AMBER Archive (2007)

Subject: Re: AMBER: frcmod

From: David A. Case (case_at_scripps.edu)
Date: Fri Jun 15 2007 - 16:43:48 CDT

On Fri, Jun 15, 2007, Brooke Elizabeth Adams wrote:

> Here are the files,
> and the command for antechamber
>
> antechamber -i tabun_2_A02.pdb -fi pdb -o TAB.prepi -fo prepi -at AMBER
                                                                ^^^^^^^^^

Remove this flag. Generally, the gaff forcefield is *much* more complete
than is the attempt to use AMBER atom types for strange environments. The
only time -at AMBER should be used (in my view, Junmei may want to weigh in
here) is if you have a minor modification of an amino acid or nucleotide, and
want to see if the modified residue can be reasonably accommated with the
existing Amber types.

I ran your files using gaff types, and there were no missing parameters. If
you *really* need Amber types, you might still run with GAFF, and use the GAFF
values as a first guess for what the corresponding Amber types would be. But
I am not recommending this, just pointing is out as a possibility.

...hope this helps...dac

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