Dear professors:
I constructed a system consisted with a amino acids and Mg2+ and then performed MD simulation and energy calculation for the testing, and the MMPBSA.py run normally. But the result is same as before:
| Run on Tue Feb 15 23:11:09 CST 2011
|Input file:
|--------------------------------------------------------------
|Input file for running PB and GB in serial
|&general
| keep_files=2,
|/
|&gb
| igb=2, saltcon=0.100,
|/
|&pb
| istrng=0.100,
|/
|--------------------------------------------------------------
|Complex topology file: ../com.prmtop
|Receptor topology file: ../rec.prmtop
|Ligand topology file: ../lig.prmtop
|Initial mdcrd(s): ../pr.mdcrd
|
|Best guess for receptor mask: ":1"
|Best guess for ligand mask: ":2"
|Ligand residue name is "MG2"
|
|Calculations performed using 20 frames.
|Poisson Boltzmann calculations performed using internal PBSA solver in sander.
|
|All units are reported in kcal/mole.
-------------------------------------------------------------------------------
-------------------------------------------------------------------------------
GENERALIZED BORN:
Complex:
Energy Component Average Std. Dev. Std. Err. of Mean
-------------------------------------------------------------------------------
VDWAALS 11.7436 3.3066 0.7394
EEL -440.8740 8.7575 1.9582
EGB -210.2815 4.1016 0.9171
ESURF 1.8272 0.0124 0.0028
G gas -429.1304 9.3610 2.0932
G solv -208.4543 4.1016 0.9171
TOTAL -637.5847 2.0415 0.4565
Receptor:
Energy Component Average Std. Dev. Std. Err. of Mean
-------------------------------------------------------------------------------
VDWAALS -0.1891 0.0793 0.0177
EEL -68.8525 5.2618 1.1766
EGB -92.7749 2.4576 0.5495
ESURF 1.7446 0.0121 0.0027
G gas -69.0416 5.2624 1.1767
G solv -91.0303 2.4577 0.5496
TOTAL -160.0719 3.2939 0.7365
Ligand:
Energy Component Average Std. Dev. Std. Err. of Mean
-------------------------------------------------------------------------------
VDWAALS 0.0000 0.0000 0.0000
EEL 0.0000 0.0000 0.0000
EGB -465.5912 0.0000 0.0000
ESURF 0.0000 0.0000 0.0000
G gas 0.0000 0.0000 0.0000
G solv -465.5912 0.0000 0.0000
TOTAL -465.5912 0.0000 0.0000
Differences (Complex - Receptor - Ligand):
Energy Component Average Std. Dev. Std. Err. of Mean
-------------------------------------------------------------------------------
VDWAALS 11.9327 3.2727 0.7318
EEL -372.0216 9.4748 2.1186
EGB 348.0846 5.5626 1.2438
ESURF 0.0827 0.0034 0.0008
DELTA G gas -360.0889 10.0241 2.2415
DELTA G solv 348.1673 5.5626 1.2438
DELTA G binding = -11.9216 +/- 2.0066 0.4487
-------------------------------------------------------------------------------
-------------------------------------------------------------------------------
POISSON BOLTZMANN:
Complex:
Energy Component Average Std. Dev. Std. Err. of Mean
-------------------------------------------------------------------------------
VDWAALS 11.7436 3.3066 0.7394
EEL -440.8740 8.7575 1.9582
EPB -196.5595 3.2913 0.7360
ECAVITY 0.4399 0.0123 0.0028
G gas -429.1304 9.3610 2.0932
G solv -196.1196 3.2914 0.7360
TOTAL -625.2500 1.8921 0.4231
Receptor:
Energy Component Average Std. Dev. Std. Err. of Mean
-------------------------------------------------------------------------------
VDWAALS -0.1891 0.0793 0.0177
EEL -68.8525 5.2618 1.1766
EPB -88.6789 2.3973 0.5361
ECAVITY 0.3362 0.0113 0.0025
G gas -69.0416 5.2624 1.1767
G solv -88.3427 2.3973 0.5361
TOTAL -157.3843 3.2472 0.7261
