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

From: 475649770 <475649770.qq.com>
Date: Sun, 30 Jan 2011 17:18:00 +0800

Dear professors,
     Thanks very much for your reply. For convenience, I built a system including two amino acids and a MG2+ and then performed a short MD simulation. The protein and MG2+ were destined to the receptor and ligand, respectively. Then, I calculated MMPBSA using the 'MMPBSA.py' program and got the following errors:
     [tony.tony py_mmpbsa]$ MMPBSA.py -O -i mmpbsa.in -o MMPBSA_result.dat -sp ../com_solvated.prmtop -cp ../com.prmtop -rp ../rec.prmtop -lp ../lig.prmtop -y ../prod1.mdcrd
 

 
ptraj found! Using /home/tony/program/amber11/exe/ptraj
 

 
sander found! Using /home/tony/program/amber11/exe/sander (serial only!)
 

 
Warning: igb=2 should be used with mbondi2 pbradii set. Yours are modified Bondi radii (mbondi)
 
Preparing trajectories with ptraj...
 

 
checkCoordinates(): Could not predict number of frames for AMBER trajectory file: _MMPBSA_complex.mdcrd
 

 
       If this is not a compressed file then there is a problem
 

 
checkCoordinates(): Could not predict number of frames for AMBER trajectory file: _MMPBSA_complex.mdcrd
 

 
       If this is not a compressed file then there is a problem
 

 
checkCoordinates(): Could not predict number of frames for AMBER trajectory file: _MMPBSA_complex.mdcrd
 

 
       If this is not a compressed file then there is a problem
 

 
readAmberRestart(): topology/coordinates file are inconsist with
 

 
NATOMS = -2 (1)
 

 
Error! Ptraj failed. Check coordinate and topology files for the complex.
 

 NOTE: All files have been retained for debugging purposes. Type MMPBSA.py --clean to erase these files.



I checked the file named "_MMPBSA_ptraj6.out" and found following informations:

  \-/ Residue labels:
 

 
 
MG2

 

 
 
PTRAJ: Processing input from file _MMPBSA_ligandinpcrd.in

 

 
 
PTRAJ: trajin _MMPBSA_ligand.mdcrd 1 1 1

 

 
  Checking coordinates: _MMPBSA_ligand.mdcrd
 

 
       Could not process trajectory _MMPBSA_ligand.mdcrd

I also run the mm_pbsa.pl using the input file similar to the MMPBSA tutorial but the script interrupted, the snapshot_lig.all file showed as flowing:


MM
 
 
GB

 
 
PB

 
 
MS

 
 
PB_SURFTEN 0.0072

 
 
PB_SURFOFF 0.00

 
 
GB_SURFTEN 0.0072

 
 
GB_SURFOFF 0.00

 
 
1

 
 
 BOND = 0.0000 ANGLE = 0.0000 DIHED = 0.0000

 
 
 VDWAALS = 0.0000 EEL = 0.0000 EGB = -465.1086

 
 
 1-4 VDW = 0.0000 1-4 EEL = 0.0000 RESTRAINT = 0.0000

 
 
corrected reaction field energy: -733.423395

 
 
surface area = 83.647

 
 
ECAVITY = 83.647

 
 
EDISPER = 0.0000

 
 
2

 
 
 BOND = 0.0000 ANGLE = 0.0000 DIHED = 0.0000

 
 
 VDWAALS = 0.0000 EEL = 0.0000 EGB = -465.1086

 
 
 1-4 VDW = 0.0000 1-4 EEL = 0.0000 RESTRAINT = 0.0000

 
 
corrected reaction field energy: -733.423227

 
 
surface area = 83.647

 
 
ECAVITY = 83.647

 
 
EDISPER = 0.0000


and the snapshot_statistics.out file showed as flowing:
 
 
# COMPLEX RECEPTOR LIGAND

 
 
# ----------------------- ----------------------- -----------------------

 
 
# MEAN STD MEAN STD MEAN STD

 
 
# ======================= ======================= ======================

 
 
ELE -137.41 163.23 0.00 0.00 -76.08 56.90

 
 
VDW 50986.49 82978.20 0.00 0.00 50985.07 82979.48

 
 
INT 280795.09 191390.71 0.00 0.00 280795.09 191390.71

 
 
GAS 331644.18 249493.62 0.00 0.00 331704.08 249428.77

 
 
PBSUR 6.77 2.50 0.60 0.00 6.64 2.38

 
 
PBCAL -652.88 232.67 -437.21 0.00 -299.30 127.24

 
 
PBSOL -646.11 230.94 -436.61 0.00 -292.66 125.52

 
 
PBELE -790.29 77.59 -437.21 0.00 -375.38 77.39

 
 
PBTOT 330998.07 249337.32 -436.61 0.00 331411.42 249344.52

 
 
GBSUR 6.77 2.50 0.60 0.00 6.64 2.38

 
 
GB -734.84 266.96 -465.11 0.00 -345.33 150.53

 
 
GBSOL -728.07 265.16 -464.51 0.00 -338.69 148.65

 
 
GBELE -872.25 113.65 -465.11 0.00 -421.41 104.22

 
 
GBTOT 330916.11 249304.55 -464.51 0.00 331365.39 249317.52

 
 
 

# DELTA



 
 
# -----------------------

 
 
# MEAN STD

 
 
# =======================

 
 
ELE -61.33 118.71

 
 
VDW 1.42 3.26

 
 
INT 0.00 0.00

 
 
GAS -59.90 115.91

 
 
PBSUR -0.47 0.14

 
 
PBCAL 83.64 115.53

 
 
PBSOL 83.17 115.47

 
 
PBELE 22.31 8.87

 
 
PBTOT 23.26 9.42

 
 
GBSUR -0.47 0.14

 
 
GB 75.60 124.91

 
 
GBSOL 75.13 124.86

 
 
GBELE 14.27 10.33

 
 
GBTOT 15.23 13.23

 
thank you very much!

 ------------------ ԭʼʼ ------------------
: "Jason Swails"<jason.swails.gmail.com>;
ʱ: 2011128() 9:55
ռ: "AMBER Mailing List"<amber.ambermd.org>;

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

 
 http://archive.ambermd.org/201101/0449.html

On Fri, Jan 28, 2011 at 2:47 AM, Ф <xzt41.126.com> wrote:

> Dear amber professors,
> I am doing the free energy calculation between the protein and Mg2+
> using MM-PBSA with Amber10(both mm_pbsa.pl and MMPBSA.py),
> but many trials failed, when i check the temporary files, the following
> results were found in the "snapshot_lig.all.out":
> MM
> GB
> PB
> MS
> 1
> BOND = 0.0000 ANGLE = 0.0000 DIHED =
> 0.0000
> VDWAALS = 0.0000 EEL = 0.0000 EGB =
> -465.1086
> 1-4 VDW = 0.0000 1-4 EEL = 0.0000 RESTRAINT =
> 0.0000
> corrected reaction field energy: -733.413162
> surface area = 83.647
> ECAVITY = 83.647
> EDISPER = 0.0000
>
>
>
>
> I am confused with this, then i calculated the MM-PBSA energy of protein
> and the Na+, the same results was produced. Little information about this
> can be found by google, so i hope you can help me and give me some advices.
> thank you and best wishes to you!!
>
>
> Xiao Zhengtao ,
>
> Department of bioinformatics in Northwest Sci-Tech
> University of Agriculture and Forestry
>
>
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>



--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-4032
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Received on Sun Jan 30 2011 - 01:30:03 PST
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