Dear Amber user group
I met a problem when I generated prmtop and inpcrp files for a complex
system of a protein with coligand: Tetrabromobisphenol A (PDB ligand ID:XDI)
I generated .lib and .frcmod for the coligand successively.
However, tleap reported these lines when generating prmtop and inpcrp files
for the complex system.
Added missing heavy atom: .R<TBP 723>.A<BrAH 32>
Added missing heavy atom: .R<TBP 723>.A<BrAG 27>
Added missing heavy atom: .R<TBP 723>.A<BrAF 8>
Added missing heavy atom: .R<TBP 723>.A<BrAE 4>
Checking Unit.
FATAL: Atom .R<TBP 723>.A<BRAE 33> does not have a type.
FATAL: Atom .R<TBP 723>.A<BRAF 34> does not have a type.
FATAL: Atom .R<TBP 723>.A<BRAG 35> does not have a type.
FATAL: Atom .R<TBP 723>.A<BRAH 36> does not have a type.
Checking parameters for unit 'Complex'.
Checking for bond parameters.
Could not find bond parameter for: ca -
Could not find bond parameter for: ca -
Could not find bond parameter for: ca -
Could not find bond parameter for: ca -
Checking for angle parameters.
Could not find angle parameter: br - ca -
Could not find angle parameter: ca - ca -
Could not find angle parameter: ca - ca -
Could not find angle parameter: br - ca -
Could not find angle parameter: ca - ca -
Could not find angle parameter: ca - ca -
Could not find angle parameter: ca - ca -
Could not find angle parameter: br - ca -
Could not find angle parameter: ca - ca -
Could not find angle parameter: ca - ca -
Could not find angle parameter: br - ca -
Could not find angle parameter: ca - ca -
Does this indicates that there are no atom type for bromine atom attaching
to aromatic system?
Could you please instruct me how to solve this issue?
Thanks a lot for your help!
Cheers
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Received on Thu Oct 15 2015 - 10:00:05 PDT
