Re: [AMBER] ظ MM-PBSA error about protein + Mg2+

From: Bill Miller III <brmilleriii.gmail.com>
Date: Sun, 30 Jan 2011 08:52:20 -0500

What does your MMPBSA.py input file look like? Remember, by default
MMPBSA.py strips out *all* ions in the original trajectory file unless you
specify otherwise (see the strip_mdcrd (or initial_traj, depending on the
version of MMPBSA.py you have) and strip_mask variables in the manual). It
looks like MMPBSA.py is automatically stripping out the Mg2+ ion, and thus
gets confused later when there are no atoms in the ligand trajectory file,
and the complex trajectory file has no ligand atoms. Obviously, you will not
want MMPBSA.py to remove this ion, so you will have to specifically set
strip_mdcrd and strip_mask in your input file to remove the default
settings.

Good luck!

-Bill

2011/1/30 475649770 <475649770.qq.com>

> Dear professors,
> Thanks very much for your reply. For convenience, I built a system
> including two amino acids and a MG2+ and then performed a short MD
> simulation. The protein and MG2+ were destined to the receptor and ligand,
> respectively. Then, I calculated MMPBSA using the 'MMPBSA.py' program and
> got the following errors:
> [tony.tony py_mmpbsa]$ MMPBSA.py -O -i mmpbsa.in -o MMPBSA_result.dat
> -sp ../com_solvated.prmtop -cp ../com.prmtop -rp ../rec.prmtop -lp
> ../lig.prmtop -y ../prod1.mdcrd
>
>
>
> ptraj found! Using /home/tony/program/amber11/exe/ptraj
>
>
>
> sander found! Using /home/tony/program/amber11/exe/sander (serial only!)
>
>
>
> Warning: igb=2 should be used with mbondi2 pbradii set. Yours are modified
> Bondi radii (mbondi)
>
> Preparing trajectories with ptraj...
>
>
>
> checkCoordinates(): Could not predict number of frames for AMBER trajectory
> file: _MMPBSA_complex.mdcrd
>
>
>
> If this is not a compressed file then there is a problem
>
>
>
> checkCoordinates(): Could not predict number of frames for AMBER trajectory
> file: _MMPBSA_complex.mdcrd
>
>
>
> If this is not a compressed file then there is a problem
>
>
>
> checkCoordinates(): Could not predict number of frames for AMBER trajectory
> file: _MMPBSA_complex.mdcrd
>
>
>
> If this is not a compressed file then there is a problem
>
>
>
> readAmberRestart(): topology/coordinates file are inconsist with
>
>
>
> NATOMS = -2 (1)
>
>
>
> Error! Ptraj failed. Check coordinate and topology files for the complex.
>
>
> NOTE: All files have been retained for debugging purposes. Type MMPBSA.py
> --clean to erase these files.
>
>
>
> I checked the file named "_MMPBSA_ptraj6.out" and found following
> informations:
>
> \-/ Residue labels:
>
>
>
>
> MG2
>
>
>
>
>
> PTRAJ: Processing input from file _MMPBSA_ligandinpcrd.in
>
>
>
>
>
> PTRAJ: trajin _MMPBSA_ligand.mdcrd 1 1 1
>
>
>
>
> Checking coordinates: _MMPBSA_ligand.mdcrd
>
>
>
> Could not process trajectory _MMPBSA_ligand.mdcrd
>
> I also run the mm_pbsa.pl using the input file similar to the MMPBSA
> tutorial but the script interrupted, the snapshot_lig.all file showed as
> flowing:
>
>
> MM
>
>
> GB
>
>
>
> PB
>
>
>
> MS
>
>
>
> PB_SURFTEN 0.0072
>
>
>
> PB_SURFOFF 0.00
>
>
>
> GB_SURFTEN 0.0072
>
>
>
> GB_SURFOFF 0.00
>
>
>
> 1
>
>
>
> BOND = 0.0000 ANGLE = 0.0000 DIHED =
> 0.0000
>
>
>
> VDWAALS = 0.0000 EEL = 0.0000 EGB =
> -465.1086
>
>
>
> 1-4 VDW = 0.0000 1-4 EEL = 0.0000 RESTRAINT =
> 0.0000
>
>
>
> corrected reaction field energy: -733.423395
>
>
>
> surface area = 83.647
>
>
>
> ECAVITY = 83.647
>
>
>
> EDISPER = 0.0000
>
>
>
> 2
>
>
>
> BOND = 0.0000 ANGLE = 0.0000 DIHED =
> 0.0000
>
>
>
> VDWAALS = 0.0000 EEL = 0.0000 EGB =
> -465.1086
>
>
>
