VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Wed Sep 17 2008 - 21:46:39 CDT

Hi,
  The result will be affected by the values of x/y/z that you
specify in the second call. Both commands are using the same
padding size, so I would expect that you should only see a difference
if you specify different x/y/z coordinates for minmax than what
solvate computes for itself automatically (e.g. via "measure minmax"
in the code, as I recall).

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Wed, Sep 17, 2008 at 02:28:55PM -0400, Mamta Mohan wrote:
> Dear VMD team
>
> If I solvate protein using command listed below
>
> filename.psf filename.pdb -t 15 -o filename
>
> or
> filename.psf filename.pdb -minmax {{x y z} {x y z}} -t 15 -o filename
>
> ideally I should get identical files or they will be different?
>
> If they are different, what is the difference?
>
> Thank you.
> Mamta Mohan 

-- 
NIH Resource for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
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