VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Wed Sep 14 2011 - 13:38:40 CDT

On Wed, 2011-09-14 at 11:48 -0500, snoze pa wrote:
> Dear VMD Users,
>
> I want to connect two residues using LINK or a patch command. They
> are 10A apart in pdb file but I want to connect them using C-N bond.
> How can I connect them? or how to use LINK or PATCH command in vmd or
> psfgen

psfgen is overkill in this case. just load your psf file and
a matching coordinate file and use the addbond command from
the topotools plugin to add a specific bond.

http:://sites.google.com/site/akohlmey/software/topotools/topotools---documentation#TOC-addbond-id1-id2-

and then save the modified .psf file. that should do the trick.

cheers,
    axel.

> thank you
>
> S