Dear all,
I am trying to create topology for the protein abundant in
selenomethionine (MSE). Despite loading additional force field
parameters (apart from ff19SB and GAFF) - mod_amino19.lib - creating
topology using tleap returns an error:
> prot = loadpdb rec.pdb
Loading PDB file: ./rec.pdb
Created a new atom named: SE within residue: .R<MSE 43>
Added missing heavy atom: .R<MSE 43>.A<SED 11>
Created a new atom named: SE within residue: .R<MSE 66>
Added missing heavy atom: .R<MSE 66>.A<SED 11>
Created a new atom named: SE within residue: .R<MSE 79>
Added missing heavy atom: .R<MSE 79>.A<SED 11>
Created a new atom named: SE within residue: .R<MSE 80>
Added missing heavy atom: .R<MSE 80>.A<SED 11>
Created a new atom named: SE within residue: .R<MSE 164>
Added missing heavy atom: .R<MSE 164>.A<SED 11>
Created a new atom named: SE within residue: .R<MSE 184>
Added missing heavy atom: .R<MSE 184>.A<SED 11>
Created a new atom named: SE within residue: .R<MSE 210>
Added missing heavy atom: .R<MSE 210>.A<SED 11>
Created a new atom named: SE within residue: .R<MSE 263>
Added missing heavy atom: .R<MSE 263>.A<SED 11>
Created a new atom named: SE within residue: .R<MSE 272>
Added missing heavy atom: .R<MSE 272>.A<SED 11>
Added missing heavy atom: .R<CLYS 287>.A<OXT 23>
total atoms in file: 2269
Leap added 2239 missing atoms according to residue templates:
10 Heavy
2229 H / lone pairs
The file contained 9 atoms not in residue templates
Typical fragment of pdb file containing this residue:
ATOM 337 C ASP A 42 56.212 30.757 19.570 1.00 26.81
A C
ATOM 338 O ASP A 42 57.289 30.153 19.632 1.00 26.38
A O
ATOM 339 CB ASP A 42 57.337 32.954 19.317 1.00 32.60
A C
ATOM 340 CG ASP A 42 57.467 33.033 20.824 1.00 35.76
A C
ATOM 341 OD1 ASP A 42 56.474 33.397 21.492 1.00 36.69
A O
ATOM 342 OD2 ASP A 42 58.565 32.729 21.341 1.00 39.27
A O1-
HETATM 343 N MSE A 43 55.091 30.273 20.097 1.00 22.74
A N
HETATM 344 CA MSE A 43 55.098 28.977 20.766 1.00 21.05
A C
HETATM 345 C MSE A 43 55.320 27.849 19.773 1.00 18.33
A C
HETATM 346 O MSE A 43 54.976 27.967 18.595 1.00 17.94
A O
HETATM 347 CB MSE A 43 53.770 28.706 21.472 1.00 22.04
A C
HETATM 348 CG MSE A 43 53.342 29.737 22.484 1.00 22.27
A C
HETATM 349 CE MSE A 43 52.449 29.121 25.207 1.00 24.40
A C
HETATM 350 SE MSE A 43 51.772 29.090 23.392 1.00 21.41
A SE
ATOM 351 N THR A 44 55.891 26.753 20.260 1.00 16.37
A N
ATOM 352 CA THR A 44 56.108 25.572 19.436 1.00 14.24
A C
ATOM 353 C THR A 44 54.771 24.837 19.468 1.00 14.92
A C
ATOM 354 O THR A 44 53.898 25.173 20.269 1.00 15.67
A O
ATOM 355 CB THR A 44 57.182 24.657 20.039 1.00 13.80
A C
ATOM 356 CG2 THR A 44 58.541 25.369 20.072 1.00 11.54
A C
ATOM 357 OG1 THR A 44 56.795 24.292 21.370 1.00 11.42
A O
Do you have any suggestions how to overcome this problem?
Best regards,
Rafal
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Received on Thu May 13 2021 - 11:00:02 PDT
