Try:
image center familiar
All the best
Ross
/\
\/
|\oss Walker
| Department of Molecular Biology TPC15 |
| The Scripps Research Institute |
| Tel: +1 858 784 8889 | EMail:- ross.rosswalker.co.uk |
|
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> -----Original Message-----
> From: owner-amber.scripps.edu
> [mailto:owner-amber.scripps.edu] On Behalf Of Grzegorz Jezierski
> Sent: Tuesday, July 26, 2005 06:26
> To: amber.scripps.edu
> Subject: AMBER: Periodic box imaging using ptraj
>
> Dear AMBER users,
> I ran a 2-ns of DNA in rectilinear water box. I had the
> wrapping option
> OFF (iwrap=0) throughout the entire run.
> After transforming my trajectory (generated by AMBER8) with
> ptraj, I am
> getting a strange box shape:
> * if I use command: "image center byres :WAT" - then I get something
> like two intersecting (at right angles) narrow boxes merged into one,
> or,
> ** if I use command: "image origin :WAT byres :*" - then I
> get a "nice"
> rectilinear box, but the solute is displaced out of the box. Other
> combinations of the above command produce either of these 2
> types of system.
> Before I used AMBER6 with wrapping ON and didn't have this
> type of problem.
>
> Thank you in advance,
> Grzegorz
>
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Received on Wed Jul 27 2005 - 17:53:00 PDT
