VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Mon Oct 07 2013 - 09:37:35 CDT

Hi,
  If you see the extra bonds on your waters, and you loaded the PSF into
VMD, it is because the bond is explicitly listed in the PSF file.
If I'm not mistaken, this is likely related to the particular water
model you are likely using, and it's "normal" for that water model.

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Mon, Oct 07, 2013 at 04:23:19AM -0700, Ramin Ekhteiari wrote:
> ----------------------------------------------------------------------
>
> Hi dears,
>
> I embedded protein into the phospholipid bilayer, and generated psf and
> pdb file via charmm gui membrane builder, but when I try to load it into
> VMD,
> I see bond between the hydrogens of water molecule, as normal it should
> not be..
>
> Would be grateful for any help..
>
> Cheers,
> Ramin 

-- 
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/