You are running out of available memory to perform the PB calculation. I
would suggest you increase the amount of memory allocated to this
calculation. If this is not a possibility for you, then you can decrease
'fillratio' from 4 (default) to 2 which will utilize less memory, but this
may cause a different error during the ligand PB calculation.
Good luck!
-Bill
On Sun, Jun 6, 2010 at 5:37 AM, vaibhav dixit <vaibhavadixit.gmail.com>wrote:
> Dear Amber community members, Bill, Jimm and Ross,
> Thanks for your inputs and suggestions.
>
> I have rerun the job in another folder.
> The gb calculation is running ok and only gb results are written to the
> FINAL_RESULTS_MMPBSA.dat files and corresponding mdout files are also ok.
> But there is follwoing error in the _MMPBSA_complex_pb.mdout and
> _MMPBSA_receptor_pb.mdout files. This error is not seen in the
> _MMPBSA_ligand_pb.mdout file. (please check the attached files).
>
> I'm unable to understand what this error means. Please find time and see if
> you can suggest some solution to the problem.
> --------
> POST-PROCESSING OF TRAJECTORY ENERGIES
> trajectory generated by
> ptraj
> minimizing coord set # 1
> SA Bomb in sa_arc(): Allocation aborted 0 210 210 0 0
> ----------------
>
>
> On 6/5/10, Bill Miller III <brmilleriii.gmail.com> wrote:
>>
>> What is in your _MMPBSA_complex_pb.mdout, _MMPBSA_receptor_pb.mdout, and
>> _MMPBSA_ligand_pb.mdout? If there is something going wrong with the PB
>> calculation, the error message will most likely be in one of these files
>> when you are running the PB calculation. Take a look at these files and see
>> if you can find the error, or at least something that will point to the
>> error.
>>
>> Good luck!
>>
>> -Bill
>>
>>
>> On Sat, Jun 5, 2010 at 1:25 AM, vaibhav dixit <vaibhavadixit.gmail.com>wrote:
>>
>>> Dear Amber community members, Bill, Jim and Ross,
>>> Thanks for your comments and suggestions on MMPBSA earlier,
>>> After solving the receptor and ligand mask issue, I was getting "No
>>> potential terms in sander output error"
>>>
>>> I doubt that the prmtop file is an issue here because when I'm adjusting
>>> the input for doing only gb calculation, it is working properly and giving
>>>
>>> DELTA G binding = -42.0688 +/- 3.4141
>>> 0.4828 (please check the attached file)
>>>
>>> So there is a problem with the pb calculation. If I'm correct here, could
>>> you please point to what is going wrong in the pb calculation and how to fix
>>> that?
>>>
>>> Input file:
>>> |--------------------------------------------------------------
>>> |Input file for running PB and GB in serial
>>> |&general
>>> | endframe=50, keep_files=2,
>>> | receptor_mask=:1-271:272-284, ligand_mask=:285
>>> |/
>>> |&gb
>>> | igb=2, saltcon=0.100,
>>> |/
>>> |--------------------------------------------------------------
>>> |Solvated complex topology file: 2PRG_rosi_solvated.prmtop
>>> |Complex topology file: 2PRG_rosi_NW.prmtop
>>> |Receptor topology file: res.prmtop
>>> |Ligand topology file: rosi.prmtop
>>> |Initial mdcrd(s): rosi_MD_1ns.mdcrd
>>>
>>> |Calculations performed using 50 frames.
>>> |
>>> |All units are reported in kcal/mole.
>>>
>>> -------------------------------------------------------------------------------
>>> On 6/2/10, Bill Miller III <brmilleriii.gmail.com> wrote:
>>>>
>>>> Your ligand is just one residue, right? If this is the case, then
>>>> MMPBSA.py should be able to guess the receptor_mask and ligand_mask without
>>>> you specifying it. If MMPBSA.py cannot guess the masks with a one residue
>>>> ligand, then more than likely there is an inconsistency with the prmtop
>>>> files.
