Heme docking in Haddock

HADDOCK
1

I am trying to use Haddock to dock heme to a couple of proteins but am having trouble with the heme pdb file, in particular how to name the Fe2+ ion. I’ve tried to use HEC as the residue name since this, as far as I understand is described in the topology files used by Haddock. I thought it was working but on close inspection Haddock is complaining about the Fe2+ ion and the last time I tried it wouldn’t run. Please find the last few lines of the heme pdb file below. I would really appreciate any help on this.

Thanks in advance,
Susanna

HETATM 40 C4C HEC A 202 0.364 -3.364 -14.250 1.00 5.95 C
ANISOU 40 C4C HEC A 202 694 666 901 -85 -24 -32 C
HETATM 41 C4D HEC A 202 -0.404 -7.457 -13.263 1.00 6.39 C
ANISOU 41 C4D HEC A 202 919 552 957 -143 2 3 C
HETATM 42 NC HEC A 202 0.117 -3.937 -15.473 1.00 5.95 N
ANISOU 42 NC HEC A 202 826 541 895 -185 -53 -52 N
HETATM 43 FE+2 HEC A 202 -0.143 -5.892 -15.842 1.00 5.79 FE
ANISOU 43 FE+2 HEC A 202 830 527 844 -134 -18 -1 FE

2

Hi Susanna

Here is an example of a heme C molecule supported by HADDOCK. Should be in the PDB as ATOM and not HETATM. The iron should thus be defined as FE

