AMBER Archive (2009)

Subject: [AMBER] EPtot for Alpha-L- methyl fucose

From: Sushil Mishra (sushilbioinfo_at_gmail.com)
Date: Fri Jul 10 2009 - 08:47:26 CDT

Hi
i want to calculate the free energy of binding of alpha - L Methyl Fucose. I
tried to carry out it in amber. when i am running the MD of methyl fucuse
seperately it returning the energy in positive. I tried to adjust dielectric
constant values. Cuold anyone explain me tha how much should be expect
energy for Methyl fucose seperately. i am posting here the method used and
the avg of 2000 runs obtained.

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

 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 ??

sincerely 

-- 
Sushil K Mishra
Computational Chemistry Laboratory
National Centre for Biomolecular Research
ILBIT, Building A4 - 2.12
Kamenice 5
625 00 Brno
CZECH REPUBLIC
Tel.   +420 549 492 521
Mob. +420 774 816 044
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