VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Mon Mar 15 2004 - 13:55:29 CST

Hi,
  I'm not aware of any atom count limitations in Solvate, though there
might be some limit in the 'psfgen' plugin it uses or something like that
that I'm not aware of presently. If so however, I'd expect you to get
some errors during the structure building process. Do you get any warnings
during the solvate run? You didn't include a transcript of your output so
I'm left having to guess what might be happening rather than reading what
you actually did. Its much more helpful if you provide a full log of all
of the commands you typed, otherwise we have nothing to go on.

  John Stone
  vmd_at_ks.uiuc.edu

On Wed, Mar 10, 2004 at 07:23:33PM -0500, Satyavani Vemparala wrote:
>
> Hello:
>
> I have a PDB file (with water already present) of ~150000 atoms. This is
> lipid bilayer file, and iam trying to add more water to this bilayer.
>
> In the past i have been successfully able to do this with the help of some
> helpful suggestions by this forum, by using "-minmax" option.
>
> But with this file, i have been having problems, and number of waters
> coordinates are set to zero after i run the solvate script.
>
> Is there a limit on number of atoms, solvate can handle?
>
> any suggestions?
>
> Thanks
> Vani
> 

-- 
NIH Resource for Macromolecular Modeling and Bioinformatics
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