Hi Bill,
After the IT department compiled AMBER they sent me this list of actions
for using amber. I dont have Sander and when I try it I get this error:
var/spool/torque/mom_priv/jobs/173680.hpc.ce.sharif.edu.SC: line 8:
/root/amber16/bin/sander: No such file or directory
addles
amber.ipython
amber.pip
cpptraj.MPI
fftw-wisdom
mdgx.MPI
mpinab
nc-config
ncdump
ncgen3
parmed
sander.LES.MPI
to_be_dispatched
xparmed
amber.conda
amber.jupyter
amber.python
dacdif
fftw-wisdom-to-conf
MMPBSA.py.MPI
mpinab2c
nccopy
ncgen
nf-config
pmemd.MPI
sander.MPI
ucpp
yacc
I attached min.out file here.
thank you
On Wed, Sep 5, 2018 at 1:33 PM Bill Ross <ross.cgl.ucsf.edu> wrote:
> First, it may not be worthwhile to use MPI for minimization, and in any
> case, to debug it is best to use plain sander.
>
> Is there anything in min1.out? min2.out?
>
> Bill
>
>
> On 9/5/18 1:54 AM, maryam azimzadehirani wrote:
> > Dear AMBER users,
> > I am trying to carry out energy minimization with sander.MPI. The latest
> > error I received is:
> >
> >
> > *At line 291 of file set.F90Fortran runtime error: Bad value during
> integer
> > read*
> >
> > There is not enough explanation for me to fix the error. Here I copied my
> > input
> > script to use sander.MPI
> >
> > #PBS -N myjob
> > #PBS -m abe
> > #PBS -M maryam.azimzadeh.sharif.edu
> > #PBS -l nodes=1:ppn=24
> > #PBS -q LSPR
> > cd $PBS_O_WORKDIR
> >
> > /root/amber16/bin/sander.MPI -O -i min1.in -o min1.out -p complex.top -c
> > complex.crd -r min1.rst -ref complex.top
> >
> > /root/amber16/bin/sander.MPI -O -i min2.in -o min2.out -p complex.top -c
> > min1.rst -r min2.rst -ref complex.top
> >
> >
> > Can you please help me to fix the issue?
> > Thank you
> >
> > *Maryam Azimzadeh *
> >
> >
> > *PhD in Computational Structural Biology *
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
*Maryam Azimzadeh *
*PhD in Computational Structural Biology *
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- application/octet-stream attachment: min1.out
Received on Wed Sep 05 2018 - 03:00:02 PDT
