From: Vermaas, Joshua (
Date: Thu Oct 04 2018 - 14:21:40 CDT

Hi Francesco,

If the only thing you are doing is adding a bond, topotools has the required machinery to alter the internal representation within VMD so that VMD will write a legal psf afterward that describes the new system. So something like:

topo addbond 1 2
topo guessangles
topo guessdihedrals
[atomselect top "all"] writepsf new.psf

What topotools doesn't do (and that psfgen will), is change atomtypes and charges as specified in the patch residue (PRES) command. So sure, you can make topotools make the bond and guess the angles and dihedral terms that need to be added from the new bond. It will not, however, check to make sure that your charges/atomtypes make sense for the new chemistry.


On 2018-10-04 09:18:15-06:00 wrote:

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


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


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.


francesco pietra