[AMBER] Unknown flag error - sander

From: Mo Rahman <mo.rahman.postgrad.manchester.ac.uk>
Date: Mon, 6 Nov 2017 13:55:00 +0000


I submitted a job with sander using the following batch script:

declare -A arr=( [alanine]=ala [asparagine]=asn [phenylalanine]=phe [serine]=ser [lysine]=lys [glutamate]=glu [cysteine]=cys )

for i in "${!arr[.]}"
      echo "
        parm ~/entropy-md/"$i"/setup/"$j"-solv.prmtop
        trajin ~/entropy-md/"$i"/production/"$j"-solv-prod.mdcrd
        strip :WAT,Cl-,Na+
        trajout "$j"-vac.mdcrd crd nobox
        " > ~/entropy-md/nm-entropies/"$j"-vac.in

for kl in "${arr[.]}"
    cd ~/entropy-md/nm-entropies/
    qsub -b y -cwd -V cpptraj -i "$kl"-vac.in

sleep 60

for m in "${!arr[@]}"
    cd ~/entropy-md/nm-entropies/
    qsub -b y -cwd -V sander.MPI -O -i input/min.in -o "$n"-min.out -p ~/entropy-md/"$m"/setup/"$n"-vac.prmtop -c "$n"-vac.mdcrd -r "$n"-min.rst -x "$n"-min.mdcrd

However, I receive an error thus:

     mdfil: Error unknown flag: ala

     usage: sander [-O|A] -i mdin -o mdout -p prmtop -c inpcrd -r restrt
                   [-ref refc -x mdcrd -v mdvel -e mden -frc mdfrc -idip inpdip -rdip rstdip -mdip mddip
                   -ng numgroup -remlog rem.log -remtype rem.type -rem [0|1|2] -rremd [0|1|2|3] -saveene saveene
                   -clusterinfo cluster.info -reservoir reserv/frame -hybridtraj hybrid.strip.crd
                   -inf mdinfo -radii radii -y inptraj -amd amd.log -scaledMD scaledMD.log] -cph-data <file>
Consult the manual for additional options.
MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD
with errorcode 1.

NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes.
You may or may not see output from other processes, depending on
exactly when Open MPI kills them.

I have tried using both the sander and sander.MPI executables and the error still persists. I’m having an almost identical problem with nmode as well. Can anybody help?

Kind regards,

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Received on Mon Nov 06 2017 - 06:00:03 PST
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