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$i=0;
while ($line=<SOLVFILE>)
...
    chop($line);  # use "chomp" here, not "chop"
    ...
}

  my_script.pl  file1  file2

#!/usr/bin/perl -w

...
        }
    }
}

for my $i ( 0 .. $natms{$f1}-1 ) {

...
        }
    }
}