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{ head -n -1 complex.gro; cat lig.gro; tail -n 1 complex.gro; } >combined.gro

Try:

awk '
NR==FNR {
if(FNR==2)
ligval=$1
if(FNR>2 && NF>3)
lig=lig $0 RS
next
}
{
if(FNR==2)
$0=$1+ligval
if(NF==3)
$0=lig $0
...

Here is an approach using awk:-
awk '
NR == FNR {
if ( FNR == 2 )
lig_atoms = $1
if ( FNR > 2 )
atom[++i]...

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