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(OP)
Good morning, fellows. I would need to ask for your help in editing my awk script. Here is the original version:

BEGIN { printf ("CRYST1 200.000 200.000 200.000 90.00 90.00 90.00 P 1 1\n")
maxatoms=1000
natom=0
found_struct = 0
found_bond = 0
}
{
if( NF == 5 )
{
foundff=0
natom++
fftype[natom]="UNKNOWN"
if ($1 ~ /CT/) { fftype[natom] = "C" foundff=1 } else if ($1 ~ /OH/)
{
fftype[natom] = "O"
foundff=1
}
else if ($1 ~ /HC/) { fftype[natom] = "H" foundff=1 } else if ($1 ~ /N/)
{
fftype[natom] = "N"
foundff=1
}

else if ($1 ~ /H1/) { fftype[natom] = "H" foundff=1 } else if ($1 ~ /HO/)
{
fftype[natom] = "H"
foundff=1
}
else if ($1 = "C") { fftype[natom] = "C" foundff=1 } else if ($1 = "O")
{
fftype[natom] = "O"
foundff=1
}

next

x[natom] = $1 y[natom] =$2
z[natom] = $3 if (foundff == 0) printf("PROBLEM : Atom ff type %s not known\n",$6)
}

}

END {
for (iatom=1; iatom <= natom; iatom++)
{
printf("HETATM %d %2s %d %14.9f %14.9f %14.9f\n" ,
iatom, fftype[iatom], iatom, x[iatom], y[iatom], z[iatom])
}
printf ("END\n")
}

And this is type of file I am working with.

0 3 186 200 75202
timestep 500 186 0 3 0.002000 1.000000
40.0000000000 0.0000000000 0.0000000000
-0.0000000034 40.0000000000 0.0000000000
-0.0000000034 -0.0000000034 40.0000000000
CT_1 1 12.011000 0.061000 1.087513
-1.961325738 1.828501682 -8.933652557
CT_1 2 12.011000 0.061000 0.789711
-3.851025437 3.495427316 -10.05849230
CT_1 3 12.011000 0.061000 0.581330
-5.804493575 4.589489777 -8.369482861

ect

I would like to get this as an output:

CRYST1 200.000 200.000 200.000 90.00 90.00 90.00 P 1 1
HETATM 1 C 1 -1.961325738 1.828501682 -8.933652557
HETATM 2 C 2 -3.851025437 3.495427316 -10.05849230
HETATM 3 C 3 -5.804493575 4.589489777 -8.369482861

ect

But coordinates are not really picking up well (next line after CT_1 1 12.011000 0.061000 1.087513). Can you please have a look and suggest any solutions. Thanks.

For starters, the following should be '==' instead of '=':

#### CODE

else if ($1 == "C") . . . else if ($1 == "O") 

----------------------------------------------------------------------------
The person who says it can't be done should not interrupt the person doing it. -- Chinese proverb

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