Hi Amber users,
I'm trying to run the following script for the production step of my simulation:
module load amber
cd /work/e280/e280/enxds6/PLP
export MPICH_FAST_MEMCPY=1
export MPI_COL_OPT_ON=1
aprun -n 96 pmemd.MPI -O -i LAMPLP_MD2.in -o LAMPLP_MD1.out -p LAMPLP.prmtop -c LAMPLP_heat2fs.rst -r LAMPLP_MD1.rst -x LAMPLP_MD1.mdcrd -ref LAMPLP.inpcrd
echo "DONE"
but it stops immediately with the message:
ModuleCmd_Load.c(226):ERROR:105: Unable to locate a modulefile for 'null'
ModuleCmd_Load.c(226):ERROR:105: Unable to locate a modulefile for 'null'
At line 463 of file mdin_ctrl_dat.F90 (unit = 5, file = 'LAMPLP_MD2.in')
Fortran runtime error: Cannot match namelist object name restraint_mask
[NID 00124] 2015-09-12 21:41:19 Apid 17488296: initiated application termination
Application 17488296 exit codes: 2
Application 17488296 exit signals: Killed
Application 17488296 resources: utime ~0s, stime ~5s, Rss ~7216, inblocks ~44814, outblocks ~121023
DONE
while the output file produced is simply a reminder of my input file I used for it:
| PMEMD implementation of SANDER, Release 12
| Run on 09/12/2015 at 21:41:19
[-O]verwriting output
File Assignments:
| MDIN: LAMPLP_MD2.in
| MDOUT: LAMPLP_MD1.out
| INPCRD: LAMPLP_heat2fs.rst
| PARM: LAMPLP.prmtop
| RESTRT: LAMPLP_MD1.rst
| REFC: LAMPLP.inpcrd
| MDVEL: mdvel
| MDEN: mden
| MDCRD: LAMPLP_MD1.mdcrd
| MDINFO: mdinfo
|LOGFILE: logfile
Here is the input file:
1ns MD with distance restraints on Fe4S4 - CYS
&cntrl
imin = 0, irest = 1, ntx = 7,
ntb = 2, pres0 = 1.0, ntp = 1,
taup = 2.0,
cut = 10.0, ntr = 1,
ntc = 2,
ntf = 2,
tempi = 300.0, temp0 = 300.0,
ntt = 3, ig = -1, gamma_ln = 1.0,
nstlim = 500000, dt = 0.002,
ioutfm=1, iwrap=1,
ntpr = 500, ntwx = 500, ntwr = 1000
restraint_mask = ':1639, 1642, 1645, 1648',
restraint_wt = 1.0
vlimit = 2.0, nmropt = 1
/
&wt type = 'END' /
Does anybody know what does exactly mean?!
Many thanks,
Damiano
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Received on Sat Sep 12 2015 - 14:00:03 PDT
