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.