Hello!
I am working on a simulation of a GPCR in membrane. My topology files
were generated by CHAMBER as I am using CHARMM force field.
Using MMPBSA.py, it failed at PB calculation stage. Following is the
error messages and _MMPBSA_complex_pb.mdout file is attached.
Thanks a lot.
Regards,
Zhi
******************************
Reading command-line arguments and input files...
Loading and checking parameter files for compatibility...
ptraj found! Using /home/zw258/code/AMBER/amber11/bin/ptraj
sander found! Using /home/zw258/code/AMBER/amber11/bin/sander for GB
calculations
sander found! Using /home/zw258/code/AMBER/amber11/bin/sander for PB
calculations
Preparing trajectories for simulation...
1000 frames were read in and processed by ptraj for use in calculation.
Beginning GB calculations with sander...
calculating complex contribution...
calculating receptor contribution...
calculating ligand contribution...
Beginning PB calculations with sander...
calculating complex contribution...
Error: sander error during PB calculations!
NOTE: All files have been retained for debugging purposes. Type
MMPBSA.py --clean to erase these files.
***********************************
-------------------------------------------------------
Amber 11 SANDER 2010
-------------------------------------------------------
| Run on 07/18/2011 at 21:32:26
[-O]verwriting output
File Assignments:
| MDIN: _MMPBSA_pb.mdin
| MDOUT: _MMPBSA_complex_pb.mdout
|INPCRD: _MMPBSA_dummycomplex.inpcrd.1
| PARM: complex_vmd.prmtop
|RESTRT: _MMPBSA_.restrt
| REFC: refc
| MDVEL: mdvel
| MDEN: mden
| MDCRD: mdcrd
|MDINFO: mdinfo
| MTMD: mtmd
|INPDIP: inpdip
|RSTDIP: rstdip
|INPTRA: _MMPBSA_complex.mdcrd
|
Here is the input file:
File generated by MMPBSA.py
&cntrl
nsnb=99999, ipb=1, ntb=0, cut=999.0,
imin=5, igb=10,
/
&pb
istrng=100.0, sprob=1.4, maxitn=1000,
fillratio=4.0, radiopt=0, dbfopt=1,
cavity_surften=0.00542,
/
--------------------------------------------------------------------------------
1. RESOURCE USE:
--------------------------------------------------------------------------------
| Flags:
PB Info in pb_read(): npopt has been overwritten with inp
| New format PARM file being parsed.
| Version = 1.000 Date = 06/11/03 Time = 12:02:08
NATOM = 5068 NTYPES = 36 NBONH = 2545 MBONA = 2596
NTHETH = 5722 MTHETA = 3538 NPHIH = 9541 MPHIA = 4639
NHPARM = 0 NPARM = 0 NNB = 28000 NRES = 314
NBONA = 2596 NTHETA = 3538 NPHIA = 4639 NUMBND = 72
NUMANG = 163 NPTRA = 302 NATYP = 36 NPHB = 0
IFBOX = 1 NMXRS = 24 IFCAP = 0 NEXTRA = 0
NCOPY = 0
Implicit solvent radii are modified Bondi radii (mbondi)
| Force field information read from topology file:
| CHARMM 31 *> CHARMM22 All-Hydrogen Topology File for Proteins and Lipi
|
|CHARMM: CHARMM force field in use.
|CHARMM: Overriding default value of chngmask.
|CHARMM: Setting chngmask = 0.
| Memory Use Allocated
| Real 341238
| Hollerith 15520
| Integer 257185
| Max Pairs 1
| nblistReal 0
| nblist Int 0
| Total 3731 kbytes
| Note: 1-4 EEL scale factors are being read from the topology file.
| Note: 1-4 VDW scale factors are being read from the topology file.
| Duplicated 0 dihedrals
| Duplicated 0 dihedrals
|CHARMM: Reticulating splines.
