AMBER Archive (2008)

Subject: Re: AMBER: saveAmberPrep in internal coordinates

From: Junmei Wang (junmwang_at_gmail.com)
Date: Wed Feb 20 2008 - 11:43:31 CST

If the residue is a small molecule, you could easily convert prepc into
prepi with antechamber (using -j 0 flag if you do not want to change atom
types).
However, if it is an amino acid like residue (not capped), antechamber still
works only if you use '-j 5', you may lose some improper dihedral
information.

Junmei

On Wed, Feb 20, 2008 at 11:02 AM, Xu, Huafeng <Huafeng.Xu_at_deshaw.com> wrote:

> 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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