Hello!
I face some issues regarding the automatic application of partial charges with EMC (v9.4.4).
Below, I attach a minimal example of an acid (p. 123 from the manual) modeled with the PCFF force field.
ITEM OPTIONS
replace true
number true
field_charge false
field pcff
#field opls
build_dir .
project pani
ITEM END
ITEM GROUPS
#acid:c=a [C](=[O])[O-1] # does not work
acid:c=a [C](=[O])[O-0.99999999] # works
ITEM END
ITEM CLUSTERS
acid acid,1
ITEM END
Note that when I set the charge to -1 I receive the error msg:
Info: groups = {ngroups -> 1, group ->
{id -> acid, chemistry -> "[C](=[O])[O-1]", depth -> 8, charges ->
additive, charge -> 0, terminator -> false}, ndeletes -> 0,
npolymers -> 0}
Info: field = {mode -> apply, style -> none, error -> true, debug -> false,
check -> {atomistic -> true, charge -> false}}
Info: applying '~/Programs/emc/v9.4.4/field/pcff/pcff.frc'
Warning: increment pair {c=2, o-} not found.
Error: core/script/field/entry.c:645 ScriptFieldEntryApply:
Missing force field parameters.
Program aborted.
Changing the option from c=a[daptive] or c=o[verwrite] does not address the issue.
On the other hand, setting the charge to -0.999999 works.
The example with the water reported in the manual works as well.
It seems that the program attempts to find a specific rule for {c=, o-} pairs which is not found in the force field; thus it results an error.
I face the same issue with other chemistries as well; e.g., charged [N+1] in emeraldine salts, chlorine with variable charge (e.g., [Cl-0.7], etc.).
The solution of using a charge equal to 0.9999999 does not work for all cases; e.g., [Cl-0.9999999] does not work.
This is not a major issue since one can correct the charges by hand posteriorly, but I’m wandering whether there is a canonical way to do this.
Thanks,
Aris