The HADDOCK category is meant to discuss any HADDOCK-related issue. For general information about HADDOCK refer to http://www.bonvinlab.org/software/haddock2.2
Hello, I am having some issue with the docking of my ligand with my protein. My ligand is a metal amino acid complex that i obtain from CSD, and it keeps loosing some atoms (the carboxylate oxygen) and dissociating from the metal after docking.
I have prepared the protein accordingly, and my ligand was obtained from both CSD which i then converted into the PDB format and making sure everything was right. The docking was run under the same condition as the tutorial. And it works, kinda, sort of… the issue is that my ligand always falls apart, and the carboxylate oxygens always go missing. I have put in distance restraint on the ligand trying to keep the distance between the coordinating ligand (N, ND1, and OXT) stays around 2 A (or whatever distance they are in the crystal structure) from the metal centre but that still doesn’t solve the issue. I am wondering if there is something i can do to resolve this, perhaps i did something wrong.
This is what i upload as the ligand onto the HADDOCK 2.4 webserver
HETATM 1 CO+2 CO2 A 1 3.910 0.000 1.717 1.00 0.00 CO
HETATM 2 N HIS A 2 3.695 -2.038 2.237 1.00 0.00 N1+
HETATM 3 CA HIS A 2 2.759 -2.624 1.247 1.00 0.00 C
HETATM 4 C HIS A 2 3.115 -2.021 -0.130 1.00 0.00 C
HETATM 5 O HIS A 2 2.747 -2.687 -1.106 1.00 0.00 O
HETATM 6 CB HIS A 2 1.260 -2.279 1.667 1.00 0.00 C
HETATM 7 CG HIS A 2 0.866 -0.919 1.644 1.00 0.00 C
HETATM 8 ND1 HIS A 2 1.749 0.216 1.705 1.00 0.00 N
HETATM 9 CD2 HIS A 2 -0.374 -0.291 1.528 1.00 0.00 C
HETATM 10 CE1 HIS A 2 1.104 1.368 1.683 1.00 0.00 C
HETATM 11 NE2 HIS A 2 -0.224 1.081 1.566 1.00 0.00 N
HETATM 12 OXT HIS A 2 3.762 -0.932 -0.183 1.00 0.00 O1-
HETATM 13 H HIS A 2 4.551 -2.530 2.450 1.00 0.00 H
HETATM 14 H2 HIS A 2 3.141 -2.356 2.983 1.00 0.00 H
HETATM 15 HA HIS A 2 2.870 -3.688 1.269 1.00 0.00 H
HETATM 16 HB2 HIS A 2 1.077 -2.664 2.697 1.00 0.00 H
HETATM 17 HB3 HIS A 2 0.509 -2.764 1.028 1.00 0.00 H
HETATM 18 HD2 HIS A 2 -1.343 -0.832 1.434 1.00 0.00 H
HETATM 19 HE1 HIS A 2 1.637 2.372 1.771 1.00 0.00 H
HETATM 20 HE2 HIS A 2 -0.966 1.748 1.485 1.00 0.00 H
HETATM 21 N HIS A 3 4.107 0.979 3.661 1.00 0.00 N1+
HETATM 22 C HIS A 3 4.778 2.712 2.002 1.00 0.00 C
HETATM 23 CA HIS A 3 5.055 2.082 3.385 1.00 0.00 C
HETATM 24 O HIS A 3 5.285 3.848 1.820 1.00 0.00 O
HETATM 25 CB HIS A 3 6.583 1.612 3.382 1.00 0.00 C
HETATM 26 CG HIS A 3 6.948 0.852 2.176 1.00 0.00 C
HETATM 27 ND1 HIS A 3 6.079 0.155 1.469 1.00 0.00 N
