On Fri, Aug 26, 2011 at 9:01 PM, Yun Shi <yunshi09.gmail.com> wrote:
> Hi all,
>
> 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.
>
Use parmchk. If you run the program with no arguments, it tells you how to
use it. By default, it will search gaff.dat and pull out reasonable
parameters, dumping them to an frcmod file. If there's anything it simply
*can't* find, it will put a placeholder (all parameters are 0) and say
"ATTN, need revision". You have to fix those parameters.
However, I would warn you that gaff dihedrals should not necessarily be
accepted. Run short simulations to make sure they make sense, as you may
have to modify some of them by hand.
HTH,
Jason
> Yun
>
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--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Fri Aug 26 2011 - 19:00:03 PDT
