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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Received on Mon Mar 01 2010 - 09:30:04 PST
