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
>>
>>
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Sat May 15 2021 - 00:00:02 PDT
