AMBER Archive (2007)

Subject: AMBER: topology for postprocessed files?

From: anna.schrey_at_gmx.de
Date: Thu Apr 12 2007 - 04:57:28 CDT

Deas Amber community,

I would like to postprocess trajectories that way that I have to remove cetrain residues (e.g. a ligand) and calculate the energies afterwerds. The trajecotries are no problem, they can be modified that way using ptraj. But how to get the corresponding topology file? And how can I calculate the energies (e.g. E_el and E_vdw) with SANDER?

kind regards,

Anna 

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