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
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> http://lists.ambermd.org/mailman/listinfo/amber
> _______________________________________________
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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
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Received on Sun Jul 17 2011 - 11:00:02 PDT
