Request: sample mdps and starting structures

The functionality of OpenMM will (eventually) include everything that one would need to run modern molecular simulation.
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Christopher Bruns
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Joined: Thu Apr 07, 2005 1:10 pm

RE: Request: sample mdps and starting structures

Post by Christopher Bruns » Mon Feb 16, 2009 2:01 pm

The warnings like

"no type found for atom=<N> type=<NL>"

are related to the GBSA implicit solvent parameters defined in the file "params.agb". If you inspect the contents of params.agb, you will see that only AMBER atom types are defined. Those parameters are for the atoms types of the ffamber force fields. The ffamber paramters for gromacs can be found at http://chemistry.csulb.edu/ffamber/

To use the OpenMM GBSA-OBC implicit solvent forces with a forcefield other than ffamber, you would need to modify params.agb file to recognize the atom types of your force field. I believe that only the first two columns of the params.agb file are used.

If you succeed in creating a params.agb file that works with another popular force field, I encourage you to share the resulting file with the community. I'm certain it will be appreciated.

--Chris Bruns
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