AMBER Archive (2006)

Subject: Re: AMBER: Pt containing complex: antechamber

From: David A. Case (case_at_scripps.edu)
Date: Tue May 30 2006 - 12:39:20 CDT

On Mon, May 29, 2006, a a wrote:
>
> I am trying to do a MD calculation for a Pt containing complex. I tried to
> run the antechamber to creat leap input files. Is it the right thing to
> use antechamber for inorganic complex? The following is the error messages
> that I encountered.
>
> [PATH]$ $AMBERHOME/exe/antechamber -i Pt_nopi.pdb -fi pdb -o Pt_nopi.prepin
> -fo prepi -c bcc -s 2

Antechamber can only deal with organic molecules, not with metal ions. My
guess is that antechamber is thinking the Pt atom is Phosphorus. You are
really going to have to generate the charges and other force field information
by hand for a molecule like this.

...good luck....dac

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