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

From: David Case <>
Date: Sun, 28 May 2017 12:09:10 -0400

On Sun, May 28, 2017, NADIA RAHMAH wrote:

> Hello, I am doing AMBER16 for simulating docked complex protein, but there
> is error while preparation:
> FATAL: Atom .R<UNL 295>.A<BR 9> does not have a type.
> 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

Check the details of your antechamber run. Assuming that you made a mol2
file for the "UNL" ligand, you can see what type the BR atom should have
inside it.

Then, in tleap, use "UNL = loadMol2 <file.mol2>

That should load the mol2 file. You can use the "desc" command to interrogate
what atoms and atom types there are.

My best guess, based on very little information (not even the complete error
messages from leap): The bromine atom in the mol2 file has a different name
than the bromine atom in the PDB file you are loading. (Names are
case-sensitive: BR is different from Br, etc.)

...hope this helps....dac

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Received on Sun May 28 2017 - 09:30:04 PDT
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