> 1-4 VDW = 0.0000 1-4 EEL = 0.0000 RESTRAINT =
> 0.0000
>
>
>
> corrected reaction field energy: -733.423227
>
>
>
> surface area = 83.647
>
>
>
> ECAVITY = 83.647
>
>
>
> EDISPER = 0.0000
>
>
> and the snapshot_statistics.out file showed as flowing:
>
>
> # COMPLEX RECEPTOR LIGAND
>
>
>
> # ----------------------- -----------------------
> -----------------------
>
>
>
> # MEAN STD MEAN STD MEAN
> STD
>
>
>
> # ======================= =======================
> ======================
>
>
>
> ELE -137.41 163.23 0.00 0.00 -76.08
> 56.90
>
>
>
> VDW 50986.49 82978.20 0.00 0.00 50985.07
> 82979.48
>
>
>
> INT 280795.09 191390.71 0.00 0.00 280795.09
> 191390.71
>
>
>
> GAS 331644.18 249493.62 0.00 0.00 331704.08
> 249428.77
>
>
>
> PBSUR 6.77 2.50 0.60 0.00 6.64
> 2.38
>
>
>
> PBCAL -652.88 232.67 -437.21 0.00 -299.30
> 127.24
>
>
>
> PBSOL -646.11 230.94 -436.61 0.00 -292.66
> 125.52
>
>
>
> PBELE -790.29 77.59 -437.21 0.00 -375.38
> 77.39
>
>
>
> PBTOT 330998.07 249337.32 -436.61 0.00 331411.42
> 249344.52
>
>
>
> GBSUR 6.77 2.50 0.60 0.00 6.64
> 2.38
>
>
>
> GB -734.84 266.96 -465.11 0.00 -345.33
> 150.53
>
>
>
> GBSOL -728.07 265.16 -464.51 0.00 -338.69
> 148.65
>
>
>
> GBELE -872.25 113.65 -465.11 0.00 -421.41
> 104.22
>
>
>
> GBTOT 330916.11 249304.55 -464.51 0.00 331365.39
> 249317.52
>
>
>
>
>
> # DELTA
>
>
>
>
>
> # -----------------------
>
>
>
> # MEAN STD
>
>
>
> # =======================
>
>
>
> ELE -61.33 118.71
>
>
>
> VDW 1.42 3.26
>
>
>
> INT 0.00 0.00
>
>
>
> GAS -59.90 115.91
>
>
>
> PBSUR -0.47 0.14
>
>
>
> PBCAL 83.64 115.53
>
>
>
> PBSOL 83.17 115.47
>
>
>
> PBELE 22.31 8.87
>
>
>
> PBTOT 23.26 9.42
>
>
>
> GBSUR -0.47 0.14
>
>
>
> GB 75.60 124.91
>
>
>
> GBSOL 75.13 124.86
>
>
>
> GBELE 14.27 10.33
>
>
>
> GBTOT 15.23 13.23
>
>
> thank you very much!
>
> ------------------ ԭʼʼ ------------------
> : "Jason Swails"<jason.swails.gmail.com>;
> ʱ: 2011128() 9:55
> ռ: "AMBER Mailing List"<amber.ambermd.org>;
>
> : Re: [AMBER] MM-PBSA error about protein + Mg2+
>
>
> http://archive.ambermd.org/201101/0449.html
>
> On Fri, Jan 28, 2011 at 2:47 AM, Ф <xzt41.126.com> wrote:
>
> > Dear amber professors,
> > I am doing the free energy calculation between the protein and Mg2+
> > using MM-PBSA with Amber10(both mm_pbsa.pl and MMPBSA.py),
> > but many trials failed, when i check the temporary files, the following
> > results were found in the "snapshot_lig.all.out":
> > MM
> > GB
> > PB
> > MS
> > 1
> > BOND = 0.0000 ANGLE = 0.0000 DIHED =
> > 0.0000
> > VDWAALS = 0.0000 EEL = 0.0000 EGB =
> > -465.1086
> > 1-4 VDW = 0.0000 1-4 EEL = 0.0000 RESTRAINT =
> > 0.0000
> > corrected reaction field energy: -733.413162
> > surface area = 83.647
> > ECAVITY = 83.647
> > EDISPER = 0.0000
> >
> >
> >
> >
> > I am confused with this, then i calculated the MM-PBSA energy of protein
> > and the Na+, the same results was produced. Little information about this
> > can be found by google, so i hope you can help me and give me some
> advices.
> > thank you and best wishes to you!!
> >
> >
> > Xiao Zhengtao ,
> >
> > Department of bioinformatics in Northwest
> Sci-Tech
> > University of Agriculture and Forestry
> >
> >
> >
> >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
>
> --
> Jason M. Swails
> Quantum Theory Project,
> University of Florida
> Ph.D. Graduate Student
> 352-392-4032
> _______________________________________________
> AMBER mailing list
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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 Jan 30 2011 - 06:00:04 PST
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