Yun,
If you run LEaP and try to save the prmtop/prmcrd files LEaP will list
the missing force field parameters as errors.
You carefully look at what correspond these missing force field
parameters in your structure and you can create by hand a frcmod file
by selecting the force field parameters you really want...
regards, Francois
> I am trying do set parameters for a ligand as shown in the attachment with
> GLYCAM, GAFF, and 99SB force fields for different parts.
>
> For the left part (one standard alpha-L-Rhamnose and a thio
> alpha-L-Rhamnose), I calculated RESP charge and used antechamber to set GAFF
> parameters for the modified thio sugar (blue part). Then I loaded GLYCAM_06
> and GAFF ff within tleap, after which I loaded the standard sugar (red part)
> and the modified thio sugar (blue part).
>
> But after I linked these two together, missing parameters remained for the
> newly-formed glycosidic bond and angles and dihedrals, as expected. So I
> wonder, technically, how to fill in these missing parameters. Should I
> manually construct a .frcmod file? Or is there a better alternative to fuse
> these different parts?
>
> Thanks for any suggestion.
>
> Yun
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Received on Fri Aug 26 2011 - 23:30:02 PDT
