I’ve had similar issues with gaff on a unique nucleobase; improper gaff atom types were chosen which then loads incorrect distance, angle, and torsion angle definitions into the frcmod file. The only solution I could find was to manually inspect and alter the frcmod file. Note, I was using a rather old version of Amber (either 8 or 9).
Not the best solution, but it worked for me in the end.
Alex
On 6/20/17, 5:10 PM, "Govind Hegde" <ghegde.mines.edu> wrote:
Dear Amber Members,
I am trying to set up a system in LEAP containing 3 molecule types: small graphene sheets, a perfluorocarbon and water. I am currently using GAFF, and my graphene sheets have two atom types ( ca and ha) and the PFC's have 6 atom types (oh, ho, o, c, c3 and f). However, when I use LEAP to set up my topology file, I see that LEAP ignores the "c" in the PFC and merges that atom type with the "ca" in graphene, even though these two atom types have pretty different parameters in gaff.dat. Has anyone else experienced such a problem, and if so, is there a way to get around it? I have tried using both mol2 files as well as prep files to import the graphene and PFC units, with the same result.
Thanks for your help!
Best regards,
Govind Hegde
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Received on Tue Jun 20 2017 - 15:30:02 PDT
