RE: [NAMD] How to build and simulate a periodic DNA in NAMD

From: Nielsen, Steven (
Date: Sat May 06 2017 - 13:49:13 CDT

Hi Sebastian,

Adding a "patch" to your topology file is the easiest way.
In my case, which is for the helical RNA strand in the TMV virus,
I wanted to make the RNA strand infinitely long.
My "pgn" file looks like:
package require psfgen
topology top_all27_prot_na_SON.inp
# add RNA
segment RNA {first none; last none; pdb rna.pdb}
coordpdb rna.pdb RNA
patch PBCrna RNA:1 RNA:150
regenerate angles dihedrals
writepdb x.pdb
writepsf x.psf

The key here is the patch command. My "PBCrna" patch, in the topology file, looks like:
PRES PBCrna 0.0
BOND 1P 2O3'

That's it!! The "regenerate" command generates the correct bends and dihedrals to
accompany the bond that I added. This patch adds a bond between atom "1P" on the
first RNA base and the atom "2O3'" on the last (#150) RNA base.

Note: in VMD the bond will be drawn across the box, but that is just how VMD displays
it, it really it across the PBC.


From: [] on behalf of The Cromicus Productions []
Sent: Saturday, May 6, 2017 1:14 PM
To: NAMD list
Subject: namd-l: [NAMD] How to build and simulate a periodic DNA in NAMD

Hi everyone,

I'd like to simulate an infinitely long, periodic dsDNA in NAMD.
To do so I read in Nano Lett., 2015, 15 (12), pp 83228330 that I must
covalently bond the ends of the DNA to their periodic copies.
Any idea of which would be the easiest way to do this?

Thank you very much,


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