You can use MMPBSA without the receptor or ligand. If they're solvated,
just run the trajectory through sander using the imin=5 functionality,
setting maxcyc = 1 (that will just extract energies), but make sure that
you're using ntb=1,ntp=0, since imin=5 won't make much sense with constant
pressure. The trajectory frames should have the box size in there, anyway,
so NVT should give you the proper behavior in either case. You just won't
be calculating the pressure.
HTH,
Jason
On Tue, Aug 23, 2011 at 7:05 AM, George Tzotzos <gtzotzos.me.com> wrote:
> Hi everybody,
>
> I'm revisiting some old MD trajectories and in a couple of cases I cannot
> trace the output file (md.out).
>
> Is there a way to re-generate such files from the corresponding topology
> and trajectory files?
>
> Regards
>
> George
>
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>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Tue Aug 23 2011 - 04:30:04 PDT
