AMBER Archive (2006)

Subject: AMBER: error while running sander

From: snoze pa (snoze.pa_at_gmail.com)
Date: Fri Mar 10 2006 - 22:23:54 CST

Dear user,
I am using parallel vesion of amber and trying to finish Molecular
Dynamics (heating) with restraints on the solute tutorial as given in
Amber website for DNA polyA-polyT decamer tutorial website. In my case
both steps of minimization are working fine, while MD heating, it is
giving me following error:

forrtl: severe (24): end-of-file during read, unit 5, file /class/fistmd.in
Image PC Routine Line Source
sander 081B7FAA Unknown Unknown Unknown
sander 081B6795 Unknown Unknown Unknown
sander 08197C2D Unknown Unknown Unknown
sander 081624DA Unknown Unknown Unknown
sander 0816220A Unknown Unknown Unknown
sander 081756B0 Unknown Unknown Unknown
sander 08100B65 Unknown Unknown Unknown
sander 080B6554 Unknown Unknown Unknown
sander 0807899E Unknown Unknown Unknown
sander 080774FE Unknown Unknown Unknown
sander 0804B591 Unknown Unknown Unknown
sander 0804B4D1 Unknown Unknown Unknown
bm_list_7475: (1.258593) wakeup_slave: unable to interrupt slave 0 pid 7474
p1_7506: p4_error: net_recv read: probable EOF on socket: 1
rm_l_1_7507: (0.920806) net_send: could not write to fd=5, errno = 32

my MD input file fistmd.in is following

 &cntrl
  imin = 0,
  irest = 0,
  ntx = 1,
  ntb = 1,
  cut = 10,
  ntr = 1,
  ntc = 2,
  ntf = 2,
  tempi = 0.0,
  temp0 = 300.0,
  ntt = 3,
  gamma_ln = 1.0,
  nstlim = 10000, dt = 0.002
  ntpr = 100, ntwx = 100, ntwr = 1000
 /
This error is comming while I am running above MD script. If I will
run following script for minimization
 &cntrl
  imin = 1,
  maxcyc = 2500,
  ncyc = 1000,
  ntb = 1,
  ntr = 0,
  cut = 10

 then it is not comming. any suggestions?

thanks in advance
snoze
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