Re: Nonstandard ligand-DNA system

From: Saaz Sakrikar (
Date: Tue Jun 11 2013 - 16:47:13 CDT


My ligand molecule is very nonstandard- it has a triazacyclononane part,
but the side chains are more standard and their files are found in the
cgenff topology files.

How should I proceed with psf generation of this nonstandard small

I have read the forcefield tutorial but there the problem was to generate
parameters for a single bond not found in the topology file, here it is an
entire ring system (which will be linked to side chains, which are

Is molefacture reliable in cases like this?

Thank you,

On Fri, Jun 7, 2013 at 2:45 AM, Saaz Sakrikar <> wrote:

> Hi,
> 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
> systems.
> 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
> errors.
> Thank you,
> Saaz Sakrikar
> 3rd year UG

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