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.pl also
>>>> 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 - 09:30:03 PST
