AMBER Archive (2006)

Subject: AMBER: about the std of computational alanine scanning

From: tongli (tong.li_at_rega.kuleuven.be)
Date: Fri Dec 01 2006 - 05:50:11 CST

Dear colleagues
  I have met a problem when I used Computational Alanine Scanning to
calculate the binding free energy. Normally we can calculate the
ÄGwild-type and ÄGmutant respectively and only got the final values of
ÄG with their own std and we calculate the ÄÄG by this equation
ÄÄG=ÄGwild-type-ÄGmutant. But it seems difficult to get the std of ÄÄG
automatically because we just use two values, one from the ÄGwild-type
and one from the ÄGmutant. It will be very complex to extract every term
from the ÄGwild-type and ÄGmutant separately and calculate the std
manually. Can I modify the mm_pbsa.pl to make this calculation
automatically or some other suggestions?
 
 
Thanks in advance!
Tong Li

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