On Tue, Jun 30, 2015 at 8:59 AM, MOHD HOMAIDUR RAHMAN <rahmanhpu.gmail.com>
wrote:
> 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
>
Sander is using PME, whereas pairwise is using a simple cutoff. PME is
much better in this case. (I am assuming you mean the "pairwise" command
in cpptraj).
> 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.
>
PME gives much closer to the theoretically correct electrostatic energy
*for the forcefield*.
HTH,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Tue Jun 30 2015 - 08:30:03 PDT
