GMX: clashes after energy minimization / serine2 copies

mini.mdp

integrator              = steep
emtol                   = 100.0
nsteps                  = 10000
nstlist                 = 10
nstxout = 5
nstenergy               = 10
cutoff-scheme           = verlet
ns_type                 = grid
vdw-type                = cut-off
coulombtype             = pme
rcoulomb                = 1.0
rvdw                    = 1.0
pbc                     = xyz

Sdipep.pdb

ATOM      1  N   SER A   1      -1.435  -2.375   0.469  1.00  0.00           N
ATOM      2  CA  SER A   1       0.014  -2.375   0.469  1.00  0.00           C
ATOM      3  C   SER A   1       0.537  -0.946   0.469  1.00  0.00           C
ATOM      4  O   SER A   1       1.430  -0.610   1.244  1.00  0.00           O
ATOM      5  CB  SER A   1       0.566  -3.075  -0.764  1.00  0.00           C
ATOM      6  OG  SER A   1       0.205  -2.342  -1.937  1.00  0.00           O
ATOM      7  N   SER A   2      -0.022  -0.104  -0.404  1.00  0.00           N
ATOM      8  CA  SER A   2       0.388   1.282  -0.502  1.00  0.00           C
ATOM      9  C   SER A   2       0.234   1.969   0.847  1.00  0.00           C
ATOM     10  O   SER A   2       1.180   2.651   1.237  1.00  0.00           O
ATOM     11  OXT SER A   2      -0.824   1.792   1.446  1.00  0.00           O
ATOM     12  CB  SER A   2      -0.460   2.038  -1.513  1.00  0.00           C
ATOM     13  OG  SER A   2      -1.815   2.094  -1.059  1.00  0.00           O
END

setup_serine_dipep.sh

#!/bin/bash

proot="Sdipep"
ff="ff03"
wat="tip3p"

out="${proot}_${ff}_${wat}"
top="${proot}_${ff}_${wat}"
#gmx pdb2gmx -f ${proot}.pdb -o $out -p $top -ignh <<EOF
#1
#1
#EOF

inp=$out
nmol=4
out="${proot}${nmol}_${ff}_${wat}"
nmo=$(expr $nmol - 1)
gmx insert-molecules -f $inp -ci $inp -nmol $nmo -box 3 -o $out

topn="${proot}${nmol}_${ff}_${wat}.top"
awk -v nmol=$nmol -v itp=$itp '/Protein_chain_A/ {print "Protein_chain_A    ", nmol; next} 
	{print}' "${top}.top" > $topn

#inp=$out
#out="${proot}${nmol}_${ff}_${wat}_solv"
#gmx solvate -p $topn -cp $inp -o $out
#
#mdp="mini.mdp"
#inp=$out
#out="${proot}${nmol}_${ff}_${wat}_ions"
#gmx grompp -f $mdp -c $inp -p $topn -o $out -maxwarn 1
#
#gmx genion -s $out -o $out -p $topn -pname NA -nname CL -neutral <<EOF
#13
#EOF

mdp="mini.mdp"
inp=$out
out="${proot}${nmol}_${ff}_${wat}_mini"
gmx grompp -p $topn -c $inp -f $mdp -o $out -pp -maxwarn 1

inp=$out
out=$inp
gmx mdrun -v -s $inp -deffnm $out