[AMBER] Post processing of trajectory with sander

From: MOHD HOMAIDUR RAHMAN <rahmanhpu.gmail.com>
Date: Tue, 30 Jun 2015 18:29:02 +0530

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

‚ÄčIn 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
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