BOX TYPE: RECTILINEAR
--------------------------------------------------------------------------------
2. CONTROL DATA FOR THE RUN
--------------------------------------------------------------------------------
General flags:
imin = 5, nmropt = 0
Nature and format of input:
ntx = 1, irest = 0, ntrx = 1
Nature and format of output:
ntxo = 1, ntpr = 50, ntrx = 1, ntwr = 500
iwrap = 0, ntwx = 0, ntwv = 0, ntwe = 0
ioutfm = 0, ntwprt = 0, idecomp = 0, rbornstat= 0
Potential function:
ntf = 1, ntb = 0, igb = 10, nsnb = 99999
ipol = 0, gbsa = 0, iesp = 0
dielc = 1.00000, cut = 999.00000, intdiel = 1.00000
Frozen or restrained atoms:
ibelly = 0, ntr = 0
Energy minimization:
maxcyc = 1, ncyc = 10, ntmin = 1
dx0 = 0.01000, drms = 0.00010
| INFO: Old style inpcrd file read
--------------------------------------------------------------------------------
3. ATOMIC COORDINATES AND VELOCITIES
--------------------------------------------------------------------------------
trajectory generated by ptraj
begin time read from input coords = 0.000 ps
Number of triangulated 3-point waters found: 0
--------------------------------------------------------------------------------
4. RESULTS
--------------------------------------------------------------------------------
POST-PROCESSING OF TRAJECTORY ENERGIES
trajectory generated by ptraj
minimizing coord set # 1
Total surface charge -6.9062
Reaction field energy -3785.5658
Cavity solvation energy 95.2130
Maximum number of minimization cycles reached.
FINAL RESULTS
NSTEP ENERGY RMS GMAX NAME NUMBER
1 -3.8663E+03 1.7229E+01 1.2763E+02 C 3019
BOND = 1099.3618 ANGLE = 2514.9576 DIHED = 1727.1072
UB = 307.7066 IMP = 144.9070 CMAP = -343.5526
VDWAALS = -2140.7162 EEL = -16166.5478 EPB = -3785.5698
1-4 VDW = 1116.7688 1-4 EEL = 11564.0399 RESTRAINT = 0.0000
ECAVITY = 95.2130 EDISPER = 0.0000
minimization completed, ENE= -.38663245E+04 RMS= 0.172292E+02
minimizing coord set # 2
Total surface charge -7.1518
Reaction field energy -4178.5283
Cavity solvation energy 96.6241
Maximum number of minimization cycles reached.
FINAL RESULTS
NSTEP ENERGY RMS GMAX NAME NUMBER
1 -4.3244E+03 2.7545E+01 1.2338E+03 NE2 15
BOND = 1091.2305 ANGLE = 2567.0512 DIHED = 1750.6803
UB = 302.8783 IMP = 170.6923 CMAP = -377.5378
VDWAALS = -2142.6715 EEL = -16029.9812 EPB = -4178.5495
1-4 VDW = 1063.7607 1-4 EEL = 11361.4440 RESTRAINT = 0.0000
ECAVITY = 96.6241 EDISPER = 0.0000
minimization completed, ENE= -.43243786E+04 RMS= 0.275451E+02
minimizing coord set # 3
Total surface charge -7.1933
Reaction field energy -4846.2793
Cavity solvation energy 97.5741
Maximum number of minimization cycles reached.
FINAL RESULTS
NSTEP ENERGY RMS GMAX NAME NUMBER
1 -5.0565E+03 4.1209E+01 2.3276E+03 HE22 17
BOND = 1026.2478 ANGLE = 2471.6314 DIHED = 1770.7979
UB = 297.7850 IMP = 158.3008 CMAP = -370.6401
VDWAALS = -2134.3262 EEL = -16138.2931 EPB = -4846.2582
1-4 VDW = 1107.2937 1-4 EEL = 11503.3707 RESTRAINT = 0.0000
ECAVITY = 97.5741 EDISPER = 0.0000
minimization completed, ENE= -.50565163E+04 RMS= 0.412091E+02
minimizing coord set # 4
Total surface charge -6.9240
Reaction field energy -3781.5458
Cavity solvation energy 99.0276
Maximum number of minimization cycles reached.
