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
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Received on Sat Jun 05 2010 - 04:00:04 PDT
