AMBER Archive (2003)

Subject: Sander help

From: tianxiao yang (yang.984_at_osu.edu)
Date: Tue May 13 2003 - 18:47:17 CDT

Dear Amber Users,

I am moving to run Sander from Amber6 to Amber7 and met big difficulties to
proceed the calculation. The following is my input file. It is no problem
to run on V6. But on V7, md.out output file is empty and the error message
pointed out that there are mistakes in the input file.

I heard that many commands in V7 and V6 are quite different, but I could
not find them in manual. Would you please like to help me out? I greatly
appreciate your kind help.

Tianxiao Yang

Tianxiao Yang, Ph.D
Department of Chemistry, The Ohio State University

  &cntrl
   imin = 0,
   nsnb = 10, ntpr = 100, ntwx =200, ntwv =100, ntwe =100,
   ntx = 2, irest =0,
   ntc = 2, ntf = 2, ntb = 2,
   nstlim =500000,
   dielc = 1.0,
   ntmin = 1,
   cut = 9.0, nsnb = 10, scee = 1.20,
   ibelly = 0, ntr =1,
   temp0 = 300.0, tempi = 300.0,
   ntt = 1,
   dt = 0.001, t = 0.0, tautp = 0.1,
   ntp = 1, pres0 = 1.0, taup = 0.5, npscal = 1,
  iewald=1,
  &end
27.7619180 27.1948140 26.1915520 90.0000000 90.0000000 90.0000000
32 32 32 4 0 0 0
0.00001
Hold the solute fixed
500
RES 1
END
END