Protein-Protein Docking with bound ligands

HADDOCK
1

Dear Dr. Bonvin and Haddock team,

Today, I have tried to run Protein-Protein docking with Easy interface on HADDOCK web server. As per conversion with Dr. Bonvin, HADDOCK is directly using PRODRG for small molecules parameter generation. I have prepared ligand file in each protein with “ATOM” and “LIG”. Totally I have prepared two proteins file. (One protein as receptor plus bound ligand and second protein as ligand with bound ligand). I have given active residue number those are directly involve in interaction between two protein. I got following error message in my email. Please help me to solve this problem. Where I did mistake ??

There was an inconsistency in your data

Error message

First pdb file contains an unknown amino acid or nucleic acid base LIG

Make sure to use three letter code for bases and amino acid

For supported modified amino acids see http://haddock.science.uu.nl/services/HADDOCK/library.html
Directory of the run: http://milou.science.uu.nl/serviceresults/HADDOCK2.2/5785077997/Test_run4

Here is the ligand file in end of protein.

ATOM 2267 HG22 THR C 202 -17.762 10.377 -6.367 1.00 0.00 H
ATOM 2268 HG23 THR C 202 -16.123 10.094 -5.794 1.00 0.00 H
TER 2269 THR C 202
ATOM 2270 N01 LIG D 203 -4.388 32.768 -4.316 1.00 36.12 N
ATOM 2271 C02 LIG D 203 -5.491 33.502 -3.872 1.00 34.09 C
ATOM 2272 C03 LIG D 203 -5.628 33.900 -2.527 1.00 31.89 C
ATOM 2273 C04 LIG D 203 -4.518 33.552 -1.525 1.00 31.58 C
ATOM 2274 C05 LIG D 203 -6.779 34.632 -2.145 1.00 30.21 C
ATOM 2275 C06 LIG D 203 -6.985 35.142 -0.743 1.00 30.17 C
ATOM 2276 N07 LIG D 203 -7.346 34.251 0.216 1.00 25.41 N
ATOM 2277 C08 LIG D 203 -7.530 34.592 1.643 1.00 25.10 C
ATOM 2278 C09 LIG D 203 -6.274 35.144 2.354 1.00 27.85 C
ATOM 2279 N10 LIG D 203 -6.502 36.002 3.361 1.00 30.13 N
ATOM 2280 C11 LIG D 203 -5.492 36.448 4.320 1.00 34.64 C
ATOM 2281 C12 LIG D 203 -5.250 35.502 5.500 1.00 34.82 C
ATOM 2282 C13 LIG D 203 -4.063 35.625 6.225 1.00 37.37 C
ATOM 2283 C14 LIG D 203 -3.836 34.824 7.340 1.00 38.76 C
ATOM 2284 C15 LIG D 203 -4.794 33.891 7.743 1.00 37.12 C
ATOM 2285 C16 LIG D 203 -4.611 33.137 9.016 1.00 39.63 C
ATOM 2286 C17 LIG D 203 -4.080 33.539 10.253 1.00 42.54 C
ATOM 2287 C18 LIG D 203 -3.513 34.885 10.653 1.00 42.06 C
ATOM 2288 N19 LIG D 203 -4.100 32.630 11.209 1.00 43.68 N
ATOM 2289 C20 LIG D 203 -4.633 31.511 10.805 1.00 41.51 C
ATOM 2290 S21 LIG D 203 -5.130 31.476 9.154 1.00 39.14 S
ATOM 2291 C22 LIG D 203 -5.949 33.716 6.976 1.00 33.60 C
ATOM 2292 C23 LIG D 203 -6.178 34.519 5.863 1.00 32.51 C
ATOM 2293 O24 LIG D 203 -5.152 34.719 2.073 1.00 29.88 O
ATOM 2294 C25 LIG D 203 -7.964 33.262 2.291 1.00 25.78 C
ATOM 2295 C26 LIG D 203 -8.527 32.427 1.153 1.00 25.54 C
ATOM 2296 O27 LIG D 203 -9.864 32.821 0.911 1.00 23.51 O
ATOM 2297 C28 LIG D 203 -7.628 32.828 -0.022 1.00 23.90 C
ATOM 2298 O29 LIG D 203 -6.816 36.342 -0.518 1.00 29.90 O
ATOM 2299 C30 LIG D 203 -7.748 34.953 -3.103 1.00 30.19 C
ATOM 2300 C31 LIG D 203 -7.597 34.553 -4.425 1.00 32.40 C
ATOM 2301 C32 LIG D 203 -6.472 33.831 -4.808 1.00 33.75 C
ATOM 2302 H011 LIG D 203 -4.319 32.498 -5.287 1.00 0.00 H
ATOM 2303 H012 LIG D 203 -3.660 32.508 -3.666 1.00 0.00 H
ATOM 2304 H041 LIG D 203 -4.785 33.933 -0.539 1.00 0.00 H
ATOM 2305 H042 LIG D 203 -4.398 32.470 -1.476 1.00 0.00 H
ATOM 2306 H043 LIG D 203 -3.581 34.006 -1.848 1.00 0.00 H
ATOM 2307 H08 LIG D 203 -8.340 35.315 1.736 1.00 0.00 H
ATOM 2308 HN10 LIG D 203 -7.426 36.387 3.496 1.00 0.00 H
ATOM 2309 H111 LIG D 203 -5.764 37.434 4.698 1.00 0.00 H
ATOM 2310 H112 LIG D 203 -4.551 36.621 3.797 1.00 0.00 H
ATOM 2311 H13 LIG D 203 -3.316 36.345 5.922 1.00 0.00 H
ATOM 2312 H14 LIG D 203 -2.917 34.923 7.898 1.00 0.00 H
ATOM 2313 H181 LIG D 203 -3.187 34.848 11.692 1.00 0.00 H
ATOM 2314 H182 LIG D 203 -2.662 35.126 10.014 1.00 0.00 H
ATOM 2315 H183 LIG D 203 -4.280 35.651 10.539 1.00 0.00 H
ATOM 2316 H20 LIG D 203 -4.739 30.685 11.493 1.00 0.00 H
ATOM 2317 H22 LIG D 203 -6.667 32.956 7.247 1.00 0.00 H
ATOM 2318 H23 LIG D 203 -7.076 34.381 5.278 1.00 0.00 H
ATOM 2319 H251 LIG D 203 -8.750 33.456 3.021 1.00 0.00 H
ATOM 2320 H252 LIG D 203 -7.091 32.762 2.710 1.00 0.00 H
ATOM 2321 H26 LIG D 203 -8.456 31.360 1.366 1.00 0.00 H
ATOM 2322 HO27 LIG D 203 -10.228 32.298 0.193 1.00 0.00 H
ATOM 2323 H281 LIG D 203 -6.698 32.262 0.026 1.00 0.00 H
ATOM 2324 H282 LIG D 203 -8.184 32.721 -0.954 1.00 0.00 H
ATOM 2325 H30 LIG D 203 -8.623 35.517 -2.817 1.00 0.00 H
ATOM 2326 H31 LIG D 203 -8.353 34.804 -5.155 1.00 0.00 H
ATOM 2327 H32 LIG D 203 -6.360 33.525 -5.837 1.00 0.00 H

2

Read again my email… The ligand should be defined using HETATM instead of ATOM (and make sure to keep the correct column formatting.

3

Thanks Prof. Bonvin. Now its working fine.