AMBER Archive (2009)

Subject: Re: [AMBER] Ligand covalent bonds appear to be broken

From: Thomas Cheatham (
Date: Fri Oct 30 2009 - 10:48:07 CDT

> 1. I convert my crds to pdbs using ptraj. The script for it using the following
> actions:
> rms first out rms @CA
> center @CA
> image
> strip :WAT

You need to center and image prior to doing the RMS fit... --tec3

center @CA
rms first out rms @CA
strip :WAT

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