On Sat, Oct 22, 2016, windy wrote:
>
> I had a protein with ligands. When I put it into MD, it reported in heat step:
> Error: unspecified launch failure launching kernel kNLSkinTest
> cudaFree GpuBuffer::Deallocate failed unspecified launch failure
IHP is a very difficult ligand to model. As Bill pointed out, your version
of this ligand is fully protonated, which is both chemically unreasonable, and
is likely causing problems that are peculiar to protonated phosphates that
try to use standard Amber-like or gaff parameters.
You should do a Google search on something like "inositol hexaphosphate
molecular mechanics" to get some insight into what others have done. A
caution: you should expect a significant learning curve here: you will need to
learn about the acid-base properties of IHP, and be prepared to do a lot of
(computer) experiments. Be sure you are comfortable with Amber calculations
on more standard systems as well.
....dac
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Received on Sun Oct 23 2016 - 18:30:02 PDT
