Great!
Will do. Thank you very much!
Cristina
Billy Miller III wrote:
> 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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Received on Mon Mar 01 2010 - 09:30:05 PST
