VMD-L Mailing List

From: Vermaas, Joshua (Joshua.Vermaas_at_nrel.gov)
Date: Tue Jul 31 2018 - 13:22:47 CDT

Hi Manikandan,

If I understand this correctly, you used a SPCE waterbox passed along with the non-water options, correct? If so, in addition to making the resname QQQ in the psf/pdb pair, you also should make sure that all the molecules are in the positive octant of 3D space (ie. x, y, z all greater than 0). If not, you can run into problems with the safety check code when too many/not enough atoms are deleted.

-Josh

On 2018-07-31 11:46:36-06:00 owner-vmd-l_at_ks.uiuc.edu wrote:

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<mailto: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<mailto: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<mailto: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<mailto: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/data=r9Kx%2FBQ866DCuTKmbrdjvtZBdn7jmqGUpXsBvTCgAXc%3D&reserved=0> Phone: 217-244-3349
> http://www.ks.uiuc.edu/Research/vmd/86559957429500&sdata=1jkEijEREYodDT1IxVJYKsJHHtd5zwtVIPdVUTTGEMw%3D&reserved=0> 

--
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/data=SGwbIh2oFUaxQQs4PKmPNsqA1CJA56z%2Faz4piDR0Ii8%3D&reserved=0>           Phone: 217-244-3349
http://www.ks.uiuc.edu/Research/vmd/86559957439505&sdata=Z1J%2Bg3seeRwm2Nd%2BcA4SLVkwd%2BZHFeChTcnQ71rz8kA%3D&reserved=0>