AMBER Archive (2006)

Subject: AMBER: Problem in running umbrella sampling

From: Sai Kumar Ramadugu (compchem123_at_gmail.com)
Date: Sun Feb 12 2006 - 22:28:09 CST

Dear All,
   I'm running sander for umbrella sampling. My system has a peptide wit 40
residues and 7000+ water molecules. I'm using distance betrween two atoms as
my reaction coordinate. But when I submit the input file, it will not be
submitted. Instead it gives in following error.

ATTENTION: 0031-606 Unrecognized environment variable, MP_RSH.

1525-090 The NAMELIST READ statement cannot be completed because an
incorrect ch
aracter was encountered in a NAMELIST group name or item name. The program
will
 recover by discontinuing further processing of the READ statement.
1525-090 The NAMELIST READ statement cannot be completed because an
incorrect ch
aracter was encountered in a NAMELIST group name or item name. The program
will
 recover by discontinuing further processing of the READ statement.
1525-090 The NAMELIST READ statement cannot be completed because an
incorrect ch
aracter was encountered in a NAMELIST group name or item name. The program
will
 recover by discontinuing further processing of the READ statement.
ERROR: 0031-250 task 3: Terminated
ERROR: 0031-250 task 7: Terminated
ERROR: 0031-250 task 6: Terminated
ERROR: 0031-250 task 5: Terminated
ERROR: 0031-250 task 4: Terminated
ERROR: 0031-250 task 2: Terminated
ERROR: 0031-250 task 1: Terminated

   We have regetta 16 processors machine from IBM. I'm submitting job with 8
processors.
My input file for sander is as follows:

 Abeta-peptide: 1.8ns of MD
  &cntrl
    imin = 0, nmropt = 1, irest = 1, ntx = 7,
    ntb = 2, pres0 = 1.0, ntp = 1,
    taup = 2.0,
    cut = 9 , ntr = 0,
    ntc = 2, ntf = 2,
    tempi = 300.0, temp0 = 300.0,
    ntt = 3, gamma_ln = 1.0,
    nstlim = 500000, dt = 0.002,
    ntpr = 500, ntwx = 500, ntwr = 5000,
  /
  &wt type='DUMPFREQ', istep1=100 /
  &wt type='END' /
DISANG=dist_res.RST
DUMPAVE=dis_vs_t.5.8

   My .RST file is as follows:
# 23 ASP HB2 28 LYS NZ 5.8 6.8 (# comments go here
)
 &rst
  ixpk= 0, nxpk= 0, iat= 361, -1, r1= 2.30, r2= 5.80, r3= 5.80, r4= 8.67,

      rk2=20.0, rk3=20.0, ir6=1, ialtd=0,
 igr2= 433, 434, 435,
 &end

  The mdout file is not being generated at all. Please help me in this
regard.

Thanks in advance,
Sai K. Ramadugu

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