A couple comments here. Bugfix.43 for Amber 9 fixes the -y flag, so make
sure that all bug fixes are applied. See
http://ambermd.org/bugfixes90.htmlfor details about the Amber 9 bug
fixes and how to apply them.
As for the AmberTools 12 MMPBSA.py version, you will need to install the
full AmberTools 12 suite in order to take advantage of it (indeed, the
error you're seeing is an unpatched sander issue, not an MMPBSA.py issue).
Note that since AmberTools 12 was released, MMPBSA.py no longer depends on
sander for many of its common analyses. This means that at the very least,
NAB and two NAB programs written with MMPBSA.py need to be compiled in
order to use it.
AmberTools 12 is a free download released as open source, so there is no
financial cost for downloading it. If you are having trouble compiling
AmberTools 12, google your error message to see if the problem has been
resolved in the past. If you still need help, write back to this list with
the exact series of commands you used along with the error messages you got
(simply saying "it doesn't work" provides no help for those of us trying to
diagnose your issue remotely).
HTH,
Jason
On Tue, Jul 3, 2012 at 10:03 AM, <rajeevy.iitk.ac.in> wrote:
> Dear Jason,
> Thank you for your reply.
> yes, I have used Amber 9 for MD run (all minimization and equilibration).
> I am unable to install MMPBSA.py from ambertools 12, so please can you
> sand me the MMPBSA.py script file so that i can use for my calculations.
>
> Thanks
> Rajeev
>
> > 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
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
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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 Jul 03 2012 - 08:00:03 PDT