HETATM 28 CD2 HIS A 3 8.158 0.852 1.505 1.00 0.00 C
HETATM 29 CE1 HIS A 3 6.671 -0.434 0.485 1.00 0.00 C
HETATM 30 NE2 HIS A 3 7.987 0.049 0.426 1.00 0.00 N
HETATM 31 OXT HIS A 3 3.989 2.088 1.334 1.00 0.00 O1-
HETATM 32 H HIS A 3 3.288 0.941 4.189 1.00 0.00 H
HETATM 33 H2 HIS A 3 4.490 0.250 4.297 1.00 0.00 H
HETATM 34 HA HIS A 3 4.893 2.755 4.253 1.00 0.00 H
HETATM 35 HB2 HIS A 3 6.877 1.040 4.265 1.00 0.00 H
HETATM 36 HB3 HIS A 3 7.219 2.422 3.719 1.00 0.00 H
HETATM 37 HD2 HIS A 3 9.053 1.382 1.847 1.00 0.00 H
HETATM 38 HE1 HIS A 3 6.185 -1.157 -0.222 1.00 0.00 H
HETATM 39 HE2 HIS A 3 8.646 -0.241 -0.267 1.00 0.00 H
CONECT 1 21 2 8 27
CONECT 1 31 12
CONECT 22 23 31 24
CONECT 4 3 12 5
CONECT 3 4 6 15 2
CONECT 6 3 7 16 17
CONECT 7 6 9 8
CONECT 10 19 8 11
CONECT 9 7 18 11
CONECT 23 22 25 34 21
CONECT 25 23 26 35 36
CONECT 26 25 28 27
CONECT 29 38 27 30
CONECT 28 26 37 30
CONECT 34 23
CONECT 15 3
CONECT 13 2
CONECT 14 2
CONECT 16 6
CONECT 17 6
CONECT 19 10
CONECT 20 11
CONECT 18 9
CONECT 32 21
CONECT 33 21
CONECT 35 25
CONECT 36 25
CONECT 38 29
CONECT 39 30
CONECT 37 28
CONECT 21 1 23 32 33
CONECT 2 1 3 13 14
CONECT 8 1 7 10
CONECT 11 10 9 20
CONECT 27 1 26 29
CONECT 30 29 28 39
CONECT 31 1 22
CONECT 12 1 4
CONECT 5 4
CONECT 24 22
MASTER 0 0 0 0 0 0 0 0 39 0 39 0
END
and this is the restraint TBL file
assign (name CO2 and segid A and resi 1) (name N and segid A and resi 2) 2.19 2.19 0
assign (name CO2 and segid A and resi 1) (name OXT and segid A and resi 2) 2.12 2.12 0
assign (name CO2 and segid A and resi 1) (name ND1 and segid A and resi 2) 2.19 2.19 0
assign (name CO2 and segid A and resi 1) (name N and segid A and resi 3) 2.11 2.11 0
assign (name CO2 and segid A and resi 1) (name OXT and segid A and resi 3) 2.12 2.12 0
assign (name CO2 and segid A and resi 1) (name ND1 and segid A and resi 3) 2.17 2.17 0
but this is the file for the ligand in the begin folder after i download the run
REMARK FILENAME=“protein2.pdb”
REMARK peptide link removed (applied DPEP): from 2 to 3
REMARK coordinates built for atom: HIS 2 HN
REMARK coordinates built for atom: HIS 2 HD1
REMARK coordinates built for atom: HIS 2 HE2
REMARK coordinates built for atom: HIS 3 HN
REMARK coordinates built for atom: HIS 3 HD1
REMARK coordinates built for atom: HIS 3 HE2
REMARK DATE:18-Apr-2020 20:04:19 created by user: enmr
REMARK VERSION:1.3U
ATOM 1 CO+2 CO2 B 1 3.910 0.000 1.717 1.00 15.00 B CO+2
ATOM 2 N HIS B 2 3.695 -2.038 2.237 1.00 15.00 B N
ATOM 3 HN HIS B 2 4.657 -2.043 2.048 1.00 15.00 B H
ATOM 4 CA HIS B 2 2.759 -2.624 1.247 1.00 15.00 B C
ATOM 5 CB HIS B 2 1.260 -2.279 1.667 1.00 15.00 B C
