AMBER: ptraj and quasi harmonic analysis

From: Chris Moth <>
Date: Thu, 19 Apr 2007 14:58:52 -0500

When you perform normal mode analysis, I must assume you have separate,
minimized, structures for complex, receptor, and ligand from which you
are calculating the Hessian Matrix, and then diagonalizing this matrix
to get normal modes.

Is this right?

If so, in order for a comparable number to emerge from quasih-harmonic
analysis, I believe you will need to run three lengthy trajectories, one
for each of receptor, complex, and ligand.
Then, you perform ptraj on these separate trajectories.

I look forward to learning more about your reasoning though.

Do you have a literature reference that is guiding you in the
extract-all-from-one trajectory concept?

Keep us posted - and thanks


Hans Lee wrote:
> Can anybody give some clues on the quasiharmonic analysis using ptraj?
> Thanks!
> -Hans
> */Hans Lee <>/* wrote:
> Dear amber users,
> I was trying to calculate the entropic component of a ligand
> binding. However, the numbers I got from normal mode analysis is
> way off from quasi harmonic analysis. TdS = -26.4 kcal/mol for the
> former and TdS = -49.2 kcal/mol for the latter. I'm wondering if I
> made any mistakes in the ptraj input file for the quasi harmonic
> analysis. I am truly grateful if somebody can help me out. Thanks!
> The receptor has 131 residues and the ligand is residue 132. Here
> is my input file. Water has been stripped off from the trajectory.
> The TdS was calculated from the output file based on the principle
> of TdS = T ( S(complex) - S(receptor) - S(ligand)). Here S is the
> total entropy from the output of ptraj.
> trajin ./md_prod.mdcrd 1000 5000 1
> rms first .CA,C,N
> matrix mwcovar name com-var :1-131,132
> analyze matrix com-var out com-cov thermo reduce
> matrix mwcovar name rec-var :1-131
> analyze matrix rec-var out rec-cov thermo reduce
> matrix mwcovar name lig-var :132
> analyze matrix lig-var out lig-cov thermo reduce
> go
> Hans
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Received on Sun Apr 22 2007 - 06:07:33 PDT
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