GROMACS

#!/bin/bash

gmx='/tmp/current/bin/gmx'

pdb='chainTer.pdb'

itpA='topol_Protein_chain_A.itp'

itpB='topol_Protein_chain_B.itp'

$gmx pdb2gmx -f $pdb -ff 'amber03' -water 'tip3p'

#works

protein_ca_sel='chain A and name CA'

current='ca-A'

$gmx select   -s $pdb -on $current.ndx -select "$protein_ca_sel"

$gmx genrestr -f $pdb -n  $current.ndx -o posre_$current.itp

echo -e "; Include Position restraint file

#ifdef POSRES_CA

#include \"posre_$current.itp\"

#endif\n" >> $itpA

$gmx grompp -f ca.mdp -c conf.gro -p topol.top -o ca-A.tpr -r conf.gro

#fails

protein_ca_sel='chain B and name CA'

current='ca-B'

$gmx select   -s $pdb -on $current.ndx -select "$protein_ca_sel"

$gmx genrestr -f $pdb -n  $current.ndx -o posre_$current.itp

echo -e "; Include Position restraint file

#ifdef POSRES_CA

#include \"posre_$current.itp\"

#endif\n" >> $itpB

$gmx grompp -f ca.mdp -c conf.gro -p topol.top -o ca-B.tpr -r conf.gro