# Re: AMBER: ptraj and quasi harmonic analysis

From: Hans Lee <indyhans2000.yahoo.com>
Date: Thu, 19 Apr 2007 18:46:38 -0700 (PDT)

Chris Moth <chris.moth.vanderbilt.edu> wrote: >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?

Yes. I have 200 frames for complex, receptor and ligand respectively. Instead of running separate trajectories, simulation was carried out on the complex only. Snapshots for receptor and ligand were extracted from the complex trajectories. I am not sure how the results will improve if simulations were carried out on complex, receptor and ligand respectively. The structures were minimized before Matrix calculation.

>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.

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

I learned this right from the Amber mailing list.

-Hans

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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>
>
>
> ------------------------------------------------------------------------
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Received on Sun Apr 22 2007 - 06:07:37 PDT
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