Hi Rafi,
The MMPBSA.py section of the Amber11 manual corresponds to the version that
was released with Amber11, which has since been updated. The manual that
you should consult for MMPBSA.py is the one released alongside the source
code on the tutorial website. (
http://ambermd.org/tutorials/advanced/tutorial3/py_script/files/MMPBSA_Python_Manual.pdf).
Time constraints led to this "staggering" of MMPBSA.py/Amber releases, but
future versions will be improved in this regard (including installation,
dependencies, etc.).
All the best,
Jason
On Thu, Oct 28, 2010 at 9:58 AM, Rafi Ahmad <rafi.ahmad.uit.no> wrote:
> Hi Folks,
>
> I have been using the perl script of MMPSA for a longtime now and I
> recently
> started to use the python version, so I used the AMBER 11 manual. I have a
> complex model where I have some water-mediated contacts to the inhibitor so
> I used the initial_traj=1 option. However, every time I tried it gave me
> the
> error:
>
> Warning: Input error! "initial_traj=1" is an invalid option.
>
> After checking it up and looking at the AMBER mailing, I could not get any
> post about this, and there were posts from few months back where people had
> used the same option. But, than spending 45 mins and further digging into
> the mailing list I came to know that the "initial_traj" has been renamed to
> "strip_mdcrd".
>
> I think that I would be good, if this is updated in the AMBER 11 User
> manual
> as well ( pages 227, 230, 231 and 236) which will save sometime and
> questions to the mailing list.
>
> Regards
>
> Rafi
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>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-4032
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Received on Thu Oct 28 2010 - 07:30:02 PDT
