One word: tutorials.
Three words: not that hard.
Bill
On 6/17/19 10:45 PM, Mustafa Alhaji Isa 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.
>
>
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Received on Mon Jun 17 2019 - 23:00:03 PDT
