Re: [AMBER] Fwd: Error while preparing docked complex for minimization

From: Bill Ross <>
Date: Sun, 28 May 2017 13:53:17 -0700

Your BR atom sounds like an attempt at a Bromine ion? In any case it
needs an atom type, see manual or tutorials for an example.

It seems like your UNL residue needs work, since it also has the long bond.


On 5/28/17 3:59 AM, NADIA RAHMAH wrote:
> Hello, I am doing AMBER16 for simulating docked complex protein, but there
> is error while preparation:
> WARNING: There is a bond of 3.687021 angstroms between:
> ------- .R<UNL 295>.A<C 1> and .R<UNL 295>.A<O 2>
> FATAL: Atom .R<UNL 295>.A<BR 9> does not have a type.
> Failed to generate parameters
> Parameter file was not saved.
> my ligand name unl, before i do peparation for complex, i did antechamber
> for the ligand and get unl.lib, unl.frcmod that i use for loadamberparams
> in preparation script but i still get error when preparation complex. I
> need to fix it, because it's my undergraduate thesis, i hope anybody can
> help me. Thanks

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Received on Sun May 28 2017 - 14:00:02 PDT
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