[Chimera-users] Ligand parametrization
miromoman at gmail.com
Tue Sep 4 05:40:53 PDT 2012
When energy minimising protein-ligand complexes, I have observed that
Chimera seldom, if ever, complains about missing parameters.
However, when I try to generate a Pmrtop file for the same complexes,
quite often sLeap is unable to complete the request due to its inability
to recognise certain atom types..
Provided that the minimization engine (MMTK) is using the Amber force
filed, I was wondering:
Are parameters computed in the same way?
If not, what are the differences? Maybe a different forcefield version?
In addition, is there a way to inspect the parameters that have been
generated for minimising a given ligand or non-standard residue?
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