Free energy with amber topology

From: Stefano Corni (
Date: Fri May 26 2006 - 02:53:28 CDT


I would like to calculate a free energy difference between two
conformations of a protein via the thermodynamic integration method. I'm
using the topology of the system in amber parmtop format, and this seems
to create a problem to the free energy module while reading the
restraint atoms (probably because the segment name is undefined).
a) Does anyone know how to set the segment name when using the amber top?
b) Is there a script to convert the amber (7) parmtop file in a psf file?
Thank you in advance.

Best regards,

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