Dear Amber Users.
I am trying to calculate non bonded interaction between two residue. I was
post process trajectory with imin=5 in sander
The input file I was taken from Amber test directory (trajene.in with box)
TIP3P PP
&cntrl
imin = 5, ntx = 1, irest = 0,
ntt = 1, tautp = 0.5, temp0 = 298.0, tempi = 298.0,
ntc = 2, ntf = 1, ntb = 2,
ntp = 1, taup = 0.5,
ntwx = 10, ntwe = 0, ntwr = 10, ntpr = 10, ioutfm = 0,
cut = 10.0, iwrap = 1,
&end
I am getting the following output
Maximum number of minimization cycles reached.
FINAL RESULTS
NSTEP ENERGY RMS GMAX NAME NUMBER
1 -5.5677E+03 1.9509E+01 5.9144E+01 O 385
BOND = 0.0000 ANGLE = 0.0000 DIHED =
0.0000
VDWAALS = 1083.7829 EEL = -6651.5116 HBOND =
0.0000
1-4 VDW = 0.0000 1-4 EEL = 0.0000 RESTRAINT =
0.0000
minimization completed, ENE= -.55677286E+04 RMS= 0.195088E+02
TRAJENE: Trajectory file ended
TRAJENE: Trajene complete.
As I understand from output Total nonbonded interaction = VDWAALS + EEL
+ 1-4 VDW + 1-4 EEL.
The value is + 1083.7829 - 6651.5116 = - 5567.7287 Kcal /mol
The same trajectory I proceeded with pairwise AmberTool. Now I am getting
-4444.498556 Kcal/mol
In my simulation box Total 500 no of water molecule is there and I am
using SPCE water model for simulation.
my first question is that this which value is most acceptable and second
question what parameter i have to change to achieve optimum experimental
value.
Thanks & regards
Rahman
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Received on Tue Jun 30 2015 - 06:00:02 PDT
