VMD-L Mailing List

From: Francesco Pietra (chiendarret_at_gmail.com)
Date: Thu Oct 04 2018 - 09:07:48 CDT

Hi Axel
You suggested 8 years ago, in a different context,

> francesco,
>
> this is the kind of task, the topotools plugin was written for.
>
> you can do: topo addbond <atom id1> <atom id2>
> or: topo delbond <atom id1> <atom id2>
>
> to selectively add or remove bonds. there are similar
> commands to add/delete angles and dihedrals that
> go with this bond, too. or you can use the guessangle
> guessdihedral commands to rebuild the angle/dihedral
> lists from the bond topology.
>
May I as whether

package require topotools

etc....

can be inserted into psfgen and used to create a bond between a C-atom of a
ligand and CYS-N of a protein? All that in place of using

PATCH ....

related to a specific PRES.

thanks

francesco pietra