AMBER Archive (2002)

Subject: Gibbs tutorial problem

From: yuann (yuann_at_bioinfo.ndhu.edu.tw)
Date: Wed Jul 24 2002 - 19:40:50 CDT

Greetings,
  When I follow all steps in Gibbs toturial(Valine to Alanine Free Energy
determination), the final md before gibbs run seems bad, ie. WAT diffuse
and it can't continue Gibbs run.

(If I use this coordinate, Gibbs return warnning message as follow)
 WARNING: Atom # 376 more than 1 box length from the central box image.
 WARNING: Atom # 626 more than 1 box length from the central box image.
 WARNING: Atom # 812 more than 1 box length from the central box image.
 WARNING: Atom # 1006 more than 1 box length from the central box image.

I use AMBER6, all force field files, leap source files, input script files
are the same as this toturial describes. However, I still have no idea
what mistake I made.
I'd appreciate your help and advice.

Best Regards, sychen.