Ligand:
Energy Component Average Std. Dev. Std. Err. of Mean
-------------------------------------------------------------------------------
VDWAALS 0.0000 0.0000 0.0000
EEL 0.0000 0.0000 0.0000
EPB -437.2127 0.0003 0.0001
ECAVITY -0.4352 0.0000 0.0000
G gas 0.0000 0.0000 0.0000
G solv -437.6479 0.0003 0.0001
TOTAL -437.6479 0.0003 0.0001
Differences (Complex - Receptor - Ligand):
Energy Component Average Std. Dev. Std. Err. of Mean
-------------------------------------------------------------------------------
VDWAALS 11.9327 3.2727 0.7318
EEL -372.0216 9.4748 2.1186
EPB 329.3321 4.9434 1.1054
ECAVITY 0.5389 0.0042 0.0009
DELTA G gas -360.0889 10.0241 2.2415
DELTA G solv 329.8710 4.9434 1.1054
DELTA G binding = -30.2178 +/- 2.6240 0.5867
-------------------------------------------------------------------------------
-------------------------------------------------------------------------------
WARNINGS:
igb=2 should be used with mbondi2 pbradii set. Yours are modified Bondi radii (mbondi)
the ElE and VDW was also zero, and i checked out the other _MMPBSA_complex_pb.mdout file, not error was found.
thank you !Please tell me how can i do? This system just contain a residue and a MG2+, why is the ELE and VDW energy equal to zero. The _MMPBSA_complex_pb.mdout, _MMPBSA_receptor_pb.mdout, and _MMPBSA_ligand_pb.mdout are attached to the mail.
Thank you for your kind help!
------------------ 原始邮件 ------------------
发件人: "Jason Swails"<jason.swails.gmail.com>;
发送时间: 2011年2月16日(星期三) 上午9:47
收件人: "AMBER Mailing List"<amber.ambermd.org>;
主题: Re: [AMBER]回复： 回复： 回复： 回复： 回复： 回复： MM-PBSA error about protein + Mg2+
The complex and receptor PB simulations are ending before any frames are
calculated. I'm guessing that we're missing an error message somewhere.
660 residues is a large protein, so you may be running out of memory, or the
pairlist may be overflowing; I'm not sure.
MMPBSA.py should create input files (_MMPBSA_pb.mdin) that you can try
running sander with by hand to see if you can narrow down on what the error
may be.
Alternatively, you can use sander.APBS as the PB solver and see if that
works. (Google iAPBS and APBS for instructions on installing it)
Good luck!
Jason
2011/2/15 475649770 <475649770.qq.com>
> Dear professors:
> The _MMPBSA_complex_pb.mdout, _MMPBSA_receptor_pb.mdout,
> and_MMPBSA_ligand_pb.mdout are attached to the mail. The MMPBSA.py had
> stripped out the unnecessary molecular correctly, this can be see from the
> result file as following:
> > > |--------------------------------------------------------------
> > > |Complex topology file: ../com.prmtop
> > > |Receptor topology file: ../rec.prmtop
> > > |Ligand topology file: ../lig.prmtop
> > > |Initial mdcrd(s): ../pr1.mdcrd
> > > |
> > > |Best guess for receptor mask: ":1-660"
> > > |Best guess for ligand mask: ":661"
> > > |Ligand residue name is "MG2"
> > > |
> Thank you!
>
> ------------------ 原始邮件 ------------------
> 发件人: "Jason Swails"<jason.swails.gmail.com>;
> 发送时间: 2011年2月15日(星期二) 晚上10:46
> 收件人: "AMBER Mailing List"<amber.ambermd.org>;
>
> 主题: Re: [AMBER]回复： 回复： 回复： 回复： 回复： MM-PBSA error about protein + Mg2+
>
>
> What error messages did you get in That's where the
> error is occurring, but I don't see it printed anywhere.
>
> All the best,
> Jason
>
> 2011/2/15 Bill Miller III <brmilleriii.gmail.com>
>
> > By default, MMPBSA.py strips out all ions from the original trajectory.
