AMBER Archive (2007)

Subject: Re: AMBER: Once again, "distance" command in ptraj

From: Carlos Simmerling (carlos.simmerling_at_gmail.com)
Date: Mon Jun 04 2007 - 09:15:22 CDT

is there box info in your prmtop and mdcrd files?
even then you need to use center/image commands.

On 6/4/07, Roberto Veiga <roberto.sapiens_at_gmail.com> wrote:
>
> When running the "distance" command in ptraj, I saw:
>
>
> -------------------------------------------------------------------------------------------------------
> Processing AMBER trajectory file ../prod.mdcrd
> DISTANCE: box angles are zero, disabling imaging!
>
> -------------------------------------------------------------------------------------------------------
>
> and I got a distance much larger than I expected between two residues
> (because imaging was not used). But in my inpcrd files I provided box
> information (box angles are all 90.0 degrees). In ptraj, I used the
> command box to reset the box properties, but I got the same. Anything
> missing?
>
> []s,
>
> Roberto
>

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