Re: [AMBER] PB calculation error when using MMPBSA.py

From: Bill Miller III <brmilleriii.gmail.com>
Date: Tue, 19 Jul 2011 06:28:33 -0400

This is a problem that a couple of other people have seen (myself included).
Mengjuei has written a patch for this error that worked for me. I have
attached the patch. Apply it just as you would any other Amber bugfix, and
then recompile. That should fix your problem.

-Bill

On Tue, Jul 19, 2011 at 4:03 AM, <zw258.cam.ac.uk> wrote:

> 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
>
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>
>


-- 
Bill Miller III
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-6715



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Received on Tue Jul 19 2011 - 03:30:03 PDT
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