Peptide Nucleic Acid Functionality

pmx
1

Hello,

I use pmx a lot for free energy calculations - thanks for that!

I was wondering if there are any plans to incorporate functionality to mutate peptide nucleic acid residues. I currently do so manually by copying the hybrid bases across from pmx-generated ones for DNA/RNA and use the values in ffbonded.itp to fill in any gaps.

If there’s no intention of doing this are there any instructions available for me to add them to my pmx install manually?

BW,
Jack

1 Like
2

Hey,

sorry for the late reply. I have not previously considered peptide nucleic acid support, but that actually does sound interesting. Are there any good force fields for such constructs?

Vytas

1 Like
3

Hi,

Thanks for getting back - also late reply as over Christmas! I use Charmm36m which incorporates the parameters described most recently in this paper: Improved Force Fields for Peptide Nucleic Acids with Optimized Backbone Torsion Parameters - PubMed

EDIT: The link for the forcefield port to Gromacs is MacKerell Lab

In the file forcefield.doc reference to the above paper can be seen.

Jack