Hi Damiano,
The relevant error is this one:
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
You are using PMEMD v12 and if memory serves (don't have the code or manual in front of me right now) the restraint_mask input approach is not supported in that version of pmemd - you have to use the more traditional group based input.
The alternative if it does support it is that you are missing a comma after some of your lines, ntwr for example. This does not normally cause a problem but some compiler versions can be more picky than others.
You also need an initial space before &cntrl. So ' &cntrl' rather than '&cntrl' - same goes for the trailing / and your &wt.
All the best
Ross
> On Sep 12, 2015, at 1:52 PM, Damiano Spadoni <enxds6.nottingham.ac.uk> wrote:
>
> 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 - 14:30:03 PDT