FINAL RESULTS
NSTEP ENERGY RMS GMAX NAME NUMBER
1 -4.0487E+03 1.7492E+01 2.6532E+02 HH21 931
BOND = 1037.5461 ANGLE = 2512.4890 DIHED = 1781.7092
UB = 314.0055 IMP = 156.7151 CMAP = -383.6738
VDWAALS = -2112.4389 EEL = -16363.8438 EPB = -3781.5560
1-4 VDW = 1111.3562 1-4 EEL = 11579.9868 RESTRAINT = 0.0000
ECAVITY = 99.0276 EDISPER = 0.0000
minimization completed, ENE= -.40486770E+04 RMS= 0.174922E+02
minimizing coord set # 5
Total surface charge -6.8066
Reaction field energy -4132.0448
Cavity solvation energy 100.1397
Maximum number of minimization cycles reached.
FINAL RESULTS
NSTEP ENERGY RMS GMAX NAME NUMBER
1 -4.0752E+03 2.3701E+01 1.0820E+03 HN 279
BOND = 1068.4239 ANGLE = 2542.4866 DIHED = 1752.5624
UB = 312.9327 IMP = 160.5512 CMAP = -355.1272
VDWAALS = -2108.7107 EEL = -16070.2489 EPB = -4131.9348
1-4 VDW = 1099.9538 1-4 EEL = 11553.7967 RESTRAINT = 0.0000
ECAVITY = 100.1397 EDISPER = 0.0000
minimization completed, ENE= -.40751746E+04 RMS= 0.237006E+02
minimizing coord set # 6
Total surface charge -7.2589
Reaction field energy -4482.6135
Cavity solvation energy 99.3138
Maximum number of minimization cycles reached.
FINAL RESULTS
NSTEP ENERGY RMS GMAX NAME NUMBER
1 -4.5157E+03 2.4632E+01 7.3786E+02 HE3 578
BOND = 1025.8814 ANGLE = 2598.7656 DIHED = 1750.0536
UB = 311.4308 IMP = 176.1615 CMAP = -365.6693
VDWAALS = -2110.0325 EEL = -16196.9724 EPB = -4482.6283
1-4 VDW = 1113.6909 1-4 EEL = 11564.3343 RESTRAINT = 0.0000
ECAVITY = 99.3138 EDISPER = 0.0000
minimization completed, ENE= -.45156704E+04 RMS= 0.246318E+02
minimizing coord set # 7
Total surface charge -7.8574
Reaction field energy -4675.2626
Cavity solvation energy 97.6558
Maximum number of minimization cycles reached.
FINAL RESULTS
NSTEP ENERGY RMS GMAX NAME NUMBER
1 -4.8040E+03 3.0581E+01 1.2089E+03 HG2 2176
BOND = 1088.3925 ANGLE = 2590.6020 DIHED = 1749.6480
UB = 324.7064 IMP = 153.5049 CMAP = -378.3257
VDWAALS = -2159.4928 EEL = -16136.6875 EPB = -4675.3001
1-4 VDW = 1089.9328 1-4 EEL = 11451.3271 RESTRAINT = 0.0000
ECAVITY = 97.6558 EDISPER = 0.0000
minimization completed, ENE= -.48040366E+04 RMS= 0.305811E+02
minimizing coord set # 8
Total surface charge -7.0924
Reaction field energy -5413.4434
Cavity solvation energy 99.0459
Maximum number of minimization cycles reached.
FINAL RESULTS
NSTEP ENERGY RMS GMAX NAME NUMBER
1 -5.5510E+03 5.6513E+01 3.0241E+03 NH1 36
BOND = 1076.6077 ANGLE = 2616.8717 DIHED = 1724.5112
UB = 307.8197 IMP = 151.2331 CMAP = -359.5713
VDWAALS = -2143.2190 EEL = -16160.7416 EPB = -5413.3831
1-4 VDW = 1075.5702 1-4 EEL = 11474.2433 RESTRAINT = 0.0000
ECAVITY = 99.0459 EDISPER = 0.0000
minimization completed, ENE= -.55510124E+04 RMS= 0.565131E+02
minimizing coord set # 9
-8.9359999999999999 7.5970000000000004 42.517000000000003
pb_fdfrc(): Atom out of focusing box 42 65 182
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Tue Jul 19 2011 - 01:30:02 PDT
