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Hi, I have generated ligand topology (NAG5) using the CGenFF server. However looking at the .str file, atom and bond angle penalties are all below 10, however I have several dihedrals with penalties slightly above 10 (14.5 and 11.5). How should these scores be interpreted? As they are only just above 10, would they require much reparameterization? Screenshot of the .str file are below.
The comment in the header of the file addresses this. The penalties are really quite low and unlikely to be a problem, however if they are between 10 and 50, 1-D potential energy scans along those degrees of freedom are recommended, then compare the QM and MM energies. This isn’t something done (easily at least) within GROMACS.
Thanks for the reply, i’ll look into this. Side note: Thanks for your tutorials and posts i’ve seen on RG and here - they have been invaluable in getting to (somewhat) grips with Gromacs.