VMD-L Mailing List

From: Peter Freddolino (petefred_at_ks.uiuc.edu)
Date: Tue May 30 2006 - 13:38:20 CDT

Dear Abu,
pdb files do not actually store bond information, so every time you load
this pdb file the bond will be displayed because it is formed from a
distance search. For what purpose do you need this bond deleted? If you
are trying to prepare an MD run, what will be important is the
information in your structure file.
Peter

Naser, Md Abu wrote:

> Hi All,
>
> I have broken some disulfide bond using the option Mouse->add/remove
> bonds and I want to save the
> changes as pdb files. I tried using save coordinates but when I reload
> it the bonds are still there.
>
> I would appreciate if anyone helps me out.
>
> regards,
>
> Abu Naser
>
> School Of Life Sciences
> Heriot-Watt University
> Edinburgh EH14 4AS
> Email: mn2_at_hw.ac.uk
> Phone: +44(0)1314518265
> Fax : +44(0) 131 451 3009
>
>
>
>