AMBER Archive (2009)

Subject: RE: [AMBER] Atom types

From: Ross Walker (
Date: Mon Jan 19 2009 - 09:46:10 CST

Hi George,

> I'm loading on xleap a protein/ligand complex obtained from a docking
> simulation using AutoDock v.4.
> When I do a check in xleap I get the following fatal errors:
> WARNING: The unperturbed charge of the unit: -8.000000 is not zero.
> FATAL: Atom .R<UNK 126>.A<C 1> does not have a type.
> FATAL: Atom .R<UNK 126>.A<O 2> does not have a type.
> The ligand is a simple unsaturated aliphatic aldehyde.

You need to provide parameters and charges for the aliphatic aldehyde since
it is not part of the standard library (amino acids and dna / rna etc). The
simplest way to do this is to use the GAFF force field and antechamber. The
following tutorial gives an example of using this:

You will need to build a pdb file containing just your ligand with the
hydrogens in place as well. You may also want to consider naming it
something other than UNK (3 letters max) although in your case since you
only have this one non-standard residue having it named UNK will not cause a

Good luck,

|\oss Walker

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| San Diego Supercomputer Center |
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