ATOM 6 CG HIS B 2 0.866 -0.919 1.644 1.00 15.00 B C
ATOM 7 ND1 HIS B 2 1.749 0.216 1.705 1.00 15.00 B N
ATOM 8 HD1 HIS B 2 2.723 0.149 1.759 1.00 15.00 B H
ATOM 9 CD2 HIS B 2 -0.374 -0.291 1.528 1.00 15.00 B C
ATOM 10 CE1 HIS B 2 1.104 1.368 1.683 1.00 15.00 B C
ATOM 11 NE2 HIS B 2 -0.224 1.081 1.566 1.00 15.00 B N
ATOM 12 HE2 HIS B 2 -0.948 1.740 1.517 1.00 15.00 B H
ATOM 13 C HIS B 2 3.115 -2.021 -0.130 1.00 15.00 B C
ATOM 14 O HIS B 2 2.747 -2.687 -1.106 1.00 15.00 B O
ATOM 15 N HIS B 3 4.107 0.979 3.661 1.00 15.00 B N
ATOM 16 HN HIS B 3 4.256 0.105 3.244 1.00 15.00 B H
ATOM 17 CA HIS B 3 5.055 2.082 3.385 1.00 15.00 B C
ATOM 18 CB HIS B 3 6.583 1.612 3.382 1.00 15.00 B C
ATOM 19 CG HIS B 3 6.948 0.852 2.176 1.00 15.00 B C
ATOM 20 ND1 HIS B 3 6.079 0.155 1.469 1.00 15.00 B N
ATOM 21 HD1 HIS B 3 5.122 0.088 1.658 1.00 15.00 B H
ATOM 22 CD2 HIS B 3 8.158 0.852 1.505 1.00 15.00 B C
ATOM 23 CE1 HIS B 3 6.671 -0.434 0.485 1.00 15.00 B C
ATOM 24 NE2 HIS B 3 7.987 0.049 0.426 1.00 15.00 B N
ATOM 25 HE2 HIS B 3 8.652 -0.156 -0.264 1.00 15.00 B H
ATOM 26 C HIS B 3 4.778 2.712 2.002 1.00 15.00 B C
ATOM 27 O HIS B 3 5.285 3.848 1.820 1.00 15.00 B O
END
and the ligand lost its carboxylate oxygen before the start of the docking, and is no longer coordinating the metal.
Like many others, I am turning to computational work since the beginning of the lockdown, so I am very much a novice when it comes to this. So any recommendation on this would help! Thanks!!!
Hi Wayne
First of all, probably not a good idea to call your ligand HIS… This is overlapping with amino acids and is asking for problems.
What is your ligand? Is it a tripeptide consisting of 3 Histidines coordinating a metal ion?
If this is the case, simply define it as a protein, using ATOM statements and the proper way of defining the ion as explained at:
https://bianca.science.uu.nl/haddock2.4/library
You might also want to define a few distance restraints between your metal and its coordinating atoms, to keep it in place.
Hi Alexandre,
The CCDC deposition number for my ligand is 1128809. It is bis-(L-histidino)cobalt(II) with two free histidine coordinating the cobalt ion. I put residue 1 as the cobalt ion, and residue 2 and 3 as the two free histidines. The restraint TBL file i use was the following (I am not too sure if I am doing it right, but they are the coordinating atoms)
thank you so much for the suggestion!
Your restraints seem correct to me. I would however suggest not to put the smallest molecule as first, but rather the largest.
Especially if you will be using RMSD for clustering.
