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

From: vaibhav dixit <vaibhavadixit.gmail.com>
Date: Sat, 5 Jun 2010 10:55:43 +0530

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



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Received on Fri Jun 04 2010 - 22:30:03 PDT
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