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

From: Jason Swails <jason.swails.gmail.com>
Date: Tue, 1 Feb 2011 09:44:35 -0500

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
_______________________________________________
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Received on Tue Feb 01 2011 - 07:00:03 PST
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