1 Like
Hi Alexandre,
So I have made the changes as you suggested, i.e. putting the smallest molecule last and renaming the ligand something other than HIS
I decided to try it with the original ligand, bis(L-histidinato)nickel(II) that was in the original protein crystal structure, with all your recommended adjustments. (this complex is similar to the aforementioned one, instead it has a nickel ion instead of cobalt ion)
the ligand i used in this test run:
HETATM 1 N NIH A 1 -3.684 35.402 -18.305 1.00 0.00 N
HETATM 2 CA NIH A 1 -2.632 36.391 -18.081 1.00 0.00 C
HETATM 3 C NIH A 1 -1.851 36.748 -19.342 1.00 0.00 C
HETATM 4 O NIH A 1 -1.319 37.864 -19.486 1.00 0.00 O
HETATM 5 CB NIH A 1 -1.657 35.917 -17.010 1.00 0.00 C
HETATM 6 CG NIH A 1 -0.641 34.934 -17.500 1.00 0.00 C
HETATM 7 ND1 NIH A 1 -0.943 33.914 -18.388 1.00 0.00 N1+
HETATM 8 CD2 NIH A 1 0.681 34.810 -17.234 1.00 0.00 C
HETATM 9 CE1 NIH A 1 0.140 33.205 -18.633 1.00 0.00 C
HETATM 10 NE2 NIH A 1 1.145 33.731 -17.948 1.00 0.00 N
HETATM 11 OXT NIH A 1 -1.731 35.917 -20.238 1.00 0.00 O1-
HETATM 12 H NIH A 1 -3.982 34.889 -17.444 1.00 0.00 H
HETATM 13 H2 NIH A 1 -4.502 35.849 -18.778 1.00 0.00 H
HETATM 14 HB2 NIH A 1 -1.083 36.789 -16.625 1.00 0.00 H
HETATM 15 HE2 NIH A 1 2.134 33.398 -17.968 1.00 0.00 H
HETATM 16 HE1 NIH A 1 1.283 35.435 -16.588 1.00 0.00 H
HETATM 17 HD2 NIH A 1 0.230 32.407 -19.356 1.00 0.00 H
HETATM 18 HA NIH A 1 -3.131 37.299 -17.673 1.00 0.00 H
HETATM 19 HB3 NIH A 1 -2.209 35.506 -16.138 1.00 0.00 H
HETATM 20 N NIH A 2 -4.246 34.623 -21.489 1.00 0.00 N
HETATM 21 CA NIH A 2 -4.195 34.172 -22.877 1.00 0.00 C
HETATM 22 C NIH A 2 -5.573 34.183 -23.551 1.00 0.00 C
HETATM 23 OXT NIH A 2 -6.572 33.781 -22.948 1.00 0.00 O1-
HETATM 24 CB NIH A 2 -3.582 32.774 -22.952 1.00 0.00 C
HETATM 25 CG NIH A 2 -2.102 32.760 -22.745 1.00 0.00 C
HETATM 26 ND1 NIH A 2 -1.470 33.576 -21.834 1.00 0.00 N1+
HETATM 27 CD2 NIH A 2 -1.126 32.032 -23.340 1.00 0.00 C
HETATM 28 CE1 NIH A 2 -0.167 33.355 -21.875 1.00 0.00 C
HETATM 29 NE2 NIH A 2 0.066 32.421 -22.780 1.00 0.00 N
HETATM 30 O NIH A 2 -5.724 34.590 -24.711 1.00 0.00 O
HETATM 31 H NIH A 2 -4.410 35.656 -21.498 1.00 0.00 H
HETATM 32 H2 NIH A 2 -5.101 34.208 -21.054 1.00 0.00 H
HETATM 33 HB2 NIH A 2 -3.751 32.338 -23.961 1.00 0.00 H
HETATM 34 HD2 NIH A 2 -1.240 31.277 -24.107 1.00 0.00 H
HETATM 35 HE1 NIH A 2 0.573 33.762 -21.203 1.00 0.00 H
HETATM 36 HE2 NIH A 2 1.002 32.020 -23.010 1.00 0.00 H
HETATM 37 HB3 NIH A 2 -4.085 32.104 -22.221 1.00 0.00 H
HETATM 38 HA NIH A 2 -3.529 34.830 -23.482 1.00 0.00 H
HETATM 39 NI+2 NI2 A 3 -2.666 34.185 -19.767 1.00 0.00 Ni2+
END
and the distance constraint
assign (name NI2 and segid A and resi 3) (name N and segid A and resi 1) 2.158 2.158 0
assign (name NI2 and segid A and resi 3) (name OXT and segid A and resi 1) 2.024 2.024 0
assign (name NI2 and segid A and resi 3) (name ND1 and segid A and resi 1) 2.223 2.223 0
assign (name NI2 and segid A and resi 3) (name N and segid A and resi 2) 2.378 2.378 0
