On Mon, Feb 15, 2010 at 8:10 PM, Jason Swails <jason.swails.gmail.com> wrote:
[...snip...]
> The problem you have to fix is getting sander to recognize the -y
> flag. All of the calculations are done using this flag (inptraj), so
> that all frames are analyzed from a single trajectory file rather than
> having separate inpcrds for each file.
>
> I'm pretty sure this was a bug in a pre-patched amber9. Make sure
> that all of the patches are applied, then you must recompile. Don't
> forget to do "make clean" before you do "make serial" again.
>
> Sander must be fixed before MMPBSA.py will work.
SOLVED!
I had applied all the bugfixes and recompiled it already. Turns out
there was some residual installation of amber in another directory
without the bugfixes, and due to path setting in some file, MMPBSA was
picking up sander from that directory. That path was overridden, and
sander worked.
Thank you Jason and Billy for your help.
Regards,
arvind
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Received on Tue Feb 16 2010 - 01:30:03 PST
