AMBER Archive (2006)

Subject: Re: AMBER: Could not find atom type.

From: David A. Case (case_at_scripps.edu)
Date: Tue Apr 18 2006 - 18:06:21 CDT

On Tue, Apr 18, 2006, Sergey Krishtal wrote:

>
> Ethanol molecule is supposed to be a rigid one with
> two united atoms: CH3 and CH2.

The straightforward approach in Amber is to treat ethanol as two carbons, one
oxygen and 6 hydrogen atoms. The antechamber program can be used to create a
forcefield for this that is consistent with the rest of the Amber force
fields.

It is not clear why you think that ethanol is "supposed" to have two united
atoms, as above. This description might be consistent with ff03ua, but you
should be sure that you have the background and experience to start creating
a new forcefield when existing ones are already available.

...dac

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