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
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Received on Wed Jun 02 2010 - 05:00:05 PDT
