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
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Received on Sun Sep 22 2024 - 01:00:02 PDT
