you have a few issues here:
1) your histidine is named HIE but you have an HD1 atom, so it must be HID.
Renames it and it should be ok.
2) you have a residue named UNK that appears to be a small molecule ligand.
There are coordinates in the PDB file but leap is building them anyway - do
the atom names and residue name match up properly with the library files
that you made for the ligand? You didn't show all of the Leap output so we
can't tell what you've done for the ligand.
good luck!
On Tue, Jun 18, 2019 at 1:45 AM Mustafa Alhaji Isa <
mustafaisa.unimaid.edu.ng> wrote:
> Dear Amber users
> I want to create topology and coordinate files of a protein-ligand
> complex when I try to upload the complex using tleap, it displays the
> below output which eventually fails to create the coordinates.
> Attached is the complex
>
>
>
> Loading PDB file: ./tslp.pdb
> (starting new molecule for chain C)
> (starting new molecule for chain N)
> -- residue 528: duplicate [ C] atoms (total 20)
> -- residue 528: duplicate [ H] atoms (total 2)
> -- residue 528: duplicate [ O] atoms (total 8)
>
> Warning: Atom names in each residue should be unique.
> (Same-name atoms are handled by using the first
> occurrence and by ignoring the rest.
> Frequently duplicate atom names stem from alternate
> conformations in the PDB file.)
>
> Created a new atom named: HD1 within residue: .R<HIE 259>
> Created a new atom named: HD1 within residue: .R<HIE 285>
> Added missing heavy atom: .R<CASN 337>.A<OXT 15>
> Created a new atom named: HD1 within residue: .R<HIE 368>
> Created a new atom named: HD1 within residue: .R<HIE 389>
> Created a new atom named: HD1 within residue: .R<HIE 413>
> Added missing heavy atom: .R<CCYS 527>.A<OXT 12>
> Added missing heavy atom: .R<UNK1 528>.A<C 1>
> Added missing heavy atom: .R<UNK1 528>.A<C 2>
> Added missing heavy atom: .R<UNK1 528>.A<C 11>
> Added missing heavy atom: .R<UNK1 528>.A<C 3>
> Added missing heavy atom: .R<UNK1 528>.A<C 10>
> Added missing heavy atom: .R<UNK1 528>.A<O 12>
> Added missing heavy atom: .R<UNK1 528>.A<C 4>
> Added missing heavy atom: .R<UNK1 528>.A<C 9>
> Added missing heavy atom: .R<UNK1 528>.A<O 15>
> Added missing heavy atom: .R<UNK1 528>.A<C 13>
> Added missing heavy atom: .R<UNK1 528>.A<C 5>
> Added missing heavy atom: .R<UNK1 528>.A<O 8>
> Added missing heavy atom: .R<UNK1 528>.A<C 14>
> Added missing heavy atom: .R<UNK1 528>.A<C 16>
> Added missing heavy atom: .R<UNK1 528>.A<C 6>
> Added missing heavy atom: .R<UNK1 528>.A<C 26>
> Added missing heavy atom: .R<UNK1 528>.A<C 17>
> Added missing heavy atom: .R<UNK1 528>.A<C 21>
> Added missing heavy atom: .R<UNK1 528>.A<O 7>
> Added missing heavy atom: .R<UNK1 528>.A<O 27>
> Added missing heavy atom: .R<UNK1 528>.A<C 18>
> Added missing heavy atom: .R<UNK1 528>.A<C 20>
> Added missing heavy atom: .R<UNK1 528>.A<C 19>
> Added missing heavy atom: .R<UNK1 528>.A<O 22>
> Added missing heavy atom: .R<UNK1 528>.A<O 24>
> Added missing heavy atom: .R<UNK1 528>.A<C 23>
> total atoms in file: 7819
> Leap added 303 missing atoms according to residue templates:
> 28 Heavy
> 275 H / lone pairs
>
> saveamberparm complex tslpz.prmtop tslpz.inpcrd
> Checking Unit.
> WARNING: There is a bond of 26.351692 angstroms between:
> ------- .R<GLU 115>.A<C 14> and .R<THR 116>.A<N 1>
> WARNING: The unperturbed charge of the unit: -0.999700 is not zero.
> FATAL: Atom .R<HIE 259>.A<HD1 18> does not have a type.
> FATAL: Atom .R<HIE 285>.A<HD1 18> does not have a type.
> FATAL: Atom .R<HIE 368>.A<HD1 18> does not have a type.
> FATAL: Atom .R<HIE 389>.A<HD1 18> does not have a type.
> FATAL: Atom .R<HIE 413>.A<HD1 18> does not have a type.
> Failed to generate parameters
> Parameter file was not saved.
>
> --
> Warm regards
>
>
> Mustafa Alhaji Isa, Ph.D.
> Department of Microbiology,
> Faculty of Sciences
> University of Maiduguri
> P.M.B. 1069
> Borno State, Nigeria
> Mob No.: +2348032069491
> _______________________________________________
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> AMBER.ambermd.org
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>
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Received on Wed Jun 19 2019 - 05:00:03 PDT
