Typically error and output files are given as pbs directives in the qsub script or as command line options to the qsub script like so:
#! /bin/bash
#PBS -q queue_name
#PBS -A account_name
#PBS -l nodes=12:ppn=12
#PBS -l walltime=18:00:00
#PBS -e /mypath/error.txt
#PBS -o /mypath/output.txt
or as a command line option to qsub like so:
qsub -o /mypath/output.txt -e /mypath/error.txt submit_job.sh
With the first option I don’t think you can use a variable as the shell won’t look at lines that are commented. Plus I think PBS deals with the commented lines before the shell would. If you know the path when you’re invoking qsub, you could try the second option.
Alternatively you could try simply redirecting the output and error in the script itself:
/home/user1/run.sh $SEED > ${SEED}/output.txt 2> ${SEED}/error.txt
The third option is probably the easiest. Output and error files might still be created in the run directory, though they’d likely be empty.