Dear AMBER Community,
I am new to biological simulations. Can anybody please help me to understand why I am getting below error, and how to solve it.
Thank you.
> complex = loadpdb complex_H.pdb
Loading PDB file: ./complex_H.pdb
-- residue 835: duplicate [ C] atoms (total 18)
-- residue 835: duplicate [ N] atoms (total 3)
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: CL within residue: .R<UNL 835>
Added missing heavy atom: .R<UNL 835>.A<C1 5>
Added missing heavy atom: .R<UNL 835>.A<C8 12>
Added missing heavy atom: .R<UNL 835>.A<Cl 23>
Added missing heavy atom: .R<UNL 835>.A<C2 6>
Added missing heavy atom: .R<UNL 835>.A<C4 8>
Added missing heavy atom: .R<UNL 835>.A<C3 7>
Added missing heavy atom: .R<UNL 835>.A<N1 2>
Added missing heavy atom: .R<UNL 835>.A<C7 11>
Added missing heavy atom: .R<UNL 835>.A<C5 9>
Added missing heavy atom: .R<UNL 835>.A<C6 10>
Added missing heavy atom: .R<UNL 835>.A<C17 21>
Added missing heavy atom: .R<UNL 835>.A<C16 20>
Added missing heavy atom: .R<UNL 835>.A<N2 3>
Added missing heavy atom: .R<UNL 835>.A<C13 17>
Added missing heavy atom: .R<UNL 835>.A<C14 18>
Added missing heavy atom: .R<UNL 835>.A<C12 16>
Added missing heavy atom: .R<UNL 835>.A<C15 19>
Added missing heavy atom: .R<UNL 835>.A<C11 15>
Added missing heavy atom: .R<UNL 835>.A<C9 13>
Added missing heavy atom: .R<UNL 835>.A<C10 14>
total atoms in file: 13242
Leap added 45 missing atoms according to residue templates:
20 Heavy
25 H / lone pairs
The file contained 1 atoms not in residue templates
> saveamberparm complex complex_H.prmtop complex_H.rst7
Checking Unit.
Warning: The unperturbed charge of the unit (-8.001000) is not zero.
FATAL: Atom .R<UNL 835>.A<CL 24> does not have a type.
Error: Failed to generate parameters
Warning: Parameter file was not saved.
——
Jatin Kashyap
Ph.D. Student
Dr. Dibakar Datta Group
Department of Mechanical and Industrial Engineering
New Jersey Institute of Technology (NJIT)
University Heights
Newark, NJ 07102-1982
Phone- (201)889-5783
Email- jk435.njit.edu
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Received on Thu Oct 01 2020 - 10:00:04 PDT
