AMBER Archive (2006)

Subject: Re: AMBER: ambpdb and original PDB

From: Bill Ross (
Date: Mon Apr 17 2006 - 13:38:17 CDT

> i generate a PDB file using ambpdb, but the center of
> PDB coordinate from ambpdb seems to different from the original PDB file.

leap centers the molecule in a box that has a corner at 0,0,0.

> .. I want to compare the changes in my original PDB file
> after minization. If yes then how can I overlap these two structures?

Use ptraj with an rms fit.

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