AMBER Archive (2008)

Subject: AMBER: Entropy calculation

From: nag raj (nagaraju_chem_at_yahoo.co.in)
Date: Wed Jan 30 2008 - 03:51:26 CST

Dear Amber users,
                                 I am apology to ask very basic question about calculation of entropy for complete free energy calculation.
  I want to calculate the free energy of binding for b-cyclodextrine and ligand complex. As per the tutorial http://amber.scripps.edu/tutorials/advanced/tutorial3/index.htm , I prepared input files, simulation was done for 3ns time scale and calculated GBTOT and PBTOT using MM_PBSA (script) method. For the complete free energy of binding, ENTROPY of the system to be calculated as per section “Calculate the binding free energy and analyze the results” in the above tutorial. I am using AMBER8.0 program.
  My doubts are:
          To calculate the entropy
  (1) Only by activating NM keyword (and also using corresponding parameters) in MM_PBSA script and running this script on trajectories obtained from MD simulation.
                                                        Or
  (2) First doing normal mode analysis on trajectories obtained from MD simulation.
  Second step is, calculate the entropy using NM keyword in MM_PBSA script on trajectory obtained from normal mode analysis.
  (3) Is entropy calculated in these two cases will vary significantly?
   
     Which one is correct method and can you provide sample file for calculating normal mode analysis.
   
  Any suggestion is appreciated.
   
                              Thank you in advance,
                                                                                    With best regards,
                                                                                    Nagaraju Mulpuri.

       
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