ATOM      1  FE  HEC   400       3.565   0.487   0.949  1.00  0.00
ATOM      2  NA  HEC   400       2.428   0.067  -0.589  1.00  0.00
ATOM      3  NB  HEC   400       2.047   1.349   1.835  1.00  0.00
ATOM      4  NC  HEC   400       4.701   0.907   2.487  1.00  0.00
ATOM      5  ND  HEC   400       5.083  -0.375   0.062  1.00  0.00
ATOM      6  C1A HEC   400       2.777  -0.593  -1.748  1.00  0.00
ATOM      7  CHA HEC   400       4.031  -1.080  -2.015  1.00  0.00
ATOM      8  HA  HEC   400       4.181  -1.584  -2.970  1.00  0.00
ATOM      9  C4D HEC   400       5.111  -0.982  -1.176  1.00  0.00
ATOM     10  C1B HEC   400       0.758   1.490   1.367  1.00  0.00
ATOM     11  CHB HEC   400       0.320   1.028   0.153  1.00  0.00
ATOM     12  HB  HEC   400      -0.725   1.202  -0.104  1.00  0.00
ATOM     13  C4A HEC   400       1.093   0.363  -0.765  1.00  0.00
ATOM     14  C1C HEC   400       4.353   1.567   3.646  1.00  0.00
ATOM     15  CHC HEC   400       3.099   2.054   3.913  1.00  0.00
ATOM     16  HC  HEC   400       2.949   2.558   4.867  1.00  0.00
ATOM     17  C4B HEC   400       2.019   1.956   3.073  1.00  0.00
ATOM     18  C1D HEC   400       6.372  -0.516   0.530  1.00  0.00
ATOM     19  CHD HEC   400       6.810  -0.054   1.745  1.00  0.00
ATOM     20  HD  HEC   400       7.855  -0.228   2.001  1.00  0.00
ATOM     21  C4C HEC   400       6.037   0.611   2.662  1.00  0.00
ATOM     22  C2A HEC   400       1.657  -0.708  -2.647  1.00  0.00
ATOM     23  CAA HEC   400       1.655  -1.356  -3.989  1.00  0.00
ATOM     24 HAA1 HEC   400       0.763  -1.959  -4.084  1.00  0.00
ATOM     25 HAA2 HEC   400       2.520  -1.997  -4.069  1.00  0.00
ATOM     26  CBA HEC   400       1.688  -0.336  -5.128  1.00  0.00
ATOM     27 HBA1 HEC   400       0.817   0.300  -5.068  1.00  0.00
ATOM     28 HBA2 HEC   400       1.689  -0.855  -6.076  1.00  0.00
ATOM     29  CGA HEC   400       2.952   0.518  -5.012  1.00  0.00
ATOM     30  O1A HEC   400       3.380   1.048  -6.024  1.00  0.00
ATOM     31  O2A HEC   400       3.469   0.628  -3.913  1.00  0.00
ATOM     32  C3A HEC   400       0.609  -0.113  -2.035  1.00  0.00
ATOM     33  CMA HEC   400      -0.775   0.023  -2.569  1.00  0.00
ATOM     34 HMA1 HEC   400      -0.815  -0.376  -3.572  1.00  0.00
ATOM     35 HMA2 HEC   400      -1.053   1.067  -2.586  1.00  0.00
ATOM     36 HMA3 HEC   400      -1.460  -0.522  -1.937  1.00  0.00
ATOM     37  C2B HEC   400      -0.075   2.186   2.315  1.00  0.00
ATOM     38  CMB HEC   400      -1.518   2.521   2.156  1.00  0.00
ATOM     39 HMB1 HEC   400      -1.899   2.055   1.259  1.00  0.00
ATOM     40 HMB2 HEC   400      -1.633   3.592   2.081  1.00  0.00
ATOM     41 HMB3 HEC   400      -2.068   2.158   3.011  1.00  0.00
ATOM     42  C3B HEC   400       0.710   2.476   3.377  1.00  0.00
ATOM     43  CAB HEC   400       0.302   3.192   4.617  1.00  0.00
ATOM     44  HAB HEC   400       0.638   4.217   4.569  1.00  0.00
ATOM     45  CBB HEC   400       0.841   2.537   5.891  1.00  0.00
ATOM     46 HBB1 HEC   400       1.196   1.544   5.662  1.00  0.00
ATOM     47 HBB2 HEC   400       0.052   2.477   6.626  1.00  0.00
ATOM     48 HBB3 HEC   400       1.654   3.129   6.283  1.00  0.00
ATOM     49  C2C HEC   400       5.472   1.682   4.545  1.00  0.00
ATOM     50  CMC HEC   400       5.475   2.330   5.886  1.00  0.00
ATOM     51 HMC1 HEC   400       4.622   2.987   5.970  1.00  0.00
ATOM     52 HMC2 HEC   400       6.383   2.902   6.008  1.00  0.00
ATOM     53 HMC3 HEC   400       5.421   1.571   6.653  1.00  0.00
ATOM     54  C3C HEC   400       6.520   1.087   3.932  1.00  0.00
ATOM     55  CAC HEC   400       7.905   0.951   4.467  1.00  0.00
ATOM     56  HAC HEC   400       8.472   1.838   4.228  1.00  0.00
ATOM     57  CBC HEC   400       7.941   0.712   5.978  1.00  0.00
ATOM     58 HBC1 HEC   400       6.953   0.450   6.325  1.00  0.00
ATOM     59 HBC2 HEC   400       8.271   1.611   6.476  1.00  0.00
ATOM     60 HBC3 HEC   400       8.626  -0.094   6.198  1.00  0.00
ATOM     61  C2D HEC   400       7.204  -1.212  -0.417  1.00  0.00
ATOM     62  CMD HEC   400       8.647  -1.547  -0.258  1.00  0.00
ATOM     63 HMD1 HEC   400       8.984  -1.233   0.719  1.00  0.00
ATOM     64 HMD2 HEC   400       9.221  -1.036  -1.017  1.00  0.00
ATOM     65 HMD3 HEC   400       8.783  -2.613  -0.360  1.00  0.00
ATOM     66  C3D HEC   400       6.419  -1.502  -1.479  1.00  0.00
ATOM     67  CAD HEC   400       6.828  -2.218  -2.720  1.00  0.00
ATOM     68 HAD1 HEC   400       5.945  -2.603  -3.208  1.00  0.00
ATOM     69 HAD2 HEC   400       7.468  -3.046  -2.451  1.00  0.00
ATOM     70  CBD HEC   400       7.577  -1.310  -3.697  1.00  0.00
ATOM     71 HBD1 HEC   400       8.323  -1.887  -4.225  1.00  0.00
ATOM     72 HBD2 HEC   400       8.059  -0.513  -3.150  1.00  0.00
ATOM     73  CGD HEC   400       6.588  -0.715  -4.701  1.00  0.00
ATOM     74  O1D HEC   400       6.218  -1.418  -5.626  1.00  0.00
ATOM     75  O2D HEC   400       6.218   0.435  -4.527  1.00  0.00
END
3

