VMD-L Mailing List

From: Nitin Bhardwaj (nbhardwaj_at_gmail.com)
Date: Fri Oct 21 2005 - 12:05:09 CDT

Hi all,
  I am trying to create a bond between an oxygen and a hydrogen atom
(atom 64 and 65 as follows) in a non-standard lipid.

ATOM 64 O10 INO X 2 4.809 -7.607 -1.405 1.00 0.00
ATOM 65 H11 INO X 2 4.090 -8.131 -0.074 1.00 0.00

so at the end of the PDB file I say:

CONECT 64 65

But the bond still does not show up in VMD. It shows up fine in PyMol.

I think VMD by itself decides whether to place a bond between atoms.
The distance between the above two atoms is 1.6 Ang. What do I do to
make this bond show up in VMD?

I further need to simulate the lipid. Do I need to be worried that
this bond does now show up in VMD (although it appears in my topology
file that there is bond between O10 and H11?

Thanks a lot in advance,
Rgds,
Nitin