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

From: Jason Swails <jason.swails.gmail.com>
Date: Tue, 15 Feb 2011 09:46:42 -0500

What error messages did you get in _MMPBSA_complex_pb.mdout,
_MMPBSA_receptor_pb.mdout, and/or _MMPBSA_ligand_pb.mdout? 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
Received on Tue Feb 15 2011 - 07:00:03 PST
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