Dear All,
I want to run a 2 stage and heating minimization on Sander. I have
MT2.prmtop and MT2.inpcrd files in the working directory as my parameter
and coordinate files. I have a .sh file 'job. sh' which I have created
to run stepwise jobs. When I submit .sh file, I get error message.
Error: Could not determine format of topology MT2.prmtop
Error opening unit 30: File "min1.rst7" is missing or unreadable
The job.sh file is:
#!bin/sh
source /apps/amber18/amber.sh
cd /home/pradeepkumar/priyasha/MT2
sander -O -i min1.in -o min1.out -p MT2.prmtop -c MT2.inpcrd -r
min1.rst7 -ref MT2.inpcrd
ambpdb -p MT2.prmtop -c min1.rst7 > min1.pdb
sander -O -i min2.in -o min2.out -p MT2.prmtop -c min1.rst7 -r min2.rst7
-ref min1.rst7
ambpdb -p MT2.prmtop -c min2.rst7 > min2.pdb
sander -O -i heat.in -o heat.out -p MT2.prmtop -c min2.rst7 -r heat.rst7
-ref min2.rst7
I have all the input files inside the working directory. This is the
minimization input file.
minimise
&cntrl
imin=1,maxcyc=10000,ncyc=10000,
cut=10.0,ntb=1,
ntc=1,
ntpr=1000,
ntr=1,
restraintmask=':1-200, 264-353',
restraint_wt=200.0,
/
Please let me know where i am getting the error
Thanks
Priyasha
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Received on Wed Apr 10 2024 - 23:30:02 PDT
