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

From: Sushil Mishra <sushilbioinfo.gmail.com>
Date: Fri, 10 Jul 2009 19:26:20 +0100

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 ??