AMBER Archive (2004)

Subject: Re: AMBER: mm_pbsa energy decomposition error

From: David A. Case (
Date: Tue May 25 2004 - 10:20:13 CDT

On Tue, May 25, 2004, Fang, Jianwen wrote:

> I am trying to calculate binding energy for a protein/ligand system.
> Stability and Binding calculation worked well. But I got "bad atom
> type: oh" when I run energy decomposition. I found the error related to
> the flag "gbsa". "gbsa = 0" is OK and "gbsa=1" generates the error. My
> question is what went wrong? I used antechamber to generate "prep" file
> for second ligand which is part of complex.

You don't say what version you are running, but this sounds like the
problem addressed by bugfix.7 for Amber 7 (see the Amber web site).
(But it may well be something else, since I don't see why this would fail
only when decomposition is turned on.)

...good luck....dac

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