RE: AMBER: umbrella sampling

From: Jardas sucuriba <>
Date: Sun, 25 Nov 2007 19:32:28 +0000

When I try to run my input files for umbrella sampling I obtain the following error:
PGFIO-F-239/namelist read/unit=33/entity name is not member of group.
 File name = d1.restraint formatted, sequential access record = 5
 In source file _restal.f, at line number 311
p1_27940: p4_error: net_recv read: probable EOF on socket: 1
rm_l_1_27941: (1.203240) net_send: could not write to fd=5, errno = 32
I didn´t manage to find where is the error. Does anyone know what I am doing wrong?
Here is my input file:
  imin = 0, irest=1, ntx=5,
  nstlim=25000, dt=0.002, scee = 1.2,
  ntt=3, gamma_ln=1.0, tempi=300.0, temp0=300.0,
  ntb = 2, ntp=1, pres0=1.0,
  ntc=2, ntf=2,
  ntr = 0,
  ntwe=100, ntwx=100, ntpr=100,
  cut = 10.0
 &wt type='DUMPFREQ', istep1=1 /
 &wt type='END' /
#distance restrainst
&rst iat=-1,-1, r1=0.0, r2=4.575, r3=4.575, r4=100.0, rk2=10., rk3=10.,
 IGR1=262, IGR2=267,267,267,
 GRNAM2(1)=C19, GRNAM2(2)=C20, GRNAM2(3)=O1,
The idea is to approach the SG atom of a cysteine to the center of mass of 3 atoms of a ligand.
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Received on Wed Nov 28 2007 - 06:07:07 PST
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