syn3A.script

#! /usr/bin/env bash
#
seedinc=123
seed=1234
#
echo "------starting generate_connect------------"
echo "   "
./generate_connect << EOF
syn3A.genome
syn3A.connect
503,187,187
120
EOF

for (( step=1; step<=1; step++)); do
  seed=$((seed+seedinc))
echo "------starting step $step------"
echo "------starting generate_pol------------"
echo "   "
./generate_pol << EOF
syn3Asmall_ribosomes.pdb
6c6u_mask.pdb
4v6k_mask.pdb
7nyx_mask.pdb
syn3A.$step.pdb
187
201.26
$seed
20.
RANDOM
EOF
#
echo "------starting modularlattice------------"
echo "   "
./modularlattice << EOF
syn3A.$step.pdb
syn3A.connect
syn3A_lattice.$step.pdb
0
$seed
60.
EOF
#
echo "------starting relax------------"
echo "   "
./relax << EOF
syn3A_lattice.$step.pdb
syn3A_relax.$step.pdb
1499
EOF

done