VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Wed Feb 12 2003 - 16:08:55 CST

Dear Ioana,
  If you're loading the structure from a PDB, VMD is forced to guess
what atoms are bonded to each other. If it guesses incorrectly, the
best solution is to load the actual AMBER Parm file rather than a PDB
version of the same structure, as VMD will get the full connectivity
information from the Parm file where it will not from a PDB.
Let us know if you need more help with this. I assume you're using
VMD 1.8 right?

Thanks,
  John Stone
  vmd_at_ks.uiuc.edu

On Wed, Feb 12, 2003 at 02:03:29PM -0800, Ioana Cozmuta wrote:
> Hi,
>
> I have an RNA single strand, hydrogen terminated generated with amber.
> When I load the file in vmd however the terminal hydrogens are not
> recognized as being bonded to the neighboring oxygen atoms.
> Any idea why this is happening and what is the best way to correct this?
>
> Thank you,
> Ioana
>
>
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