On Tue, Jun 20, 2017, Govind Hegde wrote:
>
> 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...
You should run antechamber on the graphene, the perfluorocarbon and water (if
needed) as separate jobs. I can't tell what really happened from your brief
description, but antechamber only handles a single molecule at a time. You
combine separate molecules into a complete system at the leap stage.
...hope this helps....dac
p.s.: I recommend using one of the standard water files: GAFF is for getting
approximate force fields for molecules where you cannot (or do not wish to)
spend time on individual optimization. If you have optimized parameters (such
as for water) you should use them. Same comment applies to graphene: there
are probably already parameters out there that people have tested.
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Received on Wed Jun 21 2017 - 05:30:03 PDT
