VMD打不开amber中amoeba结果的问题

alystone

帮帮我

I want to use pmemd.amoeba.MPI this section to calculate my system.

Calculation process was very plain sailing, and calculation speed was vert fast.

But when I want to use VMD to see my system structure, I got some problems.

My system has PBC, and the x,y,z value is all OK in my .crd file. I first load my .pdb file, it’s OK.  And then I load .crd file and select “Amber Coordinate and Periodic Box”.  it doesn’t echo to me.

Below is my .crd file format, please help me. What should I do And any tutorial?

“

%VERSION  VERSION_STAMP = V0001.000  DATE = 05/12/16  12:11:15

%FLAG TITLE

%FORMAT(a)

solvated

%FLAG ATOMIC_COORDS_SIMULATION_TIME

%FORMAT(E16.8)

  0.20000000E+04

%FLAG ATOMIC_COORDS_NUM_LIST

%FORMAT(i8)

   19950

%FLAG ATOMIC_COORDS_LIST

%COMMENT   dimension = (3,19950)      

%FORMAT(3e20.12)

-0.798609228540E+01 -0.119485368340E+02  0.334078608257E+01

-0.738206600601E+01 -0.126157176487E+02  0.463022030229E+01

-0.691559149784E+01 -0.112381028689E+02  0.429864473143E+01

……

……

……

  0.135613364794E+02 -0.103897952190E+02  0.127555536814E+02

-0.960573868866E+01 -0.213273536574E+01  0.675275334676E+01

-0.519110859326E-02  0.677491552894E+00 -0.788188055911E+00

%FLAG UNIT_CELL_PARAMETERS

%COMMENT lengths a,b,c; then angles alpha,beta,gamma

%FORMAT(3e20.12)

  0.571041457849E+02  0.602902878769E+02  0.581308454270E+02

  0.900000000000E+02  0.900000000000E+02  0.900000000000E+02

”