assign (name NI2 and segid A and resi 3) (name ND1 and segid A and resi 2) 2.465 2.465 0
It all seems fine, (no missing atoms!), except it seems to recognize the atom named CA as calcium instead of the alpha carbon which was in the original file, as follow:
REMARK FILENAME=“protein2.pdb”
REMARK coordinates built for atom: NIH 1 HAB
REMARK coordinates built for atom: NIH 1 HAC
REMARK coordinates built for atom: NIH 1 HAA
REMARK coordinates built for atom: NIH 1 HAD
REMARK coordinates built for atom: NIH 2 HAB
REMARK coordinates built for atom: NIH 2 HAC
REMARK coordinates built for atom: NIH 2 HAA
REMARK coordinates built for atom: NIH 2 HAD
REMARK DATE:20-Apr-2020 16:28:19 created by user: enmr
REMARK VERSION:1.3U
ATOM 1 O NIH B 1 -1.319 37.864 -19.486 1.00 15.00 B O
ATOM 2 C NIH B 1 -1.851 36.748 -19.342 1.00 15.00 B C
ATOM 3 OXT NIH B 1 -1.731 35.917 -20.238 1.00 15.00 B O
ATOM 4 CA NIH B 1 -2.632 36.391 -18.081 1.00 15.00 B CA
ATOM 5 N NIH B 1 -3.684 35.402 -18.305 1.00 15.00 B N
ATOM 6 HAB NIH B 1 -4.319 35.749 -18.995 1.00 15.00 B H
ATOM 7 HAC NIH B 1 -3.278 34.550 -18.634 1.00 15.00 B H
ATOM 8 HAA NIH B 1 -4.174 35.232 -17.450 1.00 15.00 B H
ATOM 9 CB NIH B 1 -1.657 35.917 -17.010 1.00 15.00 B C
ATOM 10 CG NIH B 1 -0.641 34.934 -17.500 1.00 15.00 B C
ATOM 11 CD2 NIH B 1 0.681 34.810 -17.234 1.00 15.00 B C
ATOM 12 NE2 NIH B 1 1.145 33.731 -17.948 1.00 15.00 B N
ATOM 13 CE1 NIH B 1 0.140 33.205 -18.633 1.00 15.00 B C
ATOM 14 ND1 NIH B 1 -0.943 33.914 -18.388 1.00 15.00 B N
ATOM 15 HAD NIH B 1 -1.846 33.740 -18.780 1.00 15.00 B H
ATOM 16 O NIH B 2 -5.724 34.590 -24.711 1.00 15.00 B O
ATOM 17 C NIH B 2 -5.573 34.183 -23.551 1.00 15.00 B C
ATOM 18 OXT NIH B 2 -6.572 33.781 -22.948 1.00 15.00 B O
ATOM 19 CA NIH B 2 -4.195 34.172 -22.877 1.00 15.00 B CA
ATOM 20 N NIH B 2 -4.246 34.623 -21.489 1.00 15.00 B N
ATOM 21 HAB NIH B 2 -4.570 33.997 -20.782 1.00 15.00 B H
ATOM 22 HAC NIH B 2 -4.301 35.616 -21.371 1.00 15.00 B H
ATOM 23 HAA NIH B 2 -3.274 34.534 -21.272 1.00 15.00 B H
ATOM 24 CB NIH B 2 -3.582 32.774 -22.952 1.00 15.00 B C
ATOM 25 CG NIH B 2 -2.102 32.760 -22.745 1.00 15.00 B C
ATOM 26 CD2 NIH B 2 -1.126 32.032 -23.340 1.00 15.00 B C
ATOM 27 NE2 NIH B 2 0.066 32.421 -22.780 1.00 15.00 B N
ATOM 28 CE1 NIH B 2 -0.167 33.355 -21.875 1.00 15.00 B C
ATOM 29 ND1 NIH B 2 -1.470 33.576 -21.834 1.00 15.00 B N
ATOM 30 HAD NIH B 2 -1.926 34.233 -21.233 1.00 15.00 B H
ATOM 31 NI+2 NI2 B 3 -2.666 34.185 -19.767 1.00 15.00 B NI+2
END
So I try to fix it by renaming that atom to C1 instead of CA, but when i try to upload the file again, it gave me this error on the web server
An error has occurred, here are the details: DSSP failed to produce an output
I tried renaming all the atoms to C# (e.g. C1 C2 N1 N2 O1 …) and the error persisted. I am not too sure what I can do about this, as when I reverted back to CA, I was allowed to progress to the “input parameter” interface.
