AMBER Archive (2009)

Subject: Re: [AMBER] can antechamber convert a prep file from cartesian to internal coordinates?

From: case (case_at_biomaps.rutgers.edu)
Date: Tue Sep 15 2009 - 17:12:25 CDT

On Tue, Sep 15, 2009, Paul Ledbetter wrote:
>
> I have an AMBER prep file in cartesian coordinates which I'd like to
> convert to internal coordinates. I had to do a bunch of hand editing
> of the final prep file in cartesian coordinates, so I'd like to avoid
> doing things over from the pdb and ac files.
>
> antechamber -i pca-pB.prepc -fi prepc -o pca-pB.prepi -fo prepi
>
> and got a "Warning: the assigned bond types may be wrong, please :"

> I don't want any bonds reassigned, so I did:

Prep files don't contain any bond type information (this is not used by
Amber), so I don't see the danger here. Does the program continue to run,
after the warning?

...dac

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