> You
> > will need to change this by setting strip_mdcrd=0 in the &gen section of
> > your MMPBSA.py input file, and setting strip_mask to strip only the
> > molecules you do not want analyzed (like the water molecules and any
> other
> > ions that are not being analyzed). See the manual for more details about
> > using these variables.
> >
> > Good luck!
> >
> > -Bill
> >
> > 2011/2/15 475649770 <475649770.qq.com>
> >
> > > Dear professor,
> > > Please forgive my dumb questions. I performed MMPBSA energy between
> > > protein and mg2+ carefully again using the MMPBSA.py. Following you
> kind
> > > assistance, I know that the errors occurred because the script ignored
> > the
> > > ions by default. Then I solved this problem, and the calculation
> > completed
> > > with the following informations:
> > > ptraj found! Using /home/tony/program/amber11/exe/ptraj
> > > sander found! Using /home/tony/program/amber11/exe/sander
> > > Warning: igb=2 should be used with mbondi2 pbradii set. Yours are
> > modified
> > > Bondi radii (mbondi)
> > >
> > >
> > > Preparing trajectories with ptraj...
> > > 100 frames were read in and processed by ptraj for use in calculation.
> > >
> > >
> > > Starting calculations...
> > >
> > >
> > > Starting gb calculation...
> > >
> > >
> > > calculating ligand contribution...
> > > calculating receptor contribution...
> > > calculating complex contribution...
> > > Starting pb calculation...
> > >
> > >
> > > calculating ligand contribution...
> > > calculating receptor contribution...
> > > calculating complex contribution...
> > >
> > >
> > > Calculations complete. Writing output file(s)...
> > >
> > >
> > > 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.
> > >
> > >
> > >
> > > then, I checked the final result and found that the ELE and VDW items
> of
> > > the Mg2+ is zero,this is similar with the result calculated by
> > > mm_pbsa.pl. The result show as following:
> > > | Run on Wed Feb 16 03:30:02 CST 2011
> > >
> > >
> > > |Input file:
> > > |--------------------------------------------------------------
> > > |Input file for running PB and GB in serial
> > > |&general
> > > | keep_files=2,
> > > |/
> > > |&gb
> > > | igb=2, saltcon=0.100,
> > > |/
> > > |&pb
> > > | istrng=0.100
> > > |/
> > > |--------------------------------------------------------------
> > > |Complex topology file: ../com.prmtop
> > > |Receptor topology file: ../rec.prmtop
> > > |Ligand topology file: ../lig.prmtop
> > > |Initial mdcrd(s): ../pr1.mdcrd
> > > |
> > > |Best guess for receptor mask: ":1-660"
> > > |Best guess for ligand mask: ":661"
> > > |Ligand residue name is "MG2"
> > > |
> > > |Calculations performed using 100 frames.
> > > |Poisson Boltzmann calculations performed using internal PBSA solver in
> > > sander.
> > > |
> > > |All units are reported in kcal/mole.
> > >
> > >
> >
> -------------------------------------------------------------------------------
> > >
> > >
> >
> -------------------------------------------------------------------------------
> > >
> > >
> > > GENERALIZED BORN:
> > >
> > >
> > > Complex:
> > > Energy Component Average Std. Dev. Std. Err.
> of
> > > Mean
> > >
> > >
> >
> -------------------------------------------------------------------------------
> > > VDWAALS -5066.5497 39.0700
> > > 3.9070
> > > EEL -38199.9862 129.9569
> > > 12.9957
> > > EGB -10892.8975 106.7352
> > > 10.6735
> > > ESURF 245.3985 1.9876
> > > 0.1988
> > >
> > >
> > > G gas -43266.5359 135.7028
> > > 13.5703
> > > G solv -10647.4990 106.7537
> > > 10.6754
> > >
> > >
> > > TOTAL -53914.0349 71.2116
> > > 7.1212
> > >
> > >
> > >
> > >
> > > Receptor:
> > > Energy Component Average Std. Dev. Std. Err.
