdb 16.7689 -132.951 -70.0504 -63.0614 -69.8898 155.033 0 0 0 0 0
complex_146w.pdb -18.01 -109.23 -68.1418 -63.5765 -45.6534 91.3529 0 0 0 0 0
complex_149w.pdb -69.3405 -153.544 -58.31 -47.7284 -105.816 84.2036 0 0 0 0 0
complex_80w.pdb -2.43086 -147.25 -62.8713 -53.4958 -93.7547 144.82 0 0 0 0 0
complex_131w.pdb 48.0409 -120.91 -56.5249 -49.371 -71.5393 168.951 0 0 0 0 0
complex_85w.pdb 72.222 -102.274 -53.3828 -47.9505 -54.3233 174.496 0 0 0 0 0
complex_195w.pdb 0.948263 -136.951 -45.7366 -35.6017 -101.349 137.899 0 0 0 0 0
#struc Edesolv
complex_71w.pdb 15.3953
complex_139w.pdb 11.3715
complex_73w.pdb 10.5739
complex_105w.pdb 10.4342
complex_70w.pdb 7.59674
complex_106w.pdb 8.42244
complex_83w.pdb 10.9582
complex_113w.pdb 10.2056
complex_146w.pdb 14.0982
complex_149w.pdb 10.1108
complex_80w.pdb 9.27334
complex_131w.pdb 7.33669
complex_85w.pdb 8.01117
complex_195w.pdb 9.50466
Also was this run on the server or locally?
Note that the scoring function can include more terms depending on what kind of data you are using and also if solvated docking is used or not
Do you have other energy terms enabled? E.g. symmetry?
Other types of restraints?
It was run on HADDOCK server. And solvated docking is used. Rest options were all chosen as default. Its a Protein-DNA docking by the way.
That explains, then the interfacial water-protein energies should also be included. You find those in the header of the PDB files.
Do I find it here? Then I have add that value to the score?
REMARK FILENAME=“complex_71w.pdb0”
REMARK ===============================================================
REMARK HADDOCK run for complex
REMARK initial structure: complex_71.pdb
REMARK ===============================================================
REMARK total,bonds,angles,improper,dihe,vdw,elec,air,cdih,coup,rdcs,vean,dani,xpcs,rg
REMARK energies: -167.358, 0, 0, 0, 0, -73.1899, -151.277, 69.2096, 0, 0, 0, 0, 0, 0, 0
REMARK ===============================================================
REMARK bonds,angles,impropers,dihe,air,cdih,coup,rdcs,vean,dani,xpcs
REMARK rms-dev.: 0,0,0,0,0.365918,0,0, 0, 0, 0, 0
REMARK ===============================================================
REMARK air,cdih,coup,rdcs,vean,dani,xpcs
REMARK >0.3,>5,>1,>0,>5,>0.2,>0.2
REMARK violations.: 4, 0, 0, 0, 0, 0, 0
REMARK ===============================================================
REMARK CVpartition#,violations,rms
REMARK AIRs cross-validation: 1, 11, 1.00978
REMARK ===============================================================
REMARK NCS energy: 0
REMARK ===============================================================
REMARK Symmetry energy: 0
REMARK ===============================================================
REMARK Membrane restraining energy: 0
REMARK ===============================================================
REMARK Local cross-correlation: 0.0000
REMARK ===============================================================
REMARK Desolvation energy: 15.3953
REMARK Internal energy free molecules: -5005.46
REMARK Internal energy complex: -4785.89
REMARK Binding energy: 10.4964
REMARK ===============================================================
REMARK buried surface area: 1823.22
REMARK ===============================================================
REMARK water - chain_1: -11.2448 -5.19192 -6.05292
REMARK water - chain_2: 1.21903 -5.83981 7.05884
REMARK ===============================================================
REMARK water - water: -2.07509 -0.181703 -1.89339
REMARK ===============================================================
REMARK DATE:08-Oct-2021 12:18:16 created by user: enm009
Also, can I compare the haddock scores of the same complex from different haddock docking results (different Active Residues), after removing the Eair part of the equation?
Please note, all are solvated docking.
Thank you for your response
I would say yes
I could not find the ‘interfacial water-protein energies’ in the header of the PDB files, though. I searched the results folder all over, still could not find.
it was in one of our previous message… The last value is the electrostatic energy, the second one the van der Waals energy. And it is given per chain.