AMBER Archive (2005)

Subject: Re: Re: AMBER: Free energy calculation for protein-protein complex usingMM_PBSA

From: Zhiguo Liu (zgleo_at_tom.com)
Date: Thu Jun 30 2005 - 04:56:42 CDT

Dear Thomas,
    Thanks for your help! If I understood correctly, you mean that the vibrational part of the energy could be just ignored. Now someone tell me that the translational and rotational parts of the energy functions are independent of the conformation of the protein, i.e., it is not necessary for these calculations to sample a lot of snapshots from the md trajectory. One snapshot is enough to estimate the conformational entropy. I wonder if it is right. Could you give me some advice?
                
          
                                                             Zhiguo Liu
                                                        
                                                                  2005-6-30

___________________________________________
    
Zhiguo Liu
Ph.D candidate
Drug Discovery and Design Center
Shanghai Institute of Materia Medica
Chinese Academy of Science
Shanghai, China
zhiguo.leo_at_gmail.com
___________________________________________


----- 2005-06-30, 15:14:01, Thomas Steinbrecher wrote -----
  Re: AMBER: Free energy calculation for protein-protein complex usingMM_PBSA

>Dear Zhiguo,
>
>calculating bindung free energies between protein molecules is within the
>scope of MM-PBSA. This paper describes something similar:
>
>Gohlke H. ; Case D.A. 2003 Converging free energy estimates: MM-PB(GB)SA
>studies on the protein-protein complex Ras-Raf J. Comput. Chem. 25,
>238-250
>
>The size of the system should be no problem for the MM and PB parts of the
>calculation.
>
>You might however run into problems doing nmode calculations on so large a
>system, so you proably have to figure out a way to estimate the entropy
>contribution to binding, like assuming only the classical rotational and
>translational degrees of freedom are lost.
>
>Kind Regards,
>
>Thomas
>
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