Thanks in advance! I hope I’m not being too troublesome.
It all seems fine, (no missing atoms!), except it seems to recognize the atom named CA as calcium instead of the alpha carbon which was in the original file, as follow:
You need to define it as HETATM…
And now you will have three ligands, all with name NIH but different residue numbers, an unconnected… Probably not what you want/
Hi Alexandre,
Yep i have defined it as HETATM. Should I instead actually preparing 3 separate pdb, and just by the distance restraint, putting my ligand together into one cohesive unit?
edit 1: I uploaded it as HETATM, but it seems to convert it back to ATOM
edit 2: I tried separating the ligand into 2 different pdb, that doesn’t seem to be a good idea, and the pdb file containing both the histidine (which is labelled as HETATM) and nickel gives me the same error
An error has occurred, here are the details: DSSP failed to produce an output
I am wondering if we can bypass the DSSP for the ligand…
Please clarify what are your inputs and what is defined as ATOM and what as HETATM.
Molecule 1: Protein+Ligand?
Molecule 2: Ligand?
Also, what are you trying to achieve?
PS: A calciun ion should have CA2 as residue name and CA+2 as atom name. And in case you would define distance restraints to it, make sure to put the atom name between double quotes.
Hi Rodrigo and Alexandre,
These are the molecules I uploaded onto the webserver
Molecule 1 contains the protein alone (ATOM)
Molecule 2 contains the free amino acids (HETATM) and the metal (HETATM)
(or I split them up molecule 2 contains a free amino acid (HETATM) and the metal (HETATM), and molecule 3 contains the last free amino acid (HETATM))
If i input the free amino acid (molecule 2 or 3) as ATOM, the carboxylate oxygen disappear.
in terms of naming, i kept the amino acid atom nomenclature (N CA C O CB CG ND1 CD2 CE1 NE2 OXT H H2 HA HB2 HB3 HD1 HD2 HE1 HE2)
The alpha carbon is recognized as calcium in the docking (as i can see that in “protein2.pdb” in the “begin” folder, where the line for CA is left-shifted just like other metals, while other elements were all correct), and when i open up the pdb it is represented as a calcium atom instead of a carbon.
So i just change that CA => C1 (or any other names really) and that resulted to the DSSP error.
The DSSP error persisted if i changed all atom names to C1 C2 C3 N1 N2 … the only thing it worked was to keep it as CA.
Thank you for your help!
If i input the free amino acid (molecule 2 or 3) as ATOM, the carboxylate oxygen disappear.
Still this is the simplest way to do it.
The carboxylate disappear because by default the termini for peptides are set to uncharged. But you can change that.
Oh, thanks! I should give it a try then!
Just an update.
So I listed the two histidines as separate chain, and set them as charged N and C termini.
