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Is it a typo?

liuxz at PUBMS.PKU.EDU.CN liuxz at PUBMS.PKU.EDU.CN
Tue May 12 04:55:39 EST 1998


Dear xplorers,

Because no one has replied  me until now, I think perhaps I made mistakes
in my email. I want to know the answer to my question. So I ask again.
Any help from you will be appreciated.

In the toppar/protein_rep.param file there are some lines as following: 
------- 
{* nonbonding parameter section *} 
!  This uses a new form of the REPEL function: 
!  fVDW(R) = RCON *( Rmin ^IREX - R ^ IREX ) ^ REXP 
!  
! PROLSQ uses a function of the form: 
!  fVDW(R) = (1 / 0.5) ^ 4 * ( Rmin ^4 - R ^ 4 )  
!  
!  The epsilon values are arbitrary since the repel function does not
!depend on epsilon.  The sigma values come from converting the Van der Waals 
!  radii of the PROLSQ program into sigma values using the formula: 
!    Rmin = sigma * 2 ^ (1/6) 

... 

 NBONds
  CUTNB=7.0 WMIN=1.5
  REPEl = 1.0
  REXPonent = 4

  IREXponent = 1
  RCONst = 16.0
  TOLErance = 0.5 NBXMOD = 5
  ctonnb=5.5 ctofnb=6.0 {* for consistency only, not needed for repel *}
END
--------------------------------------------

Note the REXPonent and IREXponent values. It means that the REPEL
function is : 
    fVDW(R) = 16.0 * (Rmin^1 - R^1)^4 
Obviously this is not consistent with the PROLSQ's function. 

Is this a typo? 

Thank you very much.

Xiaozhou Liu
-------------------------------------------------------
  Xiaozhou Liu
  Biophysics and Physiology Department
  College of Life Science
  Peking University
  Beijing 100871, P.R.China
    
  E-mail: liuxz at iris.lsc.pku.edu.cn
          liuxz at pubms.pku.edu.cn
  Telephone: +86 10 62751864
-------------------------------------------------------





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