Hi Rafal,
Can you share with me your leap.in script and which version of ambertools
you are using?
On Sat, May 15, 2021, 2:59 AM Rafał Madaj <rmadaj.cbmm.lodz.pl> wrote:
> Hi Kellon,
>
> I applied changes to pdb files. As long as there are no 'unknown' heavy
> atoms, there are still some parameters missing:
>
> > prot = loadpdb 1pl6_A.pdb
> Loading PDB file: ./1pl6_A.pdb
> total atoms in file: 2677
> Leap added 2735 missing atoms according to residue templates:
> 2735 H / lone pairs
> > check prot
> Checking 'prot'....
>
> Warning: The unperturbed charge of the unit (3.066712) is not integral.
>
> Warning: The unperturbed charge of the unit (3.066712) is not zero.
>
> Warning: Close contact of 1.185506 angstroms between .R<MSE 38>.A<HE3
> 15> and .R<MSE 38>.A<HA 4>
>
> Warning: Close contact of 1.344255 angstroms between .R<SER 158>.A<HB3
> 7> and .R<THR 302>.A<HG1 12>
>
> Warning: Close contact of 0.981188 angstroms between .R<THR 322>.A<HG1
> 12> and .R<LEU 343>.A<H 2>
> Checking parameters for unit 'prot'.
> Checking for bond parameters.
>
> Error: Could not find bond parameter for: SE - CT
>
> Error: Could not find bond parameter for: SC - H1
>
> Error: Could not find bond parameter for: SC - H1
>
> Error: Could not find bond parameter for: SC - SE
>
> Error: Could not find bond parameter for: 2C - SC
>
> Error: Could not find bond parameter for: SE - CT
>
> Error: Could not find bond parameter for: SC - H1
>
> --- MSE FRAGMENT ---
>
> HETATM 278 N MSE A 38 85.991 40.099 50.845 1.00
> 14.20 N
> HETATM 279 CA MSE A 38 86.115 39.447 49.549 1.00
> 14.33 C
> HETATM 280 C MSE A 38 84.860 38.699 49.126 1.00
> 15.21 C
> HETATM 281 O MSE A 38 84.174 38.094 49.952 1.00
> 14.97 O
> HETATM 282 CB MSE A 38 87.338 38.533 49.555 1.00
> 15.33 C
> HETATM 283 CG MSE A 38 88.609 39.294 49.919 1.00
> 18.70 C
> HETATM 284 SED MSE A 38 89.048 40.703 48.611 1.00
> 21.68 SED
> HETATM 285 CE MSE A 38 87.500 41.833 48.688 1.00
> 26.20 C
>
> How to deal with that?
>
> Best,
>
> Rafal
>
>
> On 14.05.2021 02:14, Kellon Belfon wrote:
> > Hi Rafal,
> >
> > I am happy that you are trying out the MSE parameters. I made the
> decision
> > to use SED for the atom name of the Selenium based on the position of the
> > atom. The problem you are having is an atom name issue. Can you change SE
> > to SED in your pdb file and let me know if that works?
> >
> > HETATM 350 SE MSE A 43 51.772 29.090 23.392 1.00 21.41
> > A SE
> >
> > to
> > HETATM 350 SED MSE A 43 51.772 29.090 23.392 1.00 21.41
> > A SED
> >
> > Best,
> >
> > Kellon
> >
> > On Thu, May 13, 2021 at 1:51 PM Rafał Madaj <rmadaj.cbmm.lodz.pl> wrote:
> >
> >> 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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> >>
> >
>
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Received on Sat May 15 2021 - 08:00:02 PDT