>>>>
>>>> The error that you are now getting means that the sander calculations
>>>> (GB and PB) did not actually calculate any energies. The reason for this
>>>> error is probably a sander error that should be near the end of the
>>>> _MMPBSA_*.mdout files. This should have a sander error message that will be
>>>> helpful. You also might want to check the STDOUT and STDERR files for any
>>>> possibly important messages that got printed there.
>>>>
>>>> Good luck!
>>>>
>>>> -Bill
>>>>
>>>>
>>>> On Wed, Jun 2, 2010 at 6:37 AM, vaibhav dixit <vaibhavadixit.gmail.com>wrote:
>>>>
>>>>> Dear Amber community member,
>>>>> Thanks for your suggestions earlier.
>>>>> I have tried to fix the receptor and ligand masking issue as specified
>>>>> in the mail below. Please check if thats ok.
>>>>>
>>>>> But now I'm getting another error as follows. I'm not able to
>>>>> understand what is this potential terms error in sander output. I have
>>>>> attached my initial and avgcomplex pdb files here, but can't attach the
>>>>> mdcrd file as it makes the message large and is not delivered.
>>>>>
>>>>> Please find time and see if you can suggest some solution to the issue.
>>>>>
>>>>> The ERROR is given below.
>>>>> ---------------------------------------------
>>>>> [vaibhav.localhost MMPBSA]$ pwd
>>>>> /home/vaibhav/vaibhav/amber/2PRG/rosi/MMPBSA
>>>>> [vaibhav.localhost MMPBSA]$ $AMBERHOME/bin/MMPBSA.py -O -i
>>>>> mmpbsa_2b.in FINAL_RESULTS_MMPBSA.dat -sp 2PRG_rosi_solvated.prmtop
>>>>> -cp 2PRG_rosi_NW.prmtop -rp 2PRG_nolig.prmtop -lp rosi.prmtop -y *.mdcrd
>>>>> ptraj found! Using /home/vaibhav/software/amber10/exe/ptraj
>>>>> sander found! Using /home/vaibhav/software/amber10/exe/sander (serial
>>>>> only!)
>>>>> Assuming /home/vaibhav/software/amber10/exe/sander is part of
>>>>> amber9 or amber10. Using old PB input file.
>>>>> Warning: igb=2 should be used with mbondi2 pbradii set. Yours are
>>>>> modified Bondi radii (mbondi)
>>>>>
>>>>> Preparing trajectories with ptraj...
>>>>> 50 frames were read in and processed by ptraj for use in calculation.
>>>>>
>>>>> Starting sander calls
>>>>>
>>>>> Starting gb calculation...
>>>>>
>>>>> Starting pb calculation...
>>>>>
>>>>> Error: No potential terms in sander output! Check output files.
>>>>> NOTE: All files have been retained for debugging purposes. Type
>>>>> MMPBSA.py --clean to erase these files.
>>>>> [vaibhav.localhost MMPBSA]$
>>>>> ---------------------------------------------
>>>>>
>>>>> On 6/2/10, vaibhav dixit <vaibhavadixit.gmail.com> wrote:
>>>>>>
>>>>>> Dear Amber community members,
>>>>>> Thanks Bill for your comments.
>>>>>> Based on your suggestion I have given the receptor and ligand mask in
>>>>>> the following way.
>>>>>> My pdb file with receptor and ligand, mmpbsa.in and the prmtop files
>>>>>> are attached with this mail.
>>>>>>
>>>>>> (there are two chain of protein residue 207-477 and 608-627) I have
>>>>>> counted them as receptor_mask=:1-271:272-284, ligand_mask=:285
>>>>>>
>>>>>> Please check wheather this assignment is correct or not?
>>>>>> Thanks once again for your inputs and suggestions.
