Dear User,
I intend to run batch minimization of 500 pdbs hence need to generate .top
and .crd files. Here is my leap.in file to do the above mentioned task :
#! /bin/sh
for file in output*.pdb
do
source leaprc.ff99SB
x = loadpdb $file
i=`expr index $file .`
f1=`expr substr $file 1 $i`
saveamberparm x $f1.top $f1.crd
done
But the moment i execute it using "tleap -f leap.in", i end up with an
error saying
----------------------------------------------------
Substituting map OB -> O2P for OB -> O2P
Could not open file file: not found
ERROR: syntax error
ERROR: syntax error
saveAmberParm: Argument #1 is type String must be of type: [unit]
usage: saveAmberParm <unit> <topologyfile> <coordfile>
ERROR: syntax error
------------------------------------------------------------------
PLEASE REPLY WHERE I HAVE GONE WRONG!Thanks for the time you may give me!
--
Regards,
Pallavi Mohanty
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Received on Fri Apr 17 2015 - 04:30:06 PDT
