That change is fine. The error is that yoyndidnt load a mol2 or other
library defining FST.
On Sun, Sep 22, 2024, 3:41 AM Maciej Spiegel via AMBER <amber.ambermd.org>
wrote:
> Hello,
>
> I've parametrised my ligand, FST, and docked it to the protein. Cleaned
> with the pdb4amber to:
>
> ...
> ATOM 3653 C LYS A 239 49.307 17.738 85.563 1.00 0.00
> C
> ATOM 3654 O LYS A 239 49.080 18.266 86.650 1.00 0.00
> O
> ATOM 3655 OXT LYS A 239 50.054 16.757 85.385 1.00 0.00
> O
> TER 3655 LYS A 239
> HETATM 3656 O1 FST B 240 37.750 63.322 76.122 1.00 0.00
> O
> HETATM 3657 C3 FST B 240 37.797 64.573 76.595 1.00 0.00
> C
> HETATM 3658 C2 FST B 240 38.689 65.506 76.100 1.00 0.00
> C
> ...
>
> However, running the following in tleap:
>
> source leaprc.gaff2
> source leaprc.protein.ff19SB
> loadamberparams FST.frcmod
> prot = loadpdb clean.pdb
>
> yields warning:
>
> Loading PDB file: ./clean.pdb
>
> Warning: Unknown residue: FST number: 239 type: Terminal/last
> ..relaxing end constraints to try for a dbase match
>
> Warning: -no luck
> Creating new UNIT for residue: FST sequence: 240
> Created a new atom named: O1 within residue: .R<FST 240>
> Created a new atom named: C3 within residue: .R<FST 240>
> Created a new atom named: C2 within residue: .R<FST 240>
> Created a new atom named: C6 within residue: .R<FST 240>
> Created a new atom named: O3 within residue: .R<FST 240>
> Created a new atom named: C5 within residue: .R<FST 240>
> Created a new atom named: C7 within residue: .R<FST 240>
> Created a new atom named: C12 within residue: .R<FST 240>
> Created a new atom named: C11 within residue: .R<FST 240>
> Created a new atom named: C8 within residue: .R<FST 240>
> Created a new atom named: H2 within residue: .R<FST 240>
> Created a new atom named: H5 within residue: .R<FST 240>
> Created a new atom named: H1 within residue: .R<FST 240>
> Created a new atom named: C1 within residue: .R<FST 240>
> Created a new atom named: C4 within residue: .R<FST 240>
> Created a new atom named: C10 within residue: .R<FST 240>
> Created a new atom named: C14 within residue: .R<FST 240>
> Created a new atom named: H4 within residue: .R<FST 240>
> Created a new atom named: H6 within residue: .R<FST 240>
> Created a new atom named: C15 within residue: .R<FST 240>
> Created a new atom named: C13 within residue: .R<FST 240>
> Created a new atom named: C9 within residue: .R<FST 240>
> Created a new atom named: H3 within residue: .R<FST 240>
> Created a new atom named: O6 within residue: .R<FST 240>
> Created a new atom named: H10 within residue: .R<FST 240>
> Created a new atom named: O5 within residue: .R<FST 240>
> Created a new atom named: H9 within residue: .R<FST 240>
> Created a new atom named: O2 within residue: .R<FST 240>
> Created a new atom named: H7 within residue: .R<FST 240>
> Created a new atom named: O4 within residue: .R<FST 240>
> Created a new atom named: H8 within residue: .R<FST 240>
> total atoms in file: 3686
> The file contained 31 atoms not in residue templates
>
> and examining saved .pdb it appears that FST is now classified as ATOM:
>
> ...
> ATOM 3653 C LYS 239 49.307 17.738 85.563 1.00 0.00
> ATOM 3654 O LYS 239 49.080 18.266 86.650 1.00 0.00
> ATOM 3655 OXT LYS 239 50.054 16.757 85.385 1.00 0.00
> TER
> ATOM 3656 O1 FST 240 37.750 63.322 76.122 1.00 0.00
> ATOM 3657 C3 FST 240 37.797 64.573 76.595 1.00 0.00
> ATOM 3658 C2 FST 240 38.689 65.506 76.100 1.00 0.00
> ...
>
> Why that? Is it problem?
> –
> Maciej Spiegel, MPharm PhD
> assistant professor
> .GitHub <https://farmaceut.github.io/>
>
> Department of Organic Chemistry and Pharmaceutical Technology,
> Faculty of Pharmacy, Wroclaw Medical University
> Borowska 211A, 50-556 Wroclaw, Poland
> <https://www.google.com/maps/search/Borowska+211A,+50-556+Wroclaw,+Poland?entry=gmail&source=g>
>
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Received on Sun Sep 22 2024 - 04:30:02 PDT