>>>>>> ---------------------
>>>>>> Input file for running PB and GB in serial
>>>>>> &general
>>>>>> endframe=50, keep_files=2,
>>>>>> receptor_mask=:1-271:272-284, ligand_mask=:285
>>>>>> /
>>>>>> &gb
>>>>>> igb=2, saltcon=0.100,
>>>>>> /
>>>>>> &pb
>>>>>> istrng=0.100,
>>>>>> /
>>>>>> ------------------------------------
>>>>>>
>>>>>>
>>>>>> On 6/1/10, Bill Miller III <brmilleriii.gmail.com> wrote:
>>>>>>>
>>>>>>> Did you specify the receptor_mask and ligand_mask variables in your
>>>>>>> input
>>>>>>> file? MMPBSA.py has a built in function to determine which residues
>>>>>>> correspond to the receptor and which residues correspond to the
>>>>>>> ligand.
>>>>>>> However, the guesser only works if all of the ligand residues are
>>>>>>> sequential
>>>>>>> (one after the other with no receptor residues in between). If this
>>>>>>> is not
>>>>>>> the case in your system, then you will need to specify receptor_mask
>>>>>>> and
>>>>>>> ligand_mask in the &general section of the MMPBSA.py input file.
>>>>>>> Otherwise,
>>>>>>> the guesser should work just fine, and if it isn't there might be an
>>>>>>> inconsistency with the prmtops that you provided.
>>>>>>>
>>>>>>> I hope that helps explain things a little better.
>>>>>>>
>>>>>>> -Bill
>>>>>>>
>>>>>>> On Tue, Jun 1, 2010 at 10:46 AM, vaibhav dixit <
>>>>>>> vaibhavadixit.gmail.com>wrote:
>>>>>>>
>>>>>>> > Dear Amber community members,
>>>>>>>
>>>>>>> > Thanks Jason for a prompt help with the tutorial. I could use the
>>>>>>> new file
>>>>>>> > successfully.
>>>>>>> >
>>>>>>> > I'm now trying the same tutorial procedure on my target protein and
>>>>>>> ligand.
>>>>>>> > Here I'm getting a different kind of error which is given below. I
>>>>>>> could
>>>>>>> > not
>>>>>>> > understand what it exactly means and how could I fix it.
>>>>>>> >
>>>>>>> > Please find time and see if you could help me with same.
>>>>>>> >
>>>>>>> > The error is as follows:
>>>>>>> > ---------------
>>>>>>> > [vaibhav.localhost MMPBSA]$ $AMBERHOME/bin/MMPBSA.py -O -i
>>>>>>>
>>>>>>> > mmpbsa_2b.inFINAL_RESULTS_MMPBSA.dat -sp 2PRG_rosi_solvated.prmtop
>>>>>>> -cp
>>>>>>>
>>>>>>> > 2PRG_rosi_NW.prmtop -rp 2PRG_nolig.prmtop -lp rosi.prmtop -y
>>>>>>> *.mdcrd
>>>>>>> > ptraj found! Using /home/vaibhav/software/amber10/exe/ptraj
>>>>>>> > sander found! Using /home/vaibhav/software/amber10/exe/sander
>>>>>>> (serial
>>>>>>> > only!)
>>>>>>> > Assuming /home/vaibhav/software/amber10/exe/sander is part of
>>>>>>> > amber9 or amber10. Using old PB input file.
>>>>>>> > Error: Could not predict mask from topology files! Make sure ligand
>>>>>>> > residues
>>>>>>> > are
>>>>>>> > sequential or specify receptor_mask and ligand_mask in the input
>>>>>>> file.
>>>>>>> > NOTE: All files have been retained for debugging purposes. Type
>>>>>>> MMPBSA.py
>>>>>>> > --clean to erase these files.
