Dear colleagues,
I have got few complexes of my protein with different low molecular organic ligands, and now I want to assess the binding stability through MD simulation in NAMD. Of course, there are no topology for these ligands, so I used the SwissParam and CGenFF ParamChem to generate it. But even after joint work of these two servers NAMD still requires a lot of parameters (some BONDS, ANGLES, DIHEDRALS and IMPROPERS are missing in files generated by the servers, I checked it in text editor). But how can I define these parameters? I read that QM calculations can be used for such purpose, but I have not found any detail tutorials/manual on this issue. I have the GAMESS, but no idea how can it help me with parametrization of my ligands.
I would be grateful for any suggestions.
If you address the topology and parameter files generated with the SiwissParam in your input file, you will not face with any forcefield problem.
I highly suggest you not to deal with QM methods to find forcefield parameters for your non-standard residues, since it's very challenging and very high-time consuming process and it's out of the scope of your project. The mentioned servers or methods are able to roughly calculate acceptable parameters for your system and the errors, you are facing in your calculations are quite technical being solved easily..
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