Specifically, bugfix.43 for AMBER 9 adds this functionality to *sander*.
Good luck!
-Bill
On Mon, Mar 1, 2010 at 12:11 PM, Billy Miller III <brmilleriii.gmail.com>wrote:
> Christina,
>
> It looks like you have an "older" version of AMBER 9 before the -y flag was
> added to the *sander* module of AMBER. You should download the AMBER 9
> bugfixes (http://ambermd.org/bugfixes90.html) and re-compile AMBER. This
> should fix this problem.
>
> -Bill
>
>
> On Mon, Mar 1, 2010 at 12:05 PM, Cristina Sisu <csds2.cam.ac.uk> wrote:
>
>> Hi Dwight and Bill,
>>
>> I've reformated my topology files to accommodate the PBradii (Thank you
>> Dwight). The error is still there though.
>> In the error file I get:
>> > Assuming /usr/local/amber9/exe/sander is part of
>> > amber9 or amber10. Using old PB input file.
>> > Residue labels:
>> >
>> > Checking coordinates: ../JMJC-noalyprod-1.mdcrd
>> > Residue labels:
>> >
>> > Checking coordinates: _MMPBSA_complex.mdcrd
>> > Residue labels:
>> >
>> > Checking coordinates: _MMPBSA_complex.mdcrd
>> > Residue labels:
>> >
>> > Checking coordinates: _MMPBSA_complex.mdcrd
>> > Residue labels:
>> >
>> > Checking coordinates: _MMPBSA_receptor.mdcrd
>> > Residue labels:
>> >
>> > Checking coordinates: _MMPBSA_ligand.mdcrd
>> > Error: Sander error! GB mdout file was not created.
>>
>> In the .out file I get:
>> > 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.
>> > ptraj found! Using /usr/local/amber9/exe/ptraj
>> > sander found! Using /usr/local/amber9/exe/sander (serial only!)
>> >
>> > Preparing trajectories with ptraj...
>> > 347 frames were read in and processed by ptraj for use in calculation.
>> >
>> > Starting sander calls
>> >
>> > Starting gb calculation...
>> >
>> > Starting pb calculation...
>> >
>> > NOTE: All files have been retained for debugging purposes. Type
>> > MMPBSA.py --clean to erase these files.
>> >
>> Buti since I obtain 6(six) _MMPBSA_prtaj.out files that use correctly
>> the mdcrd file, i assume that the mdfil error is not too worrying.
>>
>> The first _MMPBSA_prtaj1.out show that the mdcrd file was read correctly
>> and the _MMPBSA_complex.mdcrd is created. The correct number of frames
>> is read for complex, receptor and ligand. The next two _MMPBSA_prtaj.out
>> file contain the correct information for the ligand and receptor
>> respectively. The _MMPBSA_prtraj 4, 5 and 6.out are a bit strange in the
>> way that they read only one frame.
>> Eg: _MMPBSA_ptraj4.out
>> > PTRAJ: Processing input from file _MMPBSA_complexinpcrd.in
>> >
>> > PTRAJ: trajin _MMPBSA_complex.mdcrd 1 1 1
>> >
>> > PTRAJ: trajout _MMPBSA_dummycomplex.inpcrd restart
>> >
>> > PTRAJ: Successfully read the input file.
>> > Coordinate processing will occur on 1 frames.
>> > Summary of I/O and actions follows:
>> >
>> > INPUT COORDINATE FILES
>> > File (_MMPBSA_complex.mdcrd) is an AMBER trajectory with 1 sets
>> >
>> > OUTPUT COORDINATE FILE
>> > File (_MMPBSA_dummycomplex.inpcrd) is an AMBER restart file
>> >
>> > NO ACTIONS WERE SPECIFIED
>> >
>> > Processing AMBER trajectory file _MMPBSA_complex.mdcrd
>> > going to be
>> > Set 1 .
>> >
>> > PTRAJ: Successfully read in 1 sets and processed 1 sets.
>> > Dumping accumulated results (if any)
>> Identical results are obtained for receptor and ligand. And after that
>> it stops, and get the error message.
>> That's pretty much all the information I have. Any help is highly
>> appreciated.
>>
>> Cristina
>>
>>
>> Billy Miller III wrote:
>> > There seems to be a problem with the inputs being given to the PB
>> solver.
