AMBER Archive (2004)

Subject: AMBER: minimizating complex-protein with AMBER

From: susan.costantini_at_unina2.it
Date: Sun Feb 15 2004 - 03:27:00 CST

 
 I am using Amber 7 to minimize complex-structure constituted by three
 chains (370 Amino acids).
 The minimization stops after nstep = 10 and in the file nome.min.out ais
 indicated this error:
 
 The system has extended beyond
      the extent of the virtual box.
  Restarting sander will recalculate
     a new virtual box with 30 Angstroms
     extra on each side, if there is a
     restart file for this configuration.
  EWALD BOMB in subroutine Routine: map_coords (ew_force.f)
  Atom out of bounds. If a restart has been written,
  restarting should resolve the error
 
 Can you help me?
 
 Susan Costantini
 
> --
>
>
> ...................................................................
> Costantini Susan
> Research Center of Computational and Biotechnological Sciences
> (CRISCEB), Second University of Naples
> Work address:
> Institute of Food Science and Technology - CNR
> via Roma 52 A/C -83100 Avellino (Italy)
> tel:++39.0825.299651 - Fax +39.0825.781585
> mobile: 347/9396453 - 329/5686016
> e-mail:susan.costantini_at_unina2.it & susan.costantini_at_isa.cnr.it
> ...................................................................
>
>
>
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> &nbsp;
> <br>I am using Amber 7 to minimize complex-structure constituted by three
> chains (370 Amino acids).
> <br>The minimization stops after nstep = 10 and in the file nome.min.out
> ais indicated this error:
> <p>The system has extended beyond
> <br>&nbsp;&nbsp;&nbsp;&nbsp; the extent of the virtual box.
> <br>&nbsp;Restarting sander will recalculate
> <br>&nbsp;&nbsp;&nbsp; a new virtual box with 30 Angstroms
> <br>&nbsp;&nbsp;&nbsp; extra on each side, if there is a
> <br>&nbsp;&nbsp;&nbsp; restart file for this configuration.
> <br>&nbsp;EWALD BOMB in subroutine Routine: map_coords (ew_force.f)
> <br>&nbsp;Atom out of bounds. If a restart has been written,
> <br>&nbsp;restarting should resolve the error
> <p>Can you help me?
> <p>Susan Costantini
> <pre>--&nbsp;
> &nbsp;
>
> ...................................................................
> &nbsp;Costantini Susan
> &nbsp;Research Center of Computational and Biotechnological Sciences
> &nbsp;(CRISCEB), Second University of Naples
> &nbsp;Work address:
> &nbsp;&nbsp; Institute of Food Science and Technology - CNR
> &nbsp;&nbsp; via Roma 52 A/C -83100 Avellino (Italy)
> &nbsp;&nbsp; tel:++39.0825.299651 - Fax +39.0825.781585
> &nbsp;&nbsp; mobile: 347/9396453 - 329/5686016
> &nbsp;e-mail:susan.costantini_at_unina2.it &amp; susan.costantini_at_isa.cnr.it
> ...................................................................</pre>
> &nbsp;</html>
>
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>

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