Hello Everyone, I have a AUTODOCK docking PDB file for both Protein-Ligand-DNA Complex. I want to do simulation of these complex. but simulation failed due to unrecognized ATOM TYPES present into the DNA. So, can you please have any suggestions?
Hi,
I heard that, GROMACS software is good at running protein-ligand-DNA complex simulation. Provided that ligand is Ions..Cause I have seen, Ions (Mg+) being in simulations, hvaent seen bigger ligand molecules in simulations. But i guess it should work.
Have u tried using GROMACS for it ?
i did on GROMACS but the following error is raised when i utilized the AMBER99SB protein, nucleic AMBER94.
the error massage i attached in below.
The error message is quite informative. Check the structure: Make sure that all atom names in each nucleotide correspond to their equivalents in the force field file(s).
- Badges
- Science topic
- Similar topics
- Biological Science
- Molecular Biology
- Biomolecules
- Nucleic Acids
- DNA