AMBER Archive (2007)

Subject: AMBER: Minimization amber9 segmentation fault

From: Francesco Pietra (chiendarret_at_yahoo.com)
Date: Sat Dec 01 2007 - 09:46:23 CST

Does this huge energy in trial minimization mean steric clashes or simply a bad
min.in? I am posting as I can't understand better the segmentation fault.

The system is a protein with non-covalently-bound large non-polymeric ligand,
immersed in a POPC hydrated membrane, the whole hydrated (all water is TIP3P).

>From ambmask:
1-76 POPC
77-520 protein
521 ligand
522-9999 WAT
**** WAT

(the latter corresponds to 0-4759 WAT from pdb obtained with ambpdb, otherwise
residue number and name are the same).

If relevant, should the last line of min.in end with a comma, as I did? There
are different versions to this regard on the web.

Thanks for help
francesco pietra

       -------------------------------------------------------
          Amber 9 SANDER 2006
          -------------------------------------------------------

| Run on 12/01/2007 at 16:29:59
  [-O]verwriting output

File Assignments:
| MDIN: box_min1.in
| MDOUT: box_min1.out
|INPCRD: protein_ligand_pop_box.inpcrd
   
| PARM: protein_ligand_pop_box.prmtop
   
|RESTRT: box_min1.rst
| REFC: protein_gam_pop_box.inpcrd

| MDVEL: mdvel
| MDEN: mden
| MDCRD: mdcrd
|MDINFO: mdinfo
|INPDIP: inpdip
|RSTDIP: rstdip

 
 Here is the input file:
 
1st minimization protein_ligand_pop_box80x80
   
 &cntrl
  imin=1, maxcyc=20, ncyc=10,
  cut=10, ntb=1, ntpr=1,
  ntr=1, restraintmask=":77-520, 521",
  restraint_wt=30,
  /
                                                                               
                                                                               

--------------------------------------------------------------------------------
   1. RESOURCE USE:
--------------------------------------------------------------------------------

| Flags: MPI

 getting new box info from bottom of inpcrd
| INFO: Old style inpcrd file read

| peek_ewald_inpcrd: Box info found
|Largest sphere to fit in unit cell has radius = 46.090
| New format PARM file being parsed.
| Version = 1.000 Date = 11/28/07 Time = 12:12:33
 NATOM = 89900 NTYPES = 18 NBONH = 82478 MBONA = 7441
 NTHETH = 22945 MTHETA = 9352 NPHIH = 38729 MPHIA = 20393
 NHPARM = 0 NPARM = 0 NNB = 192544 NRES = 24759
 NBONA = 7441 NTHETA = 9352 NPHIA = 20393 NUMBND = 62
 NUMANG = 130 NPTRA = 58 NATYP = 44 NPHB = 1
 IFBOX = 1 NMXRS = 134 IFCAP = 0 NEXTRA = 0
 NCOPY = 0

| Memory Use Allocated
| Real 6108229
| Hollerith 564161
| Integer 3173435
| Max Pairs 12945600
| nblistReal 1078800
| nblist Int 3319286
| Total 134283 kbytes
| Duplicated 0 dihedrals
| Duplicated 0 dihedrals

     BOX TYPE: RECTILINEAR

--------------------------------------------------------------------------------
   2. CONTROL DATA FOR THE RUN
--------------------------------------------------------------------------------

                                                                               

General flags:
     imin = 1, nmropt = 0

Nature and format of input:
     ntx = 1, irest = 0, ntrx = 1

Nature and format of output:
     ntxo = 1, ntpr = 1, 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 = 1, igb = 0, nsnb = 25
     ipol = 0, gbsa = 0, iesp = 0
     dielc = 1.00000, cut = 10.00000, intdiel = 1.00000
     scnb = 2.00000, scee = 1.20000

Frozen or restrained atoms:
     ibelly = 0, ntr = 1

Energy minimization:
     maxcyc = 20, ncyc = 10, ntmin = 1
     dx0 = 0.01000, drms = 0.00010

Ewald parameters:
     verbose = 0, ew_type = 0, nbflag = 1, use_pme = 1
     vdwmeth = 1, eedmeth = 1, netfrc = 0
     Box X = 112.533 Box Y = 109.793 Box Z = 92.179
     Alpha = 90.000 Beta = 90.000 Gamma = 90.000
     NFFT1 = 120 NFFT2 = 120 NFFT3 = 96
     Cutoff= 10.000 Tol =0.100E-04
     Ewald Coefficient = 0.27511
     Interpolation order = 4

