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

From: Thomas Cheatham <tec3.utah.edu>
Date: Fri, 30 Oct 2009 09:48:07 -0600 (Mountain Daylight Time)

> 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
image
rms first out rms .CA
strip :WAT


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Received on Fri Oct 30 2009 - 09:00:02 PDT