[Chimera-users] Ligand parametrization

Miro Moman 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?

Kind regards,


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