How to assign charge for each atom on polymer like opls or PCFF?

EMC
1

How to assign charge for each atom on polymer like opls or PCFF ?

2

Charges can be assigned using standard SMILES conventions, e.g. SPC/E water could be addressed as [O-0.8476]([H+0.4238])([H+0.4238]).

3

Thanks for reply, I konw this method, I want to konw how to assign charges by default when generating structure without assigning charge by hand?

4

The typing engine takes care of type and partial charge assignment in accordance with the chosen force field. For instance, group chemistry with SMILES O will be expanded to O(H)(H). This – in turn – will be typed as SPC/E water when selecting the OPLS-AA force field.

The method mentioned above is to override the values as provided by the force field. Coming to think of it, one would also have to set an override flag in case of overriding partial charges. This override flag is specified when defining a group, e.g.

ITEM	GROUP

water:charges=override	[O-0.8]([H+0.4])([H+0.4])

ITEM	END

will override the force field defined partial charges by the supplied values. Assume the use of OPLS-AA in which case the SPC/E values are -0.8476 for oxygen and 0.4238 for hydrogen. These are replaced by the above values of -0.8 for oxygen and 0.4 for hydrogen when toggling the charge override option. See page 43 of the EMC manual for more options ($EMC_ROOT/docs/emc.pdf).