From: John Stone (
Date: Mon Oct 07 2013 - 09:37:35 CDT

  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.

  John Stone

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

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