Hi Evangelos,
For illustrative purposes, your original script read as follows:
#!/usr/bin/env emc_setup.pl
# Options
ITEM OPTIONS
ntotal 1000
temperature 353.15
density 0.1
field_name standard
field_location .
mass true
replace true
build_dir .
ITEM END
# Shorthand
# Groups
ITEM GROUPS
water O
tfe *C2(F)(F)C2(F)(F)*,1,tfe:2
htfe *C2(F)(F)C3(F)(F)F,1,tfe:1,1,tfe:2
ITEM END
# Clusters
ITEM CLUSTERS
water water,0.054523562
poly alternate,1
ITEM END
# Polymers
ITEM POLYMERS
poly
100 tfe,98,htfe,2
ITEM END
# Force Field specification according to the B3LYP/6-13G* data
ITEM FIELD
# Definitions
ITEM DEFINE
FFNAME STANDARD
FFTYPE ATOMISTIC
LENGTH ANGSTROM
ENERGY KCAL/MOL
DENSITY G/CC
MIX BERTHELOT
CUTOFF 9.5
NBONDED 2
ANGLE COMPLETE
TORSION COMPLETE
ITEM END
# Masses
ITEM MASS
# type mass element ncons charge comment
C2 12.011 C 4 0.378 C atom for -CF2-
C3 12.011 C 4 0.567 C atom for -CFE
F 18.998 F 1 -0.189 F atom
O 15.9994 O 2 -0.8476 O atom for water
H 1.00790 H 1 0.4238 H atom for water
ITEM END
# Nonbond parameters
ITEM NONBOND
# type1 type2 sigma eps
F F 2.94 0.061
C2 F2 3.50 0.066
C3 F3 3.50 0.066
O O 3.16556 0.15539
H H 1.0 0.0
ITEM END
# Bond parameters
ITEM BOND
# type1 type2 k l0
C2 C2 259.93 1.54
C2 C3 259.93 1.54
F C2 304.82 1.38
F C3 304.82 1.38
O H 600.00 1.00
ITEM END
# Angle parameters
ITEM ANGLE
# type1 type2 type3 k theta0
F C2 F 107.64 108.72
F C3 F 107.64 108.72
F C2 C2 56.39 107.90
F C2 C3 56.39 107.90
F C3 C2 56.39 107.90
F C3 C3 56.39 107.90
C2 C2 C2 56.39 107.90
C2 C2 C3 56.39 107.90
C2 C3 C2 56.39 107.90
C2 C3 C3 56.39 107.90
C3 C2 C3 56.39 107.90
C3 C3 C3 56.39 107.90
H O H 75.00 109.47
ITEM END
# Torsion parameters
ITEM TORSION
# type1 type2 type3 type3 k n delta [...]
F C2 C2 F 1 1 1
F C2 C3 F 1 1 1
* * * * 1 1 1
ITEM END
ITEM END # FIELD
As a general remark: this script mainly contains spaces as separating characters. EMC Setup and derived modules function better when you use TABs.
Regarding your error: in general, the error occurs when a ring closure cannot be found, as is the case for the cyclodextrin question on this board. Specifically, your error has to do with how you defined your SMILES under ITEM GROUPS. You defined your tfe group with tfe *C2(F)(F)C(F)(F)*. You provided an opening link in your SMILES by providing a 2, but you never provided the accompanying closing link, hence the error. If you would have wanted not to use rules, you could have defined this group by using your types: the *[c2](f)(f)c(f)(f). Note that the field module converts used types to lower case.
Regarding using ITEM FIELD: EMC comes with an included example in $EMC_ROOT/examples/setup/chemistry/field/user, where a user defined polymer force field is used. EMC Setup uses a force field module to obtain your standard.prm and standard.top. Be aware, that this force field requires a TAB to be the separator between fields. Using spaces will cause the module to function incorrectly. Both parameters and rules can be included in the ITEM FIELD section. I included partial wild cards for your parameters. With these changes, your script looks as follows:
#!/usr/bin/env emc_setup.pl
# Options section
ITEM OPTIONS
ntotal 1000
temperature 353.15
density 1.0
field_name standard
field_location .
field_format %g
mass true
replace true
build_dir .
emc_execute true
ITEM END # OPTIONS
# Groups section
ITEM GROUPS
water O
tfe *C(F)(F)C(F)(F)*,1,tfe:2
htfe *C(F)(F)C(F)(F)F,1,tfe:1,1,tfe:2
ITEM END # GROUPS
# Clusters section
ITEM CLUSTERS
water water,0.054523562
poly alternate,1
ITEM END # CLUSTERS
# Polymers section
ITEM POLYMERS
poly
100 tfe,98,htfe,2
ITEM END # POLYMERS
# Force Field specification according to the B3LYP/6-13G* data
ITEM FIELD
# Definitions
ITEM DEFINE
FFNAME STANDARD
FFTYPE ATOMISTIC
FFDEPTH 2
LENGTH ANGSTROM
ENERGY KCAL/MOL
DENSITY G/CC
MIX BERTHELOT
CUTOFF 9.5
NBONDED 2
ANGLE ERROR
TORSION ERROR
ITEM END
# Masses
ITEM MASS
# type mass element ncons charge comment
c2 12.011 C 4 0 C atom for -CF2-
c3 12.011 C 4 0 C atom for -CFE
f 18.998 F 1 0 F atom
o 15.9994 O 2 0 O atom for water
h 1.00790 H 1 0 H atom for water
ITEM END
# Rule precedences
ITEM PRECEDENCE
(
(c2)
(c3)
(f)
(o)
(h)
)
ITEM END
# Rules
ITEM RULES
# type charge rule
c2 0.378 C(F)(F)(C)(C)
c3 0.567 C(F)(F)(F)(C)
f -0.189 F(C)
o -0.8476 [O](H)(H)
h 0.4238 H(O(H))
ITEM END
# Nonbond parameters
ITEM NONBOND
# type1 type2 sigma eps
f f 2.94 0.061
c2 c2 3.50 0.066
c3 c3 3.50 0.066
o o 3.16556 0.15539
h h 1.0 0.0
ITEM END
# Bond parameters
ITEM BOND
# type1 type2 k l0
c* c* 259.93 1.54
f c* 304.82 1.38
o h 600.00 1.00
ITEM END
# Angle parameters
ITEM ANGLE
# type1 type2 type3 k theta0
f c* f 107.64 108.72
* c* c* 56.39 107.90
h o h 75.00 109.47
ITEM END
# Torsion parameters
ITEM TORSION
# type1 type2 type3 type3 k n delta [...]
f c* c* f 1 1 1
* * * * 1 1 1
ITEM END
ITEM END # FIELD
I added ffdepth 2 since your rules have a maximum recursion depth of 2 (see your rules for water oxygen and hydrogen). I added field_format %g to change the numerical format of the resulting force field files. For completeness sake, I also attached the resulting script.
standard.esh (1.8 KB)