AMBER Archive (2007)

Subject: AMBER: PMF: WHAM result

From: Catein Catherine (askamber23_at_hotmail.com)
Date: Fri May 11 2007 - 22:28:30 CDT

Dear Sir/Madam,

In ran a test jobf for PMF type calculations, I did a total of 5 windows
with the loc_win_min (the equilibrium distances (r2 and r3) used in the
umbrella sampling calculations) set at 5, 6, 7, 8, 9 A, i.e..

=================The restraint file is set as follow=======================

# distance restrainst for test
&rst iat=4,5, r1=0.0, r2=6.0, r3=6.0, r4=50.0, rk2 =30.0, rk3 = 30.,
iresid=1, ATNAM(1)=P,
ATNAM(2)=C3 /

==========================================================

Afterall, I ran the WHAM analysis for the 5 windows and it is the results
that I got.

===========================================================================
#Coor Free Prob
4.350000 inf nan 0.000000 nan
5.050000 36.245400 nan 0.000000 nan
5.750000 28.870746 nan 0.000000 nan
6.450000 26.790462 nan 0.000000 nan
7.150000 29.584412 nan 0.000000 nan
7.850000 37.865662 nan 0.000000 nan
8.550000 35.371505 nan 0.000000 nan
9.250000 36.768326 nan 0.000000 nan
9.950000 26.409505 nan 0.000000 nan
10.650000 0.000000 nan 1.000000 nan
===========================================================================

Which number in this result should I report as the DG values for the
distance change from 5 to 9 A?

If I do the DG calculation for drug-receptor complex, should I calculation
all the windows descript the drug moving from the receptor to the free
unbounded status?

In case I could like to roughly estimate the rate of drug remove from the
receptor, which number from WHAM should I used for the estimation?

Best regards,

Cat

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