I wanted to perform a molecular dynamics simulation of a protein-ligand complex in Gromacs using the CHARMM36 force field. When generating the ligand topology file using CGenFF (https://cgenff.umaryland.edu/) following suggestion pops up in the str file:
****
! Penalties lower than 10 indicate the analogy is fair; penalties between 10
! and 50 mean some basic validation is recommended; penalties higher than
! 50 indicate poor analogy and mandate extensive validation/optimization.
****
How I can do the validation?
http://www.swissparam.ch/ try doing the same by this and then make a comparison. HTH!
http://www.swissparam.ch/ try doing the same by this and then make a comparison. HTH!
What is the geometry of your ligand? If it hasn't been properly minimized then you may be running into issues with intra-molecular steric clashing.
Thanks Anwesh Pandey for the answer. How can I do the comparison? File are of different formats for Swissparam and CGenFF.
Alexander Williams, Yes the structure was minimized with mmff94 force field in Avogadro software.
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