> of
> > > Mean
> > >
> > >
> >
> -------------------------------------------------------------------------------
> > > VDWAALS -5084.1567 38.7262
> > > 3.8726
> > > EEL -38131.5460 132.2277
> > > 13.2228
> > > EGB -10447.8583 109.4798
> > > 10.9480
> > > ESURF 245.4045 1.9876
> > > 0.1988
> > >
> > >
> > > G gas -43215.7027 137.7820
> > > 13.7782
> > > G solv -10202.4538 109.4978
> > > 10.9498
> > >
> > >
> > > TOTAL -53418.1565 70.7727
> > > 7.0773
> > >
> > >
> > >
> > >
> > > Ligand:
> > > Energy Component Average Std. Dev. Std. Err.
> of
> > > Mean
> > >
> > >
> >
> -------------------------------------------------------------------------------
> > > VDWAALS 0.0000 0.0000
> > > 0.0000
> > > EEL 0.0000 0.0000
> > > 0.0000
> > > EGB -465.5912 0.0000
> > > 0.0000
> > > ESURF 0.0000 0.0000
> > > 0.0000
> > >
> > >
> > > G gas 0.0000 0.0000
> > > 0.0000
> > > G solv -465.5912 0.0000
> > > 0.0000
> > >
> > >
> > > TOTAL -465.5912 0.0000
> > > 0.0000
> > >
> > >
> > >
> > >
> > > Differences (Complex - Receptor - Ligand):
> > > Energy Component Average Std. Dev. Std. Err.
> of
> > > Mean
> > >
> > >
> >
> -------------------------------------------------------------------------------
> > > VDWAALS 17.6070 3.5130
> > > 0.3513
> > > EEL -68.4402 24.6592
> > > 2.4659
> > > EGB 20.5520 22.3935
> > > 2.2394
> > > ESURF -0.0060 0.0048
> > > 0.0005
> > >
> > >
> > > DELTA G gas -50.8333 24.9082
> > > 2.4908
> > > DELTA G solv 20.5460 22.3935
> > > 2.2394
> > >
> > >
> > >
> > >
> > > DELTA G binding = -30.2873 +/- 4.5113
> > > 0.4511
> > >
> > >
> >
> -------------------------------------------------------------------------------
> > >
> > >
> >
> -------------------------------------------------------------------------------
> > >
> > >
> > > I also provided the complex pdb file(See attached).
> > > Will you please tell me how to solve this problem? I
> > > just built a complex system consisted with a amino acids and Mg2+ using
> > the
> > > leaprc.ff99SB forcefield as an test example to performed the
> calculation.
> > > The result is also similar.
> > >
> > >
> > >
> > > ------------------ 原始邮件 ------------------
> > > 发件人: "Jason Swails"<jason.swails.gmail.com>;
> > > 发送时间: 2011年2月1日(星期二) 晚上10:44t
> > > 收件人: "AMBER Mailing List"<amber.ambermd.org>;
> > >
> > > 主题: Re: [AMBER]回复： 回复： 回复： 回复： MM-PBSA error about protein + Mg2+
> > >
> > >
> > > 2011/2/1 475649770 <475649770.qq.com>
> > >
> > > > Dear professor,
> > > > Thank you for your kind help. I updated MMPBSA.py following your
> > > > suggestions, and changed initial_traj to strip_mdcrd. Then i
> performed
> > > > calculation again, the error is still occurred when ptraj program
> > > processed
> > > > the _MMPBSA_ligandinpcrd.in. I carried out this process by hand:
> first
> > i
> > > > produced the ligand.mdcrd using the ptraj program, this file is the
> > > > trajectory of the mg2+. Next, i processed the ligand.mdcrd using the
> > > ptraj
> > > > and using the following input option similar to the the
> > > > "_MMPBSA_ligandinpcrd.in" file,
> > > >
> > > >
> > > > trajin _MMPBSA_ligand.mdcrd 1 1 1
> > > > trajout _MMPBSA_dummyligand.inpcrd restart
> > > >
> > > >
> > > > but error occurred similar to before. The error information are as
> > > > following:
> > > >
> > > >
> > > > PTRAJ: Processing input from file _MMPBSA_ligandinpcrd.in
> > > >
> > > >
> > > > PTRAJ: trajin _MMPBSA_ligand.mdcrd 1 1 1
> > > > Checking coordinates: _MMPBSA_ligand.mdcrd
> > > > readAmberRestart(): topology/coordinates file are inconsist with
> > > > NATOMS = 0 (1)
> > > > Could not process trajectory _MMPBSA_ligand.mdcrd
> > > > PTRAJ: trajout _MMPBSA_dummyligand.inpcrd restart
> > > > WARNING in ptraj(): No input trajectories specified (trajin),
> > aborting...
