VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Tue Jul 31 2018 - 13:17:36 CDT

If you can give me the input files and a short script (calling solvate
via the script interface) so that it reproduces the problem you're having,
I should be able to fix whatever it is that has gone amiss here, or tell you
why it's not working as you expect. Just tar/zip the associated files and
email them to me and I'll take a look.

Best,
  John Stone
  vmd_at_ks.uiuc.edu

On Tue, Jul 31, 2018 at 10:38:20PM +0530, Mani Kandan wrote:
> Thanks,Â
> 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 <[1]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,
> Â John Stone
> Â [2]vmd_at_ks.uiuc.edu
> On Tue, Jul 31, 2018 at 11:53:39AM -0500, John Stone wrote:
> > Hi,
> >Â Â 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,
> >Â Â John Stone
> >Â Â [3]vmd_at_ks.uiuc.edu
> >
> > On Tue, Jul 31, 2018 at 04:54:53PM +0530, Mani Kandan wrote:
> > > Dear all,
> > >
> > >
> > >Â Â Â Â Â Â Â Â Â 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) [4]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
> > [5]http://www.ks.uiuc.edu/~johns/Â Â Â Â Â Â Phone: 217-244-3349
> > [6]http://www.ks.uiuc.edu/Research/vmd/Â Â Â
>
> --
> NIH Center for Macromolecular Modeling and Bioinformatics
> Beckman Institute for Advanced Science and Technology
> University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
> [7]http://www.ks.uiuc.edu/~johns/Â Â Â Â Â Â Phone: 217-244-3349
> [8]http://www.ks.uiuc.edu/Research/vmd/Â Â Â
>
> References
>
> Visible links
> 1. mailto:johns_at_ks.uiuc.edu
> 2. mailto:vmd_at_ks.uiuc.edu
> 3. mailto:vmd_at_ks.uiuc.edu
> 4. mailto:vmd_at_ks.uiuc.edu
> 5. http://www.ks.uiuc.edu/~johns/
> 6. http://www.ks.uiuc.edu/Research/vmd/
> 7. http://www.ks.uiuc.edu/~johns/
> 8. 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/