VMD-L Mailing List

From: Mani Kandan (manikandand5110_at_gmail.com)
Date: Tue Jul 31 2018 - 12:08:20 CDT

Thanks,

But sometimes the system is not solvated properly i.e it has some gap,
sometimes half solvated and showing this error.

Manikandan D

On Tue, Jul 31, 2018 at 10:27 PM, John Stone <johns_at_ks.uiuc.edu> wrote:

> I've made a small change to the solvate plugin that may help avoid
> this issue for custom solvents in VMD 1.9.4, we'll see how it goes when
> the next test version of VMD is posted.
>
> Best,
> John Stone
> vmd_at_ks.uiuc.edu
>
> On Tue, Jul 31, 2018 at 11:53:39AM -0500, John Stone wrote:
> > 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
> > 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/
>
> --
> 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/
>