On Tue, Mar 05, 2019, Mayank Dixit wrote:
> I have used the parmchk2 to generate frcmod file of
>azobenzene which is connected to cysteine residue.
>IMPROPER
>c3-n -c2-o 1.1 180.0 2.0 Using the
>c2-c2-n -ca 1.1 180.0 2.0 Using the
>ca-ca-ca-n 1.1 180.0 2.0 Using the
>ca-ca-ca-ha 1.1 180.0 2.0 Using general
>ca-ca-ca-nf 1.1 180.0 2.0 Using the
>ca-ca-ca-ne 1.1 180.0 2.0 Using the
>
>The parameters for improper dihedrals are not present in parm10.dat and
>gaff.dat files.
>How parmchk2 is filling these values in frcmod file?
>Please help me in fixing this issue.
I don't there is anything to "fix". You can follow the logic of what
parmchk2 is doing by looking at the chk_improper() routine in
AMBERHOME/AmberTools/src/antechamber/parmchk2.c
It's a bit complex, but steps 1 through 5 are marked by comments that
show the overview of what is going on.
...hope this helps....dac
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Received on Thu Mar 07 2019 - 06:30:04 PST
