I have a nucleic acid that has bad termini. I can use Swiss Pdb viewer to reconstruct it but i wondered what is the most precise tool for it? Gromacs has no function to do that and charmm36 does not want to work with a nucleic acid with chopped termini. Charmm GUI uses a tool for proteins but that tool is not designed for nucleic acids.
Hii
Hope the below mentioned link would help you
Sim AY, Minary P, Levitt M. Modeling nucleic acids. Curr Opin Struct Biol. 2012;22(3):273–278. doi:10.1016/j.sbi.2012.03.012
Regards
Anu
This is very simple to do in VMD software, you can select only the part that you want to take in representations tools, and then save the coordinates into a new pub or gro file. You can do the same in GROMACS too, but for that you need to know the id of the atoms that you want to remove. PyMOL is also a good option.
With nucleic acid termini i only have to add missing phosphate groups etc... but i am looking for a tool that is reliable. Removing atoms is not what i am looking for.
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