Did you strip the membrane residues out yourself before running MMPBSA.py?
-Bill
On Jul 17, 2011, at 1:48 PM, "徐见容" <gjtigergj.163.com> wrote:
> Yes, I just chose 2 frames, as I ran MMPBSA.py.MPI firstly and failed. So I tried to run a short one.
>
> the mmpbsa input files are quite simple:
> ######
> Input file for running PB and GB in serial
> &general
> endframe=1000, interval=500, keep_files=2,
> /
> &gb
> igb=2, saltcon=0.100,
> /
> &pb
> istrng=0.100,
> /
> ####################
>
> As to the residue numbers, the GPCR is :1-415, the ligand is :416, and the others are :WAT, :POP(POPC membrane) and :Cl- which have been striped.
>
> Thanks,
>
> Janker
>
>
> 2011-07-18
>
>
>
> 徐见容
>
>
>
> 发件人： Bill Miller III
> 发送时间： 2011-07-18 01:27:24
> 收件人： AMBER Mailing List
> 抄送：
> 主题： Re: [AMBER] MMPBSA calculation in complex with Membrane
>
> Are you attempting to run MMPBSA.py on only two frames? That is what
> MMPBSA.py is trying to do, so I just want to make sure that MMPBSA is
> reading that correctly. Could you also post your MMPBSA.py input file and
> exact residue numbers for the different fragments in your topology files?
> -Bill
> 2011/7/17 徐见容 <gjtigergj.163.com>
>> Thanks, Bill.
>>
>> I tried to skip GB calculation, however, the same error occurs in PB
>> calculation.
>> Actually, I checked the mdout files, finding that error occurs when
>> calculating receptor in "_MMPBSA_receptor_gb.mdout", and the process was
>> done well in "_MMPBSA_complex_gb.mdout" and other "*ptraj.out".
>>
>> In detail, information printed to screen is as following:
>> #######
>> Reading command-line arguments and input files...
>> Loading and checking parameter files for compatibility...
>> ptraj found! Using /home/Janker/Amber/amber11/bin/ptraj
>> mmpbsa_py_energy found! Using
>> /home/Janker/Amber/amber11/bin/mmpbsa_py_energy for GB calculations
>> mmpbsa_py_energy found! Using
>> /home/Janker/Amber/amber11/bin/mmpbsa_py_energy for PB calculations
>> Preparing trajectories for simulation...
>> 2 frames were read in and processed by ptraj for use in calculation.
>> Beginning GB calculations with mmpbsa_py_energy...
>> calculating complex contribution...
>> calculating receptor contribution...
>> Error: mmpbsa_py_energy error during GB calculations!
>> NOTE: All files have been retained for debugging purposes. Type MMPBSA.py
>> --clean to erase these files.
>> ##############
>>
>> And information in the uncompleted file "_MMPBSA_receptor_gb.mdout" is as
>> following:
>> #######
>> Reading parm file (M1_PBSA.top)
>> title:
>>
>> mm_options: e_debug=2
>> mm_options: gb=2
>> mm_options: rgbmax=25.000000
>> mm_options: gbsa=1
>> mm_options: surften=0.007200
>> mm_options: cut=999.000000
>> mm_options: epsext=78.300000
>> mm_options: kappa=0.103952
>> Processing ASCII trajectory (_MMPBSA_receptor.mdcrd)
>> Processing frame 1
>> iter Total bad vdW elect nonpolar genBorn
>> frms
>> eff.c(3678) enb14 --> 1527.627
>> eff.c(3679) eel14 --> 15752.779
>> eff.c(3737) enb --> -2115.367
>> eff.c(3738) eel --> -26181.477
>> eff.c(3739) e_gb --> -6160.734
>> eff.c(3740) esurf --> 194.520
>> eff.c(3741) evdwnp --> 0.000
>> ff: 0 -7871.35 9111.30 -587.74 -10428.70 194.52 -6160.73
>> 5.70e+01
>> #########################
>>
>> Do you have any other advice?
>>
>> Thanks,
>>
>> Janker
>>
>>
>> 2011-07-18
>>
>>
>>
>> 徐见容
>>
>>
>>
>> 发件人： Bill Miller III
>> 发送时间： 2011-07-18 00:47:26
>> 收件人： AMBER Mailing List
>> 抄送：
>> 主题： Re: [AMBER] MMPBSA calculation in complex with Membrane
>>
>> Does the calculation fail immediately, or does the GB calculation actually
>> progress before dying? You can check the _MMPBSA*mdout files to see if an
>> error is written to those files. Was there any error or warning messages
>> written to the screen when you were running the calculation? You almost
>> might want to look though the _MMPBSA*ptraj*out files to see if ptraj was
>> able to correctly read in your trajectory using the provided topology
>> files.
>> -Bill
>> 2011/7/17 徐见容 <gjtigergj.163.com>
>>> Dear all,
>>>
>>> I built a complex of GPCR and a small molecule ligand (X), then inserted
>>> them into a POPC membrane. After 20ns' MD, I tried to use MMPBSA.py to
>>> calculate the delta binding energy. Topology files are
>>> complex+Membrane+solvated, complex, GPCR and ligand (X). The topology
>> files
>>> are generated from complex+Membrane+solvated by ante-MMPBSA.py, or by the
>>> pdb files before inserting complex into membrane.
>>>
>>> However, the calculation failed. The error occurs during GB calculations,
>>> for mmpbsa_py_energy or sander. There's no more debuging information even
>> in
>>> the temporary files.
>>>
>>> So, is there someone who met this error before? Or, can someone provide a
>>> way to calculation binding energy in membrane system?
>>>
>>> Thanks a lot.
>>>
>>> Janker
>>>
>>> 2011-07-18
>>>
>>>
>>>
>>> Jian-Rong Xu (徐见容), PhD Student.
>>> Room 508, Building 3, Pharmacology Department
>>> Shanghai Jiao Tong University School of Medicine
>>> 280 South Chongqing Road
>>> Luwan District,Shanghai, P.R.China 200025
>>>
>>> Mobile: +86 186 2168 6069
>>> Email: janker.xu.gmail.com
>>> _______________________________________________
>>> 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
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>> 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
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
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Received on Sun Jul 17 2011 - 12:30:03 PDT
