Awesome and let me know if anything else comes up. Thank you for trying
those parameters.
On Sat, May 15, 2021, 6:06 PM Rafał Madaj <rmadaj.cbmm.lodz.pl> wrote:
> Dear Kellon,
>
> As it came out, my mistake is rather simple:
>
> I only loaded part of force field through loadoff, not whole modified
> forcefield.
>
> source leaprc.protein.ff19SB
> *loadoff $AMBERSOURCE/dat/leap/lib/mod_amino19.lib*
> prot = loadpdb ./1pl6_prep.pdb
> check prot
> <parameter errors>
>
> Once I used:
> *source leaprc.protein.ff19SB_modAA*
> and modified pdb file accordingly to your suggestions, I was able to
> generate topology and input coordinates.
>
> Thank you very much!
>
> Rafal
>
>
> On 15.05.2021 23:23, Kellon Belfon wrote:
> > Hi Rafal,
> >
> > My attachment did not go through to the listserv because of the size so I
> > am attaching a link to the folder and the forwarded email from this
> morning
> > below.
> >
> https://drive.google.com/drive/folders/1Xk3NSztUa9sRsVu1SNW0mGUwTcUA1Ysy?usp=sharing
> >
> >
> >
> > ---------- Forwarded message ---------
> > From: Kellon Belfon <kellonbelfon.gmail.com>
> > Date: Sat, May 15, 2021 at 11:40 AM
> > Subject: Re: [AMBER] Selenomethionine force field parameters
> > To: AMBER Mailing List <amber.ambermd.org>
> >
> >
> > Hi Rafal,
> >
> > I tried on my end with this leap.in script (also tried with ff14SB and
> > ff14SB_modAA)
> > source leaprc.protein.ff19SB
> > source leaprc.protein.ff19SB_modAA
> > prot = loadpdb ./1pl6_prep.pdb
> > check prot
> > saveamberparm prot 1pl6_prep.parm7 1pl6_prep.rst7
> >
> > Then converted all SE in MSE,AMSE, and BMSE units to SED and removed the
> > NAD,HOH and ligand (for testing), and run the PDB 1pl6.pdb through
> > pdb4amber to get the pdb file name 1pl6_prep.pdb
> >
> > I was able to get the topology file and rst7 file generated. This is with
> > AmberTools21.
> >
> > If you do not mind sharing, can you tell me how different your protocol
> is
> > from this or share the pdb file you load into leap along with your leap
> > commands? It would help me reproduce the error on my end.
> >
> > Thank you!
> >
> >
> > On Sat, May 15, 2021 at 10:46 AM Kellon Belfon <kellonbelfon.gmail.com>
> > wrote:
> >
> >> 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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> >>>
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Received on Sat May 15 2021 - 15:30:03 PDT
