Error information of force field appears in the construction of monomer and polymer

EMC
,
1

When I use the OPLS force field to generate a data file, I got errors.

CH3
|
C(=N-O)-CH2-CH3
|-(NH2)

(SMILES : CC(CC)C(=NO)N )

ITEM OPTIONS
replace true
mass true
ntotal 20
field opls
build_dir .
ITEM END
ITEM SHORTHAND
AO CC(CC)C(=NO)N,1
ITEM END
ITEM GROUPS
AO CC(CC)C(=NO)N
ITEM END
ITEM CLUSTERS
AO AO,1
ITEM END

There are commands that i used :

perl emc_setup.pl 1.esh

emc_win32 build.emc

then errors ccoming:

Info: variables = {seed → -1, ntotal → 20, fshape → 1, output → “1”, field
→ “opls/2012/opls-aa”, location1 → “C:/emc944/field/”, nav →
0.6022141179, temperature → 300, radius → 5, nrelax → 100,
weight_nonbond → 0.0001, weight_bond → 0.0001, weight_focus → 1,
cutoff → 9.5, charge_cutoff → 9.5, kappa → 4, density1 → 1,
lprevious → 0, lphase → 0, f_AO → 1, chem_AO → “CC(CC)C(=NO)N”}
Info: output =
{detail → 3, wide → false, expand → false, math → true, reduced →
false, info → true, strict → true, warning → true, message → true,
debug → false, exit → true, ignore → false}
Info: field = {id → opls, mode → opls, style → none, name →
{“C:/emc944/field/opls/2012/opls-aa.prm”,
“C:/emc944/field/opls/2012/opls-aa.top”}, compress → false, error
→ true, debug → false, check → {atomistic → true, charge → true}}
Info: importing ‘C:/emc944/field/opls/2012/opls-aa.prm’
Warning: undefined periodic element ‘LP’.
Warning: undefined periodic element ‘LP’.
Warning: undefined periodic element ‘OW3P’.
Warning: undefined periodic element ‘OW3F’.
Info: groups = {ngroups → 1, group →
{id → AO, chemistry → “CC(CC)C(=NO)N”, depth → 8, charges →
forcefield, charge → 0, terminator → false, bias → none},
ndeletes → 0, npolymers → 0}
Info: field = {mode → apply, style → none, error → true, debug → false,
check → {atomistic → true, charge → true}}
Info: applying ‘C:/emc944/field/opls/2012/opls-aa.prm’
Warning: missing rules for field ‘C:/emc944/field/opls/2012/opls-aa.prm’.
Warning: missing rule for {group, site} = {AO, 13}.
Warning: missing rule for {group, site} = {AO, 14}.
Warning: missing rule for {group, site} = {AO, 15}.
Warning: missing rule for {group, site} = {AO, 16}.
Warning: missing rule for {group, site} = {AO, 17}.
Warning: missing rule for {group, site} = {AO, 18}.
Warning: missing rule for {group, site} = {AO, 19}.
Error: core/fields.c:432 FieldsApply:
Missing rules.
Program aborted.

AND

If i want to use C(C)C(=NO)N （called A） and C(C)C(=O)N （called B） groups for building a polymer like methyl - [ (A)5 - (B)5 - (A)5 ] 10 - methyl with opls-aa , would you please show me some detail steps and codes?

OR
I have build some polymers pdb file , how to import those pdb files to build data files using EMC

2

The error refers to missing rules for the provided chemistry. You can get more information by adding

field_debug		reduced

to your options. This will generate output as to how rules are being applied. Your problem is, that no rules exist for part of the provided chemistry. To be more precise, the latter part of

CC(CC)C(=NO)N

i.e.

*C(=NO)N

is not represented by the rules in the provided OPLS-AA force field. Please be advised, that the OPLS-AA force field as provided by EMC is not exhaustive or representative of all chemistries for which the OPLS_AA force field has been derived in literature. Typically, CHARMM as provided by EMC is more exhaustive, but also no all-encompassing. I checked your chemistry with CGENFF and noticed, that your

*C(=NO)*

forms a problem there too. Admittedly, a double-bonded nitrogen to a carbon with a capping -OH group is not that common to begin with. You might be hard-pressed to find a canned force field covering this moiety. Alternatively, you could use quantum mechanical calculations to enhance a force field. A package called GAAMP attempts to do such for CHARMM in a more structural way.