VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Tue Jul 31 2018 - 11:53:39 CDT

Hi,
  The overlap safety check code in the solvate plugin uses a
hard-coded safety check distance tolerance, and it was only really
tested for the standard water box. I would ignore the warning assuming
that you don't see anything scary in the structure.

Best,
  John Stone
  vmd_at_ks.uiuc.edu

On Tue, Jul 31, 2018 at 04:54:53PM +0530, Mani Kandan wrote:
> Dear all,
>
>
> When I am using non-standard solvant i.e SPCE water model
> using solvate plugin, I got the following error:
>
>
> Info) Extra structure overlap safety check...
> ERROR) Found 3 water atoms near the solute! Please report this bug to
> ERROR) vmd_at_ks.uiuc.edu, including, if possible, your psf and pdb file.
> Solvate failed.
>
>
> How can I solve this problem?
>
>
> Thanks,
>
> Manikandan D 

-- 
NIH Center for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
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http://www.ks.uiuc.edu/~johns/           Phone: 217-244-3349
http://www.ks.uiuc.edu/Research/vmd/