Hi,
Thank Mr. Ursby for his kindly advice for my sigmaa weghting map problem.
I get good fo-fc map now. This mailing list is so helpful that I can
always get answers from some experienced crystallographer. I love this
mailing list.
Now I have another question to ask. I noticed that in
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 in advance.
Xiaozhou.
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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.cnliuxz at pubms.pku.edu.cn
Telephone: +86 10 62751864
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