AMBER Archive (2008)

Subject: AMBER: saveAmberPrep in internal coordinates

From: Xu, Huafeng (Huafeng.Xu_at_deshaw.com)
Date: Wed Feb 20 2008 - 11:02:00 CST

Hi,

I've built a tripeptide with a phosphoresidue using leap, and want to
save the parameters to a Amber prep.in file. I used

saveAmberPrep tripep tripep.in

It worked, except that it saved the structure in Cartesian coordinates,
whereas I'd like to have it saved in internal coordinates (z-Matrix), as
in all the default Amber prep.in files, so that I can use my scripts to
convert it to my own file format for phosphoresidue template. Does
anyone know how to instruct leap to saveAmberPrep in internal
coordinates?

Thanks very much.

Huafeng Xu
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