AMBER Archive (2009)

Subject: [AMBER] calculation of binding energy for lectin and fucuse..

From: Sushil Mishra (sushilbioinfo_at_gmail.com)
Date: Fri Jul 10 2009 - 13:26:20 CDT

Hello all first of all i thank each and every one for sharing
knowledge. i am new to amber and i want to learn from all of you. i am
facing problem from last 2 weeks and i am using this as my last weapon to
aver come from it. Please suggest me something to overcome from it.

         I want to calculate the free energy of binding of alpha - L Methyl
Fucose with lectins. I tried to carry out it in amber. fallowed the same
procedure give in amber tutorial (TUTORIAL
2<http://www.rosswalker.co.uk/tutorials/amber_workshop/Tutorial_two/index.htm>:
Using dynamics simulations to estimate binding energetics. (*Beginner*)).
         In the tutorial they are getting binding energy simply by equation
BE = Ecomplex - Eprotein - Epeptide.
But unfortunately for my case i am getting the free energy of binging very
much different. it is in +ve. I have PDB of my lectin and fucose which i
showing -9.5 Kcal/mol free energy of binding in ITC and SPR experiments.
       i am getting the EPTOP as fallows
Ecomplex = - 5164
Eprotein = - 5248
Epeptide = + 74

   so what may be problem?? Parameter Chosen by me was-

Production MD
 &cntrl
  imin=0, irest=1, ntx=5,
  nstlim=2000,dt=0.001, ntc=1,
  ntpr=20, ntwx=20,
  cut=16, ntb=0, igb=1, intdiel=4,
  ntt=3, gamma_ln=1.0,
  tempi=300.0, temp0=300.0,
 /

A V E R A G E S O V E R 2000 S T E P S (when doing MD of Methyl fucuse
seperately)

 NSTEP = 2000 TIME(PS) = 4.500 TEMP(K) = 289.64 PRESS =
0.0
 Etot = 59.8704 EKtot = 22.4469 EPtot =
37.4236
 BOND = 9.2444 ANGLE = 11.5774 DIHED =
1.5039
 1-4 NB = 4.2159 1-4 EEL = 43.5038 VDWAALS =
-1.1770
 EELEC = -22.5976 EGB = -8.8472 RESTRAINT =
0.0000

please suggest me what the problem and the energy for methyl fucose is
positive. how can i over come from it ??

I request to all member please help me and..suggest me how can i calculate
free energy of binging.

sincerely
Sushil Mishra
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