Free energy perturbation (FEP) hybrid pdb file

From: Christian Jorgensen (
Date: Tue Dec 07 2010 - 21:36:31 CST

I wish to simulate a FEP mutation in NAMD of a proline residue to a hydroxyproline residue (i.e. mutating a H into OH)

The converse (hydroxyproline to proline) is an easy process because this is simply the annihilation of H and the mutation of O into H (retaining the same coordinates)

My question: How does one write a hybrid pdb file containing the coordinates of both vanishing and appearing atoms when I do not the coordinates of the atom (H) that is to appear?

In the FEP tutorial we are always *given* the hybrid pdb file already (e.g. tyr2ala.pdb) and I want to know how this is created.

Any help on this would be appreciated.


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