Hi,
As your job script appears to use csh-like commands (setenv, limit), the problem might be fixed if you tell SGE to use csh to run the script. Add the following two lines before the "#User current working directory"
## Run using csh
#$ -S /bin/csh
Antti
PS. I don't want to start a shell war here, but in the long run it might be more practical to convert the whole script to sh/bash/ksh. All scripts related to Turbomole are also written for sh-type shells so this might help to make things less confusing.