>>>>>>> > [vaibhav.localhost MMPBSA]$ pwd
>>>>>>> > /home/vaibhav/vaibhav/amber/2PRG/rosi/MMPBSA
>>>>>>> > [vaibhav.localhost MMPBSA]$
>>>>>>> > -------------------------------------------
>>>>>>> >
>>>>>>> > --
>>>>>>> > With regards
>>>>>>> >
>>>>>>> > Vaibhav A. Dixit
>>>>>>> > Ph.D. Scholar
>>>>>>> > Department of Medicinal Chemistry
>>>>>>> > Natl. Inst. Pharm. Edu. & Res. (NIPER)
>>>>>>> > Sector 67, Phase X, S.A.S. Nagar (Mohali)
>>>>>>> > Punjab -160 062 INDIA
>>>>>>> > Phone (Mobile): +919915214408
>>>>>>> > E-mail: vaibhavadixit.gmail.com
>>>>>>> > www.niper.nic.in
>>>>>>> > _______________________________________________
>>>>>>> > AMBER mailing list
>>>>>>> > AMBER.ambermd.org
>>>>>>> > http://lists.ambermd.org/mailman/listinfo/amber
>>>>>>> >
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> --
>>>>>>>
>>>>>>> Bill Miller III
>>>>>>>
>>>>>>> Quantum Theory Project,
>>>>>>> University of Florida
>>>>>>> Ph.D. Graduate Student
>>>>>>>
>>>>>>> 352-392-6715
>>>>>>>
>>>>>>> _______________________________________________
>>>>>>> AMBER mailing list
>>>>>>> AMBER.ambermd.org
>>>>>>> http://lists.ambermd.org/mailman/listinfo/amber
>>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>> --
>>>>>> With regards
>>>>>>
>>>>>> Vaibhav A. Dixit
>>>>>> Ph.D. Scholar
>>>>>> Department of Medicinal Chemistry
>>>>>> Natl. Inst. Pharm. Edu. & Res. (NIPER)
>>>>>> Sector 67, Phase X, S.A.S. Nagar (Mohali)
>>>>>> Punjab -160 062 INDIA
>>>>>> Phone (Mobile): +919915214408
>>>>>> E-mail: vaibhavadixit.gmail.com
>>>>>> www.niper.nic.in
>>>>>>
>>>>>>
>>>>>
>>>>>
>>>>> --
>>>>> With regards
>>>>>
>>>>> Vaibhav A. Dixit
>>>>> Ph.D. Scholar
>>>>> Department of Medicinal Chemistry
>>>>> Natl. Inst. Pharm. Edu. & Res. (NIPER)
>>>>> Sector 67, Phase X, S.A.S. Nagar (Mohali)
>>>>> Punjab -160 062 INDIA
>>>>> Phone (Mobile): +919915214408
>>>>> E-mail: vaibhavadixit.gmail.com
>>>>> www.niper.nic.in
>>>>
>>>>
>>>>
>>>>
>>>> --
>>>> Bill Miller III
>>>> Quantum Theory Project,
>>>> University of Florida
>>>> Ph.D. Graduate Student
>>>> 352-392-6715
>>>>
>>>
>>>
>>>
>>> --
>>> With regards
>>>
>>> Vaibhav A. Dixit
>>> Ph.D. Scholar
>>> Department of Medicinal Chemistry
>>> Natl. Inst. Pharm. Edu. & Res. (NIPER)
>>> Sector 67, Phase X, S.A.S. Nagar (Mohali)
>>> Punjab -160 062 INDIA
>>> Phone (Mobile): +919915214408
>>> E-mail: vaibhavadixit.gmail.com
>>> www.niper.nic.in
>>
>>
>>
>>
>> --
>> Bill Miller III
>> Quantum Theory Project,
>> University of Florida
>> Ph.D. Graduate Student
>> 352-392-6715
>>
>
>
>
> --
> With regards
>
> Vaibhav A. Dixit
> Ph.D. Scholar
> Department of Medicinal Chemistry
> Natl. Inst. Pharm. Edu. & Res. (NIPER)
> Sector 67, Phase X, S.A.S. Nagar (Mohali)
> Punjab -160 062 INDIA
> Phone (Mobile): +919915214408
> E-mail: vaibhavadixit.gmail.com
> www.niper.nic.in
>
--
Bill Miller III
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-6715
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Received on Sun Jun 06 2010 - 04:30:03 PDT
