VMD-L Mailing List

From: Sergio Anis (sergioanis_at_ispwest.com)
Date: Fri Oct 21 2005 - 13:27:36 CDT

i asked this a while ago and the John said that vmd doesn't look at the connect statments, it put bonds according to the distance.
so you have to load the psf with the pdb to have vmd display the right structure.
and for the simulations, shouldn't be any problem since you will use the psf

see you
Sergio

----- Original Message -----
From: Nitin Bhardwaj [mailto:nbhardwaj_at_gmail.com]
Sent: 10/21/2005 10:05:09 AM
To: vmd-l_at_ks.uiuc.edu
Subject: vmd-l: Creating bond between two atoms

> 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
>