>> > The PB solver was not able to properly run, which is why no PB mdout
>> file
>> > created. Since the run failed, all temporary files must have been kept.
>> Did
>> > you check the ptraj output files to make sure the program stripped out
>> the
>> > proper residues and recognized the correct files? Were *any* mdout files
>> > created? What was printed in the logfile (or to the screen if ran
>> > interactively). If you submitted the run to a queue, what was printed in
>> the
>> > .out and .err files? Are you just running PB, or GB also?
>> >
>> > -Bill Miller
>> >
>> > On Mon, Mar 1, 2010 at 11:14 AM, Dwight McGee <dwight.mcgee.gmail.com
>> >wrote:
>> >
>> >
>> >> Hi Cristina,
>> >>
>> >>
>> >> If you go to the amber manual look under the igb section you will see
>> that
>> >> each generalized born model rather it be 1,2,5,7 has a suggested
>> pbradii.
>> >> MMPBSA.py simply checks your topology files to see that the pbradii you
>> >> specified matches up to the generalized born model you have chosen if
>> they
>> >> do not match to the suggested models then it prints the message which
>> you
>> >> observed.
>> >> If you want to use igb=5, I would remake my topology and coordinate
>> files
>> >> adding the command
>> >> *set default PBradii mbondi2* or *set default PBradii bondi*
>> >> Hope that helps.
>> >>
>> >> Good Luck
>> >>
>> >>
>> >> On Mon, Mar 1, 2010 at 11:04 AM, Cristina Sisu <csds2.cam.ac.uk>
>> wrote:
>> >>
>> >>
>> >>> Hi,
>> >>>
>> >>> Thank you both for the answers.
>> >>>
>> >>>>> Before to do that you could try with the new MM_PBSA.py. I don't
>> know
>> >>>>>
>> >>> how it
>> >>>
>> >>>>> works with Zinc, maybe it is more "user friendly" than the old
>> MM_PBSA
>> >>>>>
>> >>> perl
>> >>>
>> >>>> It takes the Zinc radius from the prmtop file. It does this because
>> >>>> there is no option to use molsurf, which would require an external
>> >>>> definition of the radius. However, results with/without molsurf
>> >>>> differ only very slightly in my experience. I believe mm_pbsa.plalso
>> >>>> has an option to do this, though I'm not familiar enough with using
>> >>>> that version to speak definitively on it.
>> >>>>
>> >>>>
>> >>>>
>> >>> I've tried the MM_PBSA.py and it seems to recognize both Fe and Zn and
>> >>> that's good, however I stumbled onto another problem. I set the
>> >>> MM_PBSA.py running and shortly after checking the complex. receptor
>> and
>> >>> ligand file I get the error:
>> >>>
>> >>>
>> >>>> Assuming /usr/local/amber9/exe/sander is part of
>> >>>> amber9 or amber10. Using old PB input file.
>> >>>> Warning: igb=5 should be used with either mbondi2 or bondi pbradii
>> >>>> set. Yours are modified Bondi radii (mbondi)
>> >>>> Residue labels:
>> >>>>
>> >>>> Checking coordinates: ../JMJC-noalyprod-1.mdcrd
>> >>>> Residue labels:
>> >>>>
>> >>>> Checking coordinates: _MMPBSA_complex.mdcrd
>> >>>> Residue labels:
>> >>>>
>> >>>> Checking coordinates: _MMPBSA_complex.mdcrd
>> >>>> Residue labels:
>> >>>>
>> >>>> Checking coordinates: _MMPBSA_complex.mdcrd
>> >>>> Residue labels:
>> >>>>
>> >>>> Checking coordinates: _MMPBSA_receptor.mdcrd
>> >>>> Residue labels:
>> >>>>
>> >>>> Checking coordinates: _MMPBSA_ligand.mdcrd
>> >>>> Error: Sander error! PB mdout file was not created.
>> >>>> ~
>> >>>>
>> >>> I've tried all the versions to run MM_PBSA.py in serial and parallel.
>> >>> I've checked all the input parameters. Still I have no idea of what
>> is
>> >>> happening. There is not extra information except the error: "Sander
>> >>> error! PB mdout file not created"
>> >>> Any ideas as to what can be going so wrong here?
>> >>>
>> >>>
>> >>> Cristina
>> >>>
>> >
>>
>>
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>
>
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Received on Mon Mar 01 2010 - 09:30:04 PST
