On Thu, 2014-03-20 at 15:07 +0530, BERGY wrote:
> I ran tleap, using the commands,
>
> $tleap -s -f input_prpe.txt
> which had the follwing lines.
> ---------
> source /usr/soft/amber12/dat/leap/cmd/leaprc.ff13
ff13 is not currently compatible with pmemd.cuda from Amber 12 (it will
work fine with pmemd.cuda from Amber 14).
You should also take care when choosing a force field. The general
mantra is "bigger is not always better (but sometimes is)." In
particular, ff13 is an almost complete reparametrization of the Amber
force field with a new charge model and van der Waals parametrization
strategy. As such, it's significantly less tested than other choices
like ff12SB (which is the recommended force field for Amber
simulations).
If you have a particular reason for wanting to use ff13 instead of
ff12SB, then you'll need to either wait until Amber 14 comes out to use
the GPU code or stick with the CPU code.
HTH,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Thu Mar 20 2014 - 05:00:03 PDT
