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
>> >>>>
>> >>> _______________________________________________
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>> >>> 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 - 07:30:02 PDT
