VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Thu Nov 24 2016 - 12:18:43 CST

Hi,
  It is possible that the issue you're encountering is caused by
mismatched coordinate units or something similar. Are your XYZ
file coordinates in Angstroms or nanometers? I would have expected
solvate to correctly delete waters close to your structure if it was
used properly and all of the units are consistent.

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Thu, Nov 24, 2016 at 05:30:50PM +0100, Dawid das wrote:
> Dear VMD Experts,
>
> I have a structure in XYZ file format and I would like to solavate it with
> Solvate plugin.
> However, when I choose minimum and maximum dimensions of the box, I get my
> box of
> water molecules but water molecules that are too close to my structure are
> not deleted. Is
> there a simple way to do proper solvation of structure in a XYZ file?
>
> Best regards,
> Dawid Grabarek 

-- 
NIH Center for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
http://www.ks.uiuc.edu/~johns/           Phone: 217-244-3349
http://www.ks.uiuc.edu/Research/vmd/