[AMBER] Re: gb working but not pb & gives No potential terms in sander output! error

From: vaibhav dixit <vaibhavadixit.gmail.com>
Date: Sun, 6 Jun 2010 15:07:55 +0530

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]$ $AMBERHOME/bin/MMPBSA.py -O -i mmpbsa_2b.inFINAL_RESULTS_MMPBSA.dat -sp 2PRG_rosi_solvated.prmtop -cp
>>>> 2PRG_rosi_NW.prmtop -rp 2PRG_nolig.prmtop -lp rosi.prmtop -y *.mdcrd
>>>> ptraj found! Using /home/vaibhav/software/amber10/exe/ptraj
>>>> sander found! Using /home/vaibhav/software/amber10/exe/sander (serial
>>>> only!)
>>>> Assuming /home/vaibhav/software/amber10/exe/sander is part of
>>>> amber9 or amber10. Using old PB input file.
>>>> Warning: igb=2 should be used with mbondi2 pbradii set. Yours are
>>>> modified Bondi radii (mbondi)
>>>>
>>>> Preparing trajectories with ptraj...
>>>> 50 frames were read in and processed by ptraj for use in calculation.
>>>>
>>>> Starting sander calls
>>>>
>>>> Starting gb calculation...
>>>>
>>>> Starting pb calculation...
>>>>
>>>> Error: No potential terms in sander output! Check output files.
>>>> NOTE: All files have been retained for debugging purposes. Type
>>>> MMPBSA.py --clean to erase these files.
>>>> [vaibhav.localhost MMPBSA]$
>>>> ---------------------------------------------
>>>>
>>>> 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





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Received on Sun Jun 06 2010 - 03:00:03 PDT
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