AMBER Archive (2009)

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

From: Paul Ledbetter (pjl1_at_rice.edu)
Date: Tue Sep 15 2009 - 15:25:56 CDT

Hello,

  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.

  Here is what I've tried and what I get:

First I did:

  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:

  antechamber -i pca-pB.prepc -fi prepc -o pca-pB.prepi -fo prepi -j 0

But now see just "Error happens"

Thank you,
Paul

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