Re: Adding extra bond

From: Axel Kohlmeyer (
Date: Fri Dec 17 2010 - 04:20:11 CST


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.

this functionality is fairly new, so i would strongly
advise to carefully check the results (for each bonded
interaction is a get/set XXXlist command) to make sure
you get the modification that you want/need.

please let me know, if there are any problems (or bugs?).


On Sun, Dec 12, 2010 at 5:22 AM, Francesco Oteri
<> wrote:
> Dear namd users,
> I need to simulate a circular  DNA with namd and charm force field.  I've to
> create a bond between the first nucleotide and the last nucleotide but I
> don't find any patch or command to add thi extra-bond. Autopsf don't
> recognize the bond so I obtain a linear structure.
> Is there a way to add a bond between the interested atoms or I need to
> modify the psf file by hand?
> Best regards, Francesco

Dr. Axel Kohlmeyer
Institute for Computational Molecular Science
Temple University, Philadelphia PA, USA.

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