[AMBER] sander command

From: Saeed Nasiri <s.t.nasiri.gmail.com>
Date: Tue, 10 Dec 2013 11:37:37 +0330

Dear All

I have a problem with energy minimization for ionic liquid simulation box
(amber tutorial). I run the tutorial script, I have an error. I create
input file for minimization the run sander in terminal and I have another
error. In addition I run this minimization in a directory that contains all
files from previous steps (mol2 pdb and ...).
Also thanks very much for quick and useful replying from Mr. Jason Swails
for my last problem.

Your Sincerely




# CREATE the mdin file
cat > mdin << EOF
  imin=1, ntpr=100, ntwx=100, maxcyc=10000,

   sander -O \
   -i mdin.in \ # input file
   -o min1.o \ # output file
   -p ionicbox.prmtop \ # topology file
   -c ionicbox.inpcrd \ # input coordinate file
   -r min1.x \ # restart file
   -x min1.nc \ # output coordinate sets saved in
   -e min1.dat # energy data


*$ ./runmin.sh ./runmin.sh: line 17: warning: here-document at line 3
delimited by end-of-file (wanted `EOF')*


  imin=1, ntpr=100, ntwx=100, maxcyc=10000,


*$ sander -O -i mdin.in <http://mdin.in> -o min1.o -p ionicbox.prmtop -c
ionicbox.inpcrd -r min1.x -x min1.nc <http://min1.nc> -e
min1.datSegmentation fault*
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Received on Tue Dec 10 2013 - 00:30:02 PST
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