Change qsub to echo to get the command, run that command by yourself to
debug.
Hai
On Mon, Nov 6, 2017 at 9:18 AM Hai Nguyen <nhai.qn.gmail.com> wrote:
> 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
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>
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Received on Mon Nov 06 2017 - 06:30:04 PST
