Re: Adding extra bond

From: Erik Nordgren (
Date: Thu Dec 16 2010 - 13:00:34 CST

Hi Francesco,

It sounds like what you need to do is modify your topology file and add a
new "patch residue" -- a bit of information that describes whatever new
atom(s) or bond(s) you want to create or remove, changes to the partial
charges, and so on.

Try opening the regular topology file (e.g., "top_all27_prot_na.rtf") in a
text editor and searching for occurrences of "PRES" -- this will show you
some example patch residues for reference, and based on those, you should be
able to create what you need. In fact, at the very end of this file there
is a "PRES CY35" that may already do exactly what you want. (I have no
experience with nucleic acid simulations, so I'm not sure...)

Then, you just need to add a line in your PSFGEN script (whatever you use to
build the PSF for the system) in order to manually apply your custom patch.
Note that you'll also need to specify the filename of your modified topology
file in the "topology" command. Also note that you may need to use come
care in terms of regenerating angles & dihedrals. (See the comments in the
various patch residue descriptions... sometimes it is important to
auto-generate *before* patching, and sometimes this needs to be done

hopefully helpful,

On Sun, Dec 12, 2010 at 5:22 AM, Francesco Oteri

> 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

C. Erik Nordgren, Ph.D.
Chemistry Department
University of Pennsylvania

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