and the uploaded pdb file of the ligand is as such
ATOM 1 N HIS B 1 -3.684 35.402 -18.305 1.00 0.00 N
ATOM 2 CA HIS B 1 -2.632 36.391 -18.081 1.00 0.00 C
ATOM 3 C HIS B 1 -1.851 36.748 -19.342 1.00 0.00 C
ATOM 4 O HIS B 1 -1.319 37.864 -19.486 1.00 0.00 O
ATOM 5 CB HIS B 1 -1.657 35.917 -17.010 1.00 0.00 C
ATOM 6 CG HIS B 1 -0.641 34.934 -17.500 1.00 0.00 C
ATOM 7 ND1 HIS B 1 -0.943 33.914 -18.388 1.00 0.00 N1+
ATOM 8 CD2 HIS B 1 0.681 34.810 -17.234 1.00 0.00 C
ATOM 9 CE1 HIS B 1 0.140 33.205 -18.633 1.00 0.00 C
ATOM 10 NE2 HIS B 1 1.145 33.731 -17.948 1.00 0.00 N
ATOM 11 OXT HIS B 1 -1.731 35.917 -20.238 1.00 0.00 O1-
ATOM 12 H HIS B 1 -3.982 34.889 -17.444 1.00 0.00 H
ATOM 13 H2 HIS B 1 -4.502 35.849 -18.778 1.00 0.00 H
ATOM 14 HB2 HIS B 1 -1.083 36.789 -16.625 1.00 0.00 H
ATOM 15 HE2 HIS B 1 2.134 33.398 -17.968 1.00 0.00 H
ATOM 16 HE1 HIS B 1 1.283 35.435 -16.588 1.00 0.00 H
ATOM 17 HD2 HIS B 1 0.230 32.407 -19.356 1.00 0.00 H
ATOM 18 HA HIS B 1 -3.131 37.299 -17.673 1.00 0.00 H
ATOM 19 HB3 HIS B 1 -2.209 35.506 -16.138 1.00 0.00 H
ATOM 20 N HIS C 2 -4.246 34.623 -21.489 1.00 0.00 N
ATOM 21 CA HIS C 2 -4.195 34.172 -22.877 1.00 0.00 C
ATOM 22 C HIS C 2 -5.573 34.183 -23.551 1.00 0.00 C
ATOM 23 OXT HIS C 2 -6.572 33.781 -22.948 1.00 0.00 O1-
ATOM 24 CB HIS C 2 -3.582 32.774 -22.952 1.00 0.00 C
ATOM 25 CG HIS C 2 -2.102 32.760 -22.745 1.00 0.00 C
ATOM 26 ND1 HIS C 2 -1.470 33.576 -21.834 1.00 0.00 N1+
ATOM 27 CD2 HIS C 2 -1.126 32.032 -23.340 1.00 0.00 C
ATOM 28 CE1 HIS C 2 -0.167 33.355 -21.875 1.00 0.00 C
ATOM 29 NE2 HIS C 2 0.066 32.421 -22.780 1.00 0.00 N
ATOM 30 O HIS C 2 -5.724 34.590 -24.711 1.00 0.00 O
ATOM 31 H HIS C 2 -4.410 35.656 -21.498 1.00 0.00 H
ATOM 32 H2 HIS C 2 -5.101 34.208 -21.054 1.00 0.00 H
ATOM 33 HB2 HIS C 2 -3.751 32.338 -23.961 1.00 0.00 H
ATOM 34 HD2 HIS C 2 -1.240 31.277 -24.107 1.00 0.00 H
ATOM 35 HE1 HIS C 2 0.573 33.762 -21.203 1.00 0.00 H
ATOM 36 HE2 HIS C 2 1.002 32.020 -23.010 1.00 0.00 H
ATOM 37 HB3 HIS C 2 -4.085 32.104 -22.221 1.00 0.00 H
ATOM 38 HA HIS C 2 -3.529 34.830 -23.482 1.00 0.00 H
HETATM 39 NI+2 NI2 C 3 -2.666 34.185 -19.767 1.00 0.00 Ni2+
END
The “protein2_1.pdb” file the first histidine lost its OXT (carboxylate oxygen) but still have its N (amine nitrogen), while the second histidine retains both the N and OXT
REMARK FILENAME=“protein2_1.pdb”
REMARK peptide link removed (applied DPEP): from 1 to 2
REMARK coordinates built for atom: HIS 1 HD1
REMARK coordinates built for atom: HIS 1 HE2
REMARK coordinates built for atom: HIS 1 HT1
REMARK coordinates built for atom: HIS 1 HT2
REMARK coordinates built for atom: HIS 1 HT3
REMARK coordinates built for atom: HIS 2 HN
REMARK coordinates built for atom: HIS 2 HD1
