Note that parmchk2does not produce the same frcmod output as parmchk when run in GAFF mode, i.e. running parmchk or parmchk2 without the -s 2 flag and comparing the output. I've tested with several example Mol2 files that were generated by antechamber using GAFF and there are differences in some improper terms. (I assume that these are due to changes in the methodology/algorithms used within parmchk2?)
This means that we'll need to re-run all of our existing parmchk examples with parmchk2, regardless of which force field is used. It would probably be a good idea to try GAFF and GAFF2 for the same systems. Since GAFF2 is still in beta we might want to work out cases where it is prone to failure.
Since we want to support both GAFF and GAFF2 we will need to use
parmchk2rather thanparmchk. See here or here for details.To use different force fields with
antechamberTo use different force fields with
parmchk2Note that
parmchk2does not produce the same frcmod output asparmchkwhen run in GAFF mode, i.e. runningparmchkorparmchk2without the-s 2flag and comparing the output. I've tested with several example Mol2 files that were generated byantechamberusing GAFF and there are differences in some improper terms. (I assume that these are due to changes in the methodology/algorithms used withinparmchk2?)This means that we'll need to re-run all of our existing
parmchkexamples withparmchk2, regardless of which force field is used. It would probably be a good idea to try GAFF and GAFF2 for the same systems. Since GAFF2 is still in beta we might want to work out cases where it is prone to failure.