Thanks for the reply!
I tried the docking with the heme c coordinates you sent but it still doesn’t work. I get the following error message from Haddock:

waiting for the psf files…
waiting for /home/enmr/services-enmr/HADDOCK2.2/server/run/userrun000026/run1/begin/protein2.psf…
waiting for /home/enmr/services-enmr/HADDOCK2.2/server/run/userrun000026/run1/begin/protein2.pdb…
waiting for /home/enmr/services-enmr/HADDOCK2.2/server/run/userrun000026/run1/begin/protein2.psf…
waiting for /home/enmr/services-enmr/HADDOCK2.2/server/run/userrun000026/run1/begin/protein2.pdb…
waiting for /home/enmr/services-enmr/HADDOCK2.2/server/run/userrun000026/run1/begin/protein2.psf…
waiting for /home/enmr/services-enmr/HADDOCK2.2/server/run/userrun000026/run1/begin/protein2.pdb…
waiting for /home/enmr/services-enmr/HADDOCK2.2/server/run/userrun000026/run1/begin/protein2.psf…
waiting for /home/enmr/services-enmr/HADDOCK2.2/server/run/userrun000026/run1/begin/protein2.pdb…
waiting for /home/enmr/services-enmr/HADDOCK2.2/server/run/userrun000026/run1/begin/protein2.psf…
waiting for /home/enmr/services-enmr/HADDOCK2.2/server/run/userrun000026/run1/begin/protein2.pdb…
waiting for /home/enmr/services-enmr/HADDOCK2.2/server/run/userrun000026/run1/begin/protein2.psf…
waiting for /home/enmr/services-enmr/HADDOCK2.2/server/run/userrun000026/run1/begin/protein2.pdb…
Error in the topology generation: prot_psf_B could not be created
=> HADDOCK stopped

And in generate_B.out the error message is as follows:

ASSFIL: file protein2.pdb opened.
COOR>ATOM 1 FE HEC 400 3.565 0.487 0.949 1.00 0.00
COOR>ATOM 2 NA HEC 400 2.428 0.067 -0.589 1.00 0.00
CNSsolve>
CNSsolve> show sum(1) ( not(hydrogen) and not(known) )
SELRPN: 0 atoms have been selected out of 75
SHOW: zero atoms selected
CNSsolve> if ( $select = 0 ) then
NEXTCD: condition evaluated as true
CNSsolve> display %INFO: There are no coordinates missing for non-hydrogen atoms
%INFO: There are no coordinates missing for non-hydrogen atoms
CNSsolve> end if
CNSsolve>
CNSsolve> if ( $log_level = verbose ) then
NEXTCD: condition evaluated as false
CNSsolve> set message=normal echo=on end
CNSsolve> else
CNSsolve> set message=off echo=off end
%SELRPN-BYNU-ERR: no valid number 0
%SELRPN error encountered: no valid number
(CNS is in mode: SET ABORT=NORMal END)

ABORT mode will terminate program execution.

Program will stop immediately.

Any ideas?

Thanks,
Susanna

4

Are you using the web server?
Did you define a chain to use? Does the chain exist?

Please send me in private email the link to your run.

5

Yes, I am using the web server. I added the chain name B to the file you sent and defined it in the run. I just tried again and it was the same error message. The link to the run should be arriving in an email.

Thanks!

6

Dear Susanna

You had run into an issue appearing only when docking a single heme into a protein (the result of a recent addition that should automatically recognise covalently heme groups). This has now been corrected in the production server.

Cheers
Alexandre