AMBER: ptraj and quasi harmonic analysis

From: Hans Lee <>
Date: Mon, 16 Apr 2007 14:19:34 -0700 (PDT)

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


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Received on Wed Apr 18 2007 - 06:07:21 PDT
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