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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Received on Mon Jun 17 2019 - 23:00:02 PDT
