To debug, you should try with a single command rather a complicated script
like you post. (Double check your bash script to make sure it gets what you
want).
And yes, sander does not have ala flag.
Hai
On Mon, Nov 6, 2017 at 8:56 AM Mo Rahman <
mo.rahman.postgrad.manchester.ac.uk> wrote:
> Hello,
>
> 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 "${!arr[@]}"
> do
> j="${arr[$i]}"
> echo "
> parm ~/entropy-md/"$i"/setup/"$j"-solv.prmtop
> trajin ~/entropy-md/"$i"/production/"$j"-solv-prod.mdcrd
> autoimage
> strip :WAT,Cl-,Na+
> trajout "$j"-vac.mdcrd crd nobox
> " > ~/entropy-md/nm-entropies/"$j"-vac.in
> done
>
> for kl in "${arr[@]}"
> do
> cd ~/entropy-md/nm-entropies/
> qsub -b y -cwd -V cpptraj -i "$kl"-vac.in
> done
>
> sleep 60
>
> for m in "${!arr[.]}"
> do
> n="${arr[@]}"
> cd ~/entropy-md/nm-entropies/
> qsub -b y -cwd -V sander.MPI -O -i input/min.in -o "$n"-min.out -p
> ~/entropy-md/"$m"/setup/"$n"-vac.prmtop -c "$n"-vac.mdcrd -r "$n"-min.rst
> -x "$n"-min.mdcrd
> done
>
>
> 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,
>
> Mo
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>
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Received on Mon Nov 06 2017 - 06:30:03 PST