> > > >
> > > >
> > > >
> > > > It seem to that ptraj can not process the ligand.mdcrd which only has
> > one
> > > > ion. The trajectory of the complex is correct when i check it using
> the
> > > VMD
> > > > program. I hope i state the problem clearly.
> > > > Thanks again for your kind help.
> > > >
> > >
> > > Check the trajectory of the ligand and the receptor as well. What do
> you
> > > see?
> > >
> > > All the best,
> > > Jason
> > >
> > >
> > > >
> > > > ------------------ 原始邮件 ------------------
> > > > 发件人: "Jason Swails"<jason.swails.gmail.com>;
> > > > 发送时间: 2011年1月31日(星期一) 晚上10:39
> > > > 收件人: "AMBER Mailing List"<amber.ambermd.org>;
> > > >
> > > > 主题: Re: [AMBER]回复： 回复： 回复： MM-PBSA error about protein + Mg2+
> > > >
> > > >
> > > > Is initial_traj still an input option? That was changed to
> > strip_mdcrd
> > > in
> > > > the current version available at
> > > > http://ambermd.org/tutorials/advanced/tutorial3/py_script. I'm
> > guessing
> > > > you
> > > > haven't updated since otherwise the error you would be getting would
> be
> > > > related to initial_traj not being a valid input, rather than the
> error
> > > > you're actually getting.
> > > >
> > > > As for your error: do you only have 1 ion in your entire topology
> file?
> > > It
> > > > seems as though you're keeping only the 1 ion in the topology files,
> > but
> > > > you're not stripping any according to your value of strip_mask. You
> > may
> > > > have to preprocess the trajectory in order to get it the way you want
> > > (i.e.
> > > > go through by hand and strip the residues that you want stripped).
> > > >
> > > > Hope this helps,
> > > > Jason
> > > >
> > > > 2011/1/31 475649770 <475649770.qq.com>
> > > >
> > > > > Dear professor,
> > > > > Thank you for your kind assistance. Your suggestion is very
> > > important
> > > > > for me. I modified my input file again. I seted initial_traj=0, and
> > > > > specified strip_mask as ":WAT". The input file is as following:
> > > > > Input file for running PB and GB in serial
> > > > > &general
> > > > > endframe=10,
> > > > > initial_traj=0,
> > > > > strip_mask=":WAT",
> > > > > keep_files=2,
> > > > >
> > > > >
> > > > > /
> > > > > &gb
> > > > > igb=2, saltcon=0.100,
> > > > > /
> > > > > &pb
> > > > > istrng=0.100
> > > > > /
> > > > >
> > > > > but error is still there:
> > > > > Preparing trajectories with ptraj...
> > > > > readAmberRestart(): topology/coordinates file are inconsist with
> > > > > NATOMS = 18 (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.
> > > > > this system is only composed with a protein, a MG2+ and TIP3P
> > waters.
> > > > the
> > > > > perl script "mm_pabs.pl" is also performed but error occurred. The
> > > > > snapshot_lig.all.out file is strange, all but except the EGB is
> > zero:
> > > > > 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
> > > > >
> > > > >
> > > > > Thank you for your kind help.
> > > > >
> > > > > ------------------ 原始邮件 ------------------
> > > > > 发件人: "Bill Miller III"<brmilleriii.gmail.com>;
> > > > > 发送时间: 2011年1月31日(星期一) 晚上7:46
> > > > > 收件人: "AMBER Mailing List"<amber.ambermd.org>;
> > > > >
> > > > > 主题: Re: [AMBER]回复： 回复： MM-PBSA error about protein + Mg2+
> > > > >
> > > > >
> > > > > Was your system ran in implicit or explicit solvent? Because if
> you
> > > ran
> > > > it
> > > > > in explicit solvent, then the water molecules were never stripped
> out
> > > of
> > > > > the
> > > > > original simulation, which would cause a topology/trajectory
> mismatch
> > > > > during
> > > > > the actual MM-GBSA calculations.
