Re: Adding extra bond

From: Francesco Oteri (
Date: Fri Dec 17 2010 - 05:52:46 CST

I solved the problem.
The soultion is using the patch /*lkna */that permit to link the 3' of a
segment with the 5' with another segment.

Using the same segment I obtained the circular DNA I desire.

Il 17/12/2010 11:20, Axel Kohlmeyer ha scritto:
> 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.
> 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?).
> cheers,
> axel.
> 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

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