AMBER Archive (2006)

Subject: Re: AMBER: trajout script

From: Thomas Cheatham (
Date: Mon Nov 06 2006 - 14:39:04 CST

> trajin md1.mdcrd 100 100 1
> trajout 100tobeused.pdb pdb
> center: 1-882 mass origin
> image origin center
> go
> ----
> After I run it, I got the pdb file. However I find the
> protein is already out of the water box.

If that is the script you are using, the "center:" command is ignored as
this is not a command. You want:

center :1-882 mass origin

Also, if your protein is made up of multiple subunits, likely the imaging
is more complicated. See the Amber archive and carefully read the output
produced by ptraj.

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