Nucleic acid-small molecule system

From: Saaz Sakrikar (
Date: Fri Jun 07 2013 - 01:45:49 CDT


I have previously worked with Amber and am now using NAMD.
My system is a complex nucleic acid (a three-way junction) binding a
complicated small molecule.

A lot of combined parameter/topology files have been provided dealing with
protein-NA, protein-lipid and seemingly also protein-small molecule
systems, however there seems to be no combined file for NA-small molecule
Upon reading the manual, it seems that I need to combine the small molecule
forcefield parameters and the nucleic acid parameters, however, there seems
to be no example of this on the archives or in the tutorials.

Can someone please help?
I have separated my input DNA into its component strands (saved as separate
PDB files) and also have the pdb structure of the small organic ligand. I
also have the PDB for the combined ligand-DNA system.

Also, I have heard that psfgen has a tendency to convert deoxyribose bases
into ribose bases...What should be done to avoid this?

Also, I tried using molefacture but it seems to be generating a lot of

Thank you,
Saaz Sakrikar
3rd year UG

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