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