RE: Free energy perturbation (FEP) hybrid pdb file

From: JC Gumbart (
Date: Tue Dec 07 2010 - 23:04:18 CST

You first need to create a modified topology file entry that contains both
the H and the OH groups simultaneously. This isn't as bad as it sounds,
since you can start from the entries for proline and hydroxyproline (I
assume there are parameters for it somewhere). See the file in
the FEP tutorial for an example. You can then use psfgen to mutate the
proline to the hybrid residue and generate a new psf and pdb.

-----Original Message-----
From: [] On Behalf
Of Christian Jorgensen
Sent: Tuesday, December 07, 2010 9:37 PM
Subject: namd-l: Free energy perturbation (FEP) hybrid pdb file

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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