My suggestion is to upgrade to AmberTools 12 and use the MMPBSA.py included
there.
sander from Amber 11 recognizes the '-y' flag, so I'm guessing that you are
inadvertently using an older version of MMPBSA.py and/or sander than you
are expecting.
Check the MMPBSA.py output (above the line "2480 frames were read in and
processed by ptraj for use in calculation") for the exact sander executable
that was being used, and I'll bet it's from Amber 9 or 10.
Unless you are looking to do decomposition analysis, nearly everything that
MMPBSA.py can do can be done via AmberTools 12 alone (without Amber).
HTH,
Jason
On Mon, Jul 2, 2012 at 10:36 AM, <rajeevy.iitk.ac.in> wrote:
> Dear Amber user,
> Now I am using MMPBSA.py (Amber 11) for calculations, here it was
> reading al trajectories with ptraj till....
> 2480 frames were read in and processed by ptraj for use in calculation.
>
> after that the problems is occurring like..........
> Starting sander calls
>
> Starting gb calculation...
>
> mdfil: Error unknown flag:-y
>
> usage: sander [-O|A] -i mdin -o mdout -p prmtop -c inpcrd -r restrt
> [-ref refc -x mdcrd -v mdvel -e mden -idip inpdip -rdip
> rstdip -mdip mddip -ng numgroup -remlog remlog -rem
> [0|1|2] -inf mdinfo -radii radii]
> Consult the manual for additional options.
> .
>
> Starting pb calculation...
>
>
> mdfil: Error unknown flag:-y
>
> usage: sander [-O|A] -i mdin -o mdout -p prmtop -c inpcrd -r restrt
> [-ref refc -x mdcrd -v mdvel -e mden -idip inpdip -rdip
> rstdip -mdip mddip -ng numgroup -remlog remlog -rem
> [0|1|2] -inf mdinfo -radii radii]
> Consult the manual for additional options.
>
> Error: Sander error! GB mdout file was not created.
> NOTE: All files have been retained for debugging purposes. Type MMPBSA.py
> --clean to erase these files.
>
> Regards
> Rajeev Yadav
>
> > You don't have to redo your MD, just redo your mmpbsa with the new
> > scripts that are more flexible. Let's start from there ...
> >
> > Also, the radius problem in Amber9 was reported and resolved before on
> > the mailing list. You can google it in the archive.
> >
> > Ray
> >
> > On Sun, Jul 1, 2012 at 12:10 AM, <rajeevy.iitk.ac.in> wrote:
> >> Dear Ray,
> >> In latest AmberTool, I have to use mm_pbsa.pl or any other and also
> >> the
> >> radius of F is needed or not??
> >> If i use latest AmberTool for my calculations, all the minimization and
> >> equilibration that I did in Amber9, should be done again in latest
> >> version?
> >> Since I am new in this field and not know much, so
> >> If possible please let me know the whether I can use Amber9 for
> >> mm_pbsa.pl
> >> calculations and where I should use radius of F.
> >>
> >> With Regards
> >> Rajeev Yadav
> >>
> >>
> >>> I strongly suggest you try the latest AmberTools release for your
> >>> project
> >>> ... It's free.
> >>>
> >>> Ray
> >>>
> >>> On Sat, Jun 30, 2012 at 3:36 AM, <rajeevy.iitk.ac.in> wrote:
> >>>
> >>>> Hi,
> >>>> There are three F atoms in my ligand and using mm_pbsa.pl for
> >>>> calculation
> >>>> in AMBER9. Can some one tell me how an where to set radius of F in
> >>>> MMPBSA
> >>>> calculation.
> >>>> It shows the error in the terminal window like this
> >>>> Died at /home/psen/AMBER9/amber9/src/mm_pbsa/mm_pbsa_calceneent.pm
> >>>> line
> >>>> 498, <PDB> line 9267.
> >>>> And in log file I got the following information:
> >>>> Calculating energy / entropy contributions
> >>>> Calc contrib for ./snapshot_com.crd.1
> >>>> Calc MM/GB/SAS
> >>>> Generate PDB
> >>>> Center PDB
> >>>> Calc PBSA
> >>>> Generate PQR
> >>>> No radius found for F2 9265 in residue COU 584
> >>>> Thanking You
> >>>> with regards
> >>>> Rajeev Yadav
> >>>>
> >>>> _______________________________________________
> >>>> AMBER mailing list
> >>>> AMBER.ambermd.org
> >>>> http://lists.ambermd.org/mailman/listinfo/amber
> >>>>
> >>> _______________________________________________
> >>> AMBER mailing list
> >>> AMBER.ambermd.org
> >>> http://lists.ambermd.org/mailman/listinfo/amber
> >>>
> >>
> >>
> >> _______________________________________________
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> >
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> >
>
>
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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 Mon Jul 02 2012 - 08:00:04 PDT
