# Heme docking in Haddock

**URL:** <https://ask.bioexcel.eu/t/heme-docking-in-haddock/246>\
**Category:** HADDOCK\
**Created:** [November 22, 2016, 10:11am UTC](https://ask.bioexcel.eu/t/heme-docking-in-haddock/246 "2016-11-22T10:11:53Z")\
**Posts on this page:** 6\
**Page:** 1

<div class="post-metadata">

**Author:** ![sustorn](https://avatars.discourse-cdn.com/v4/letter/s/3da27b/32.png) [@sustorn](https://ask.bioexcel.eu/u/sustorn)\
**Post date:** [November 22, 2016, 10:11am UTC](https://ask.bioexcel.eu/t/heme-docking-in-haddock/246/1 "2016-11-22T10:11:53Z")

</div>

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

---

<div class="post-metadata">

**Author:** ![amjjbonvin](https://dub1.discourse-cdn.com/flex013/user_avatar/ask.bioexcel.eu/amjjbonvin/32/23_2.png) [@amjjbonvin](https://ask.bioexcel.eu/u/amjjbonvin)\
**Post date:** [November 22, 2016, 1:56pm UTC](https://ask.bioexcel.eu/t/heme-docking-in-haddock/246/2 "2016-11-22T13:56:16Z")

</div>

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

```auto
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

```

---

<div class="post-metadata">

**Author:** ![sustorn](https://avatars.discourse-cdn.com/v4/letter/s/3da27b/32.png) [@sustorn](https://ask.bioexcel.eu/u/sustorn)\
**Post date:** [November 22, 2016, 3:00pm UTC](https://ask.bioexcel.eu/t/heme-docking-in-haddock/246/3 "2016-11-22T15:00:30Z")

</div>

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

---

<div class="post-metadata">

**Author:** ![amjjbonvin](https://dub1.discourse-cdn.com/flex013/user_avatar/ask.bioexcel.eu/amjjbonvin/32/23_2.png) [@amjjbonvin](https://ask.bioexcel.eu/u/amjjbonvin)\
**Post date:** [November 22, 2016, 3:22pm UTC](https://ask.bioexcel.eu/t/heme-docking-in-haddock/246/4 "2016-11-22T15:22:16Z")

</div>

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.

---

<div class="post-metadata">

**Author:** ![sustorn](https://avatars.discourse-cdn.com/v4/letter/s/3da27b/32.png) [@sustorn](https://ask.bioexcel.eu/u/sustorn)\
**Post date:** [November 22, 2016, 6:24pm UTC](https://ask.bioexcel.eu/t/heme-docking-in-haddock/246/5 "2016-11-22T18:24:13Z")

</div>

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!

---

<div class="post-metadata">

**Author:** ![amjjbonvin](https://dub1.discourse-cdn.com/flex013/user_avatar/ask.bioexcel.eu/amjjbonvin/32/23_2.png) [@amjjbonvin](https://ask.bioexcel.eu/u/amjjbonvin)\
**Post date:** [November 23, 2016, 8:38am UTC](https://ask.bioexcel.eu/t/heme-docking-in-haddock/246/6 "2016-11-23T08:38:16Z")

</div>

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