HI Jason.
changing from ff13 to ff12SB did work. !
thank you.
BERGY
On 3/20/14, Jason Swails <jason.swails.gmail.com> wrote:
> 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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>
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Received on Fri Mar 21 2014 - 05:00:02 PDT