> > > > >
> > > > > -Bill
> > > > >
> > > > > 2011/1/31 475649770 <475649770.qq.com>
> > > > >
> > > > > > Dear professors,
> > > > > > Thanks very much for your suggestion. I modified my MMPBSA.py
> > > input
> > > > > > file as:
> > > > > > Input file for running PB and GB in serial
> > > > > > &general
> > > > > > endframe=10,
> > > > > > initial_traj=1,
> > > > > > keep_files=2,
> > > > > > /
> > > > > > &gb
> > > > > > igb=2, saltcon=0.100,
> > > > > > /
> > > > > > &pb
> > > > > > istrng=0.100
> > > > > > /
> > > > > > but when i performed calculations angain, the flowing errors
> > > appeared:
> > > > > >
> > > > > > Preparing trajectories with ptraj...
> > > > > > checkCoordinates(): Could not predict number of frames for AMBER
> > > > > trajectory
> > > > > > file: ../pr1.mdcrd
> > > > > > If this is not a compressed file then there is a problem
> > > > > > readAmberRestart(): topology/coordinates file are inconsist with
> > > > > > NATOMS = 73 (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.
> > > > > >
> > > > > > and this time, the "_MMPBSA_ptraj6.out" file are showed as:
> > > > > > \-/ 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
> > > > > >
> > > > > >
> > > > > > PTRAJ: trajout _MMPBSA_dummyligand.inpcrd restart
> > > > > > WARNING in ptraj(): No input trajectories specified (trajin),
> > > > aborting...
> > > > > >
> > > > > > I checked the temp files, but no other errors were found. Thank
> > you
> > > > for
> > > > > > your help.
> > > > > >
> > > > > >
> > > > > > ------------------ 原始邮件 ------------------
> > > > > > 发件人: "Bill Miller III"<brmilleriii.gmail.com>;
> > > > > > 发送时间: 2011年1月30日(星期天) 晚上9:52
> > > > > > 收件人: "AMBER Mailing List"<amber.ambermd.org>;
> > > > > >
> > > > > > 主题: Re: [AMBER]回复： MM-PBSA error about protein + Mg2+
> > > > > >
> > > > > >
> > > > > > 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!
> > > > > > >
> > > > > > > ------------------ 原始邮件 ------------------
> > > > > > > 发件人: "Jason Swails"<jason.swails.gmail.com>;
> > > > > > > 发送时间: 2011年1月28日(星期五) 晚上9:55
> > > > > > > 收件人: "AMBER Mailing List"<amber.ambermd.org>;
> > > > > > >
> > > > > > > 主题: Re: [AMBER] MM-PBSA error about protein + Mg2+
> > > > > > >
> > > > > > >
> > > > > > > http://archive.ambermd.org/201101/0449.html
> > > > > > >
> > > > > > > On Fri, Jan 28, 2011 at 2:47 AM, 肖正涛 <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
> > > > > > > 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
> > > > > >
> > > > >
> > > > >
> > > > >
> > > > > --
> > > > > 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
> > > > >
> > > >
> > > >
> > > >
> > > > --
> > > > Jason M. Swails
> > > > Quantum Theory Project,
> > > > University of Florida
> > > > Ph.D. Graduate Student
> > > > 352-392-4032
> > > > _______________________________________________
> > > > 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
> > > >
> > >
> > >
> > >
> > > --
> > > Jason M. Swails
> > > Quantum Theory Project,
> > > University of Florida
> > > Ph.D. Graduate Student
> > > 352-392-4032
> > > _______________________________________________
> > > 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
> >
>
>
>
> --
> Jason M. Swails
> Quantum Theory Project,
> University of Florida
> Ph.D. Candidate
> 352-392-4032
> _______________________________________________
> 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
>
>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
_______________________________________________
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http://lists.ambermd.org/mailman/listinfo/amber
Received on Wed Feb 16 2011 - 01:00:02 PST
