Great, Bill.
Your suggestion works well. Thanks a lot.
So, the problem is POP residues cannot be dealt with in MMPBSA calculation.
I read the manual which says strip_mask (DEFAULT=":WAT:Cl-:CIO:Cs+:IB:K+:Li+:MG2:Na+:Rb+"). Then, I want to know, why these residues should be stripped from the mdcrd files.
Thanks,
Janker
2011-07-18
徐见容
发件人： Bill Miller III
发送时间： 2011-07-18 05:30:52
收件人： AMBER Mailing List
抄送：
主题： Re: [AMBER] MMPBSA calculation in complex with Membrane
That would definitely affect the validity of the calculation and would most
likely cause the calculation to end prematurely, which was the case with
your calculation. The problem is that the coordinates for the membrane were
never removed from that original mdcrd file, and thus they were improperly
included in the MMGBSA calculation. You do not necessarily need to strip
them before using MMPBSA.py, but I would advise you to define the strip_mask
variable in the &general section to include stripping out the membrane
residues in addition to the WAT and Cl- residues. So you should have a
strip_mask variable in your MMPBSA.py input file that looks something like:
strip_mask=:WAT:Cl-:POP
I hope that helps.
-Bill
2011/7/17 徐见容 <gjtigergj.163.com>
> Do you mean that the membrane residues should be striped from *.mdcrd
> files?
>
> Now, I did no further modification of the *.mdcrd files. And, the membrane
> residues exist in topology file of the solvated complex.
>
> If the membrane residues are striped from *.mdcrd files, there would be a
> large gap between complex and WAT, and does it affect the calculation of
> MMPBSA?
>
> Thanks,
>
> Janker
>
>
> 2011-07-18
>
>
>
> 徐见容
>
>
>
> 发件人： Bill Miller III
> 发送时间： 2011-07-18 03:07:10
> 收件人： AMBER Mailing List
> 抄送：
> 主题： Re: [AMBER] MMPBSA calculation in complex with Membrane
>
> 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
> >> _______________________________________________
> >> 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
> >>
> > --
> > 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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>
--
Bill Miller III
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-6715
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Received on Sun Jul 17 2011 - 17:00:02 PDT
