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

From: 475649770 <475649770.qq.com>
Date: Tue, 1 Feb 2011 14:29:30 +0800

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.

 
------------------ 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
_______________________________________________
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AMBER.ambermd.org
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Received on Mon Jan 31 2011 - 23:00:03 PST
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