problem to running command from perl
I'm trying to run the following command using perl
$SCHRODINGER/run rmsd.py -asl "not atom.element H" filename1.mol2 /mml/nfs04/reginap/renamed/filename2.mol2
this command works perfect from linux, however when I try to execute it from perl
$cmd = "$SCHRODINGER/run rmsd.py -asl "not atom.element H" filename1.mol2 /mml/nfs04/reginap/renamed/filename2.mol2";
$rmsd = system($cmd);
I'm getting the following error:
syntax error at calc_RMSD_withShrodinger.pl line 22, near ""$SCHRODINGER/run rmsd.py -asl "not "
Execution of calc_RMSD_withShrodinger.pl aborted due to compilation errors.
I tried different ways like putting \ before "not" and using `` instead of system but nothing worked.
I will appreciate very much any help.