I'm working on molecular dynamic simulation of a protein-ligand complex. I tried using GROMACS, but it gives several errors whether I allow or ignore hydrogen eg "Atom HN1 in residue GLU 221 was not found in rtp entry GLU with 17 atoms
while sorting atoms.". NAMD and VMD seem complicated to me, and CHARMMS gives me errors
is there a way to refine my complex to prevent these errors? or is there a simpler MDS program/protocol I can use?
I am not familiar with these "codes"(e.g. GORMACS), however this is an area of research that I had the opportunity to participate and contribute to. The research teams at Minnesota and at Houston I worked with utilized different simulation techniques utilized in chemical physics. If you're interested, I can point you to a few publications in that field.
I would suggest starting building your system in moltemplate and visualize it then use either gromacs or lammps.there also might be command to delete or add overlapping Hydrogen in your system.
Please see my publications with those of my co-authors at one of these sites:
Google Scholar: https://scholar.google.com/citations?user=oh-kAE4AAAAJ&hl=en
Semantic Scholar: https://www.semanticscholar.org/author/Najib-N.-Abusalbi/91989953
Academia: https://lsu.academia.edu/NajibAbusalbi
Hope this helps
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