Problem of ATP mutated to dATP in solution using FEP method

From: dbaogen (dbaogen_at_gmail.com)
Date: Mon Aug 05 2013 - 02:14:24 CDT

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Dear all,

        I have met a problem about mutating ATP to dATP in solution using FEP method. The calculation procedure and main parameters are listed as follow.

       (1) construct hybrid molecule and generate top file. Here, the sugar atoms of ATP are mutated. mutating part of fep file is:

   
      ATOM 1 C4'R ADA L2003 12.106 -18.293 -62.436 1.00 -1.00 LIG C
      ATOM 2 H4'R ADA L2003 12.692 -17.499 -62.599 1.00 -1.00 LIG H
     ATOM 3 O4'R ADA L2003 10.757 -17.889 -62.502 1.00 -1.00 LIG O
     ATOM 4 C1'R ADA L2003 10.192 -17.791 -61.196 1.00 -1.00 LIG C
     ATOM 5 H1'R ADA L2003 10.061 -16.812 -61.037 1.00 -1.00 LIG H
     ATOM 6 C4'D ADA L2003 12.106 -18.293 -62.436 1.00 1.00 LIG C
     ATOM 7 H4'D ADA L2003 12.692 -17.499 -62.599 1.00 1.00 LIG H
    ATOM 8 O4'D ADA L2003 10.757 -17.889 -62.502 1.00 1.00 LIG O
    ATOM 9 C1'D ADA L2003 10.192 -17.791 -61.196 1.00 1.00 LIG C
    ATOM 10 H1'D ADA L2003 10.061 -16.812 -61.037 1.00 1.00 LIG H
    ...
    
    ATOM 25 C2'R ADA L2003 11.182 -18.340 -60.152 1.00 -1.00 LIG C
   ATOM 26 H2'1 ADA L2003 10.783 -19.158 -59.738 1.00 -1.00 LIG H
   ATOM 27 O2'R ADA L2003 11.371 -17.537 -58.972 1.00 -1.00 LIG O
   ATOM 28 H2'R ADA L2003 10.644 -16.945 -58.764 1.00 -1.00 LIG H
   ATOM 29 C2'D ADA L2003 11.182 -18.340 -60.152 1.00 1.00 LIG C
   ATOM 30 H2'2 ADA L2003 10.783 -19.158 -59.738 1.00 1.00 LIG H
   ATOM 31 H2'D ADA L2003 11.371 -17.537 -58.972 1.00 1.00 LIG H

   (2) solvate the hybrid molecule and generating solvation box.
   (3) minimize and equilibrate the system using the fep.tcl script downloaded from NAMD official webpage
   (4)forward calculation for mutating ATP to dATP, main FEP parameters are:
           
  alch on
 alchType FEP
 alchFile ionized.fep
 alchCol B
 alchOutFile forward-on_long.fepout
 alchOutFreq 10

 alchVdwLambdaEnd 1.0
 alchElecLambdaStart 0.5
 alchVdWShiftCoeff 4.0
 alchDecouple on

 alchEquilSteps 300000
 set numSteps 1000000

 runFEP 0.0 1.0 0.025 $numSteps

  (5) extract the free energy change from lambda=0 to lambda=1 (Figure as follow). According to the above parameter settings, a turning point will occur when lambda value is 0.5. But in this case, the result is not what we expect.
       At present, I could't not find the right way to solve it. I would appreciate if you could give me some help and suggestions. Thank you!

 
 Best wishes
Duan Baogen


            

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