You could try the following shell script:

#!/bin/bash
do_modeling()
{
FILES=`ls ./`;
for f in $FILES;; do
  echo $f
  cp -f $f malign.top
  cp -f $f get-model.top
  /usr/local/modeller6v2/bin/mod6v2 malign.top
  /usr/local/modeller6v2/bin/mod6v2 get-model.top
done
}

do_modeling
do_modeling
[download]