VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Sun Feb 12 2006 - 16:33:58 CST

Lily,
  Are you just interested in knowing the min/max coordinates of the
final solvent box? If so, this is easy to determine using atom
selections with 'measure minmax' on the resulting structure file.
It's possible that some older version of solvate may have printed
some debugging messages that aren't printed in the more recent
versions of the code. You can measure min/max values like this:
  set sel [atomselect top "all"]
  measure minmax $sel

  John Stone
  vmd_at_ks.uiuc.edu

On Fri, Feb 10, 2006 at 03:07:13PM -0800, lily jin wrote:
> Hi,
>
> When I add water box on the protein by using 'solvate' I miss the information about the coordinates of the two points, which I will use in the later .conf file.
>
> When I run 'solvate', it should be finish like:
>
> Info: writing pdb file F1_ATP_in_beta_EMPTY_betadp_from_36656_WB.pdb
> Info: pdb file complete.
> Solvate 1.2 completed successfully.
> {5.14699935913 -2.42300033569 1.57500076294} {187.867996216 142.183998108 153.92199707}
>
> However, don't have the last line. It is like:
> Info: writing pdb file 1woj_test_wb.pdb
> Info: pdb file complete.
> Solvate 1.2 completed successfully.
> >Main< (work) 27 %
>
> Where else can I have the information? What might be the problem?
>
> Thanks!
>
> Lixia
>
>
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-- 
NIH Resource for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
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