On Wed, Dec 31, 2014, Pallavi Mohanty wrote:
> I am running TMD in AMBER, at this point i am done with heating and
> equilibration steps. I have an open and closed conformation and i want to
> span the transition from open to closed.
> My Input file for TMD was
>
> TMD: open->closed; target rmsd 1.6; resid 38-134 restrained
> &cntrl
> imin = 0, ntx = 1, nstlim = 5000, irest = 0,
You are using irest=0, which would not be advised if you have already done
heating and equilibration. But this is unlikely to be the cause of your
problem.
> and I got an error stating "Targeted molecular dynamics:
> tgtrmsd = 1.60000, tgtmdfrc= 1.00000
> | INFO: Old style inpcrd file read "
This is not an error message. Set ntpr=1 and see if you get any useful
information from early steps. Make sure that all energies (except the
targetted stuff, which I assume you are now turning on for the first time)
are the same in the first step of the new run compared to the final step
of the equilibration.
...hope this helps....dac
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Received on Wed Dec 31 2014 - 07:00:03 PST