REMARK coordinates built for atom: HIS 2 HE2
REMARK DATE:21-Apr-2020 16:12:19 created by user: enmr
REMARK VERSION:1.3U
ATOM 1 CB HIS B 1 -1.657 35.917 -17.010 1.00 15.00 B C
ATOM 2 CG HIS B 1 -0.641 34.934 -17.500 1.00 15.00 B C
ATOM 3 ND1 HIS B 1 -0.943 33.914 -18.388 1.00 15.00 B N
ATOM 4 HD1 HIS B 1 -1.825 33.737 -18.774 1.00 15.00 B H
ATOM 5 CD2 HIS B 1 0.681 34.810 -17.234 1.00 15.00 B C
ATOM 6 CE1 HIS B 1 0.140 33.205 -18.633 1.00 15.00 B C
ATOM 7 NE2 HIS B 1 1.145 33.731 -17.948 1.00 15.00 B N
ATOM 8 HE2 HIS B 1 2.068 33.402 -17.952 1.00 15.00 B H
ATOM 9 C HIS B 1 -1.851 36.748 -19.342 1.00 15.00 B C
ATOM 10 O HIS B 1 -1.319 37.864 -19.486 1.00 15.00 B O
ATOM 11 N HIS B 1 -3.684 35.402 -18.305 1.00 15.00 B N
ATOM 12 HT1 HIS B 1 -4.316 35.718 -19.068 1.00 15.00 B H
ATOM 13 HT2 HIS B 1 -4.244 35.274 -17.438 1.00 15.00 B H
ATOM 14 HT3 HIS B 1 -3.266 34.488 -18.571 1.00 15.00 B H
ATOM 15 CA HIS B 1 -2.632 36.391 -18.081 1.00 15.00 B C
ATOM 16 N HIS B 2 -4.246 34.623 -21.489 1.00 15.00 B N
ATOM 17 HN HIS B 2 -3.438 34.567 -20.938 1.00 15.00 B H
ATOM 18 CB HIS B 2 -3.582 32.774 -22.952 1.00 15.00 B C
ATOM 19 CG HIS B 2 -2.102 32.760 -22.745 1.00 15.00 B C
ATOM 20 ND1 HIS B 2 -1.470 33.576 -21.834 1.00 15.00 B N
ATOM 21 HD1 HIS B 2 -1.910 34.223 -21.244 1.00 15.00 B H
ATOM 22 CD2 HIS B 2 -1.126 32.032 -23.340 1.00 15.00 B C
ATOM 23 CE1 HIS B 2 -0.167 33.355 -21.875 1.00 15.00 B C
ATOM 24 NE2 HIS B 2 0.066 32.421 -22.780 1.00 15.00 B N
ATOM 25 HE2 HIS B 2 0.949 32.065 -23.012 1.00 15.00 B H
ATOM 26 CA HIS B 2 -4.195 34.172 -22.877 1.00 15.00 B C
ATOM 27 C HIS B 2 -5.573 34.183 -23.551 1.00 15.00 B C
ATOM 28 O HIS B 2 -5.724 34.590 -24.711 1.00 15.00 B O
ATOM 29 OXT HIS B 2 -6.572 33.781 -22.948 1.00 15.00 B O
ATOM 30 NI+2 NI2 B 3 -2.666 34.185 -19.767 1.00 15.00 B NI+2
END
Back to the DSSP issue, it only occurs when I add the metal to the pdb file. Once I removed the metal, even listing the histidine as HETATM, it works just fine. And likewise, if I add the metal, to say, a different ligand (such as rifampicin in the tutorial) the DSSP error is prompted.
Based on my understanding, DSSP is for secondary structure assignment, which shouldn’t be triggered regardless if I am setting the ligand as HETATM (aka as a non-proteinaceous molecule).
Is there an option to disable DSSP, either on webserver or the local?
Thanks! And I hope this isn’t too troublesome.
Wayne, please me via email your PDB files.
The ones you paste here lost completely the proper PDB formatting.
Note that the server should now properly define charged C-termini (if you specify those) for both HIS, provided they are separated by a TER statement.
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