    LOADING THE CONSTRAINED ATOMS AS GROUPS

   5. REFERENCE ATOM COORDINATES

      
     Mask :77-520, 521; matches 7002 atoms

--------------------------------------------------------------------------------
   3. ATOMIC COORDINATES AND VELOCITIES
--------------------------------------------------------------------------------

                                                                               

 begin time read from input coords = 0.000 ps

 Number of triangulated 3-point waters found: 24238
| Atom division among processors:
| 0 22475 44951 67427 89900

     Sum of charges from parm topology file = -0.00074086
     Forcing neutrality...
| Running AMBER/MPI version on 4 nodes

--------------------------------------------------------------------------------
   4. RESULTS
--------------------------------------------------------------------------------

 ---------------------------------------------------
 APPROXIMATING switch and d/dx switch using CUBIC SPLINE INTERPOLATION
 using 5000.0 points per unit in tabled values
 TESTING RELATIVE ERROR over r ranging from 0.0 to cutoff
| CHECK switch(x): max rel err = 0.2738E-14 at 2.422500
| CHECK d/dx switch(x): max rel err = 0.8314E-11 at 2.736960
 ---------------------------------------------------
| Local SIZE OF NONBOND LIST = 6454031
| TOTAL SIZE OF NONBOND LIST = 25821257

   NSTEP ENERGY RMS GMAX NAME NUMBER
      1 2.8852E+18 1.4602E+18 3.9863E+20 O 17223

 BOND = 149932.7945 ANGLE = 46211.6820 DIHED = 9161.8416
 VDWAALS = ************* EEL = -246440.0364 HBOND = 0.0000
 1-4 VDW = 29126.1421 1-4 EEL = 23905.1720 RESTRAINT = 0.0000

   NSTEP ENERGY RMS GMAX NAME NUMBER
      2 8.2905E+17 3.7817E+17 1.0324E+20 O 17223

 BOND = 149932.8374 ANGLE = 46211.6729 DIHED = 9161.8416
 VDWAALS = ************* EEL = -246403.3807 HBOND = 0.0000
 1-4 VDW = 29126.1396 1-4 EEL = 23905.1707 RESTRAINT = 0.0000

   NSTEP ENERGY RMS GMAX NAME NUMBER
      3 2.1637E+17 8.8247E+16 2.4091E+19 O 17223

 BOND = 149932.9075 ANGLE = 46211.6637 DIHED = 9161.8416
 VDWAALS = ************* EEL = -246367.9129 HBOND = 0.0000
 1-4 VDW = 29126.1367 1-4 EEL = 23905.1692 RESTRAINT = 0.0000

   NSTEP ENERGY RMS GMAX NAME NUMBER
      4 5.1492E+16 1.8633E+16 5.0866E+18 O 17223

 BOND = 149933.0186 ANGLE = 46211.6549 DIHED = 9161.8417
 VDWAALS = ************* EEL = -246334.1279 HBOND = 0.0000
 1-4 VDW = 29126.1334 1-4 EEL = 23905.1675 RESTRAINT = 0.0000

   NSTEP ENERGY RMS GMAX NAME NUMBER
      5 1.1230E+16 3.5795E+15 9.7717E+17 O 17223

 BOND = 149933.1907 ANGLE = 46211.6479 DIHED = 9161.8419
 VDWAALS = ************* EEL = -246302.4146 HBOND = 0.0000
 1-4 VDW = 29126.1294 1-4 EEL = 23905.1654 RESTRAINT = 0.0000

   NSTEP ENERGY RMS GMAX NAME NUMBER
      6 2.2583E+15 6.2972E+14 1.7191E+17 O 17223

 BOND = 149933.4532 ANGLE = 46211.6443 DIHED = 9161.8422
 VDWAALS = ************* EEL = -246273.0505 HBOND = 0.0000
 1-4 VDW = 29126.1249 1-4 EEL = 23905.1629 RESTRAINT = 0.0000

   NSTEP ENERGY RMS GMAX NAME NUMBER
      7 4.2146E+14 1.0218E+14 2.7895E+16 O 17223

 BOND = 149933.8485 ANGLE = 46211.6471 DIHED = 9161.8428
 VDWAALS = ************* EEL = -246246.1983 HBOND = 0.0000
 1-4 VDW = 29126.1198 1-4 EEL = 23905.1600 RESTRAINT = 0.0000

   NSTEP ENERGY RMS GMAX NAME NUMBER
      8 7.3514E+13 1.5407E+13 4.2061E+15 O 17223

 BOND = 149934.4390 ANGLE = 46211.6606 DIHED = 9161.8438
 VDWAALS = ************* EEL = -246221.9135 HBOND = 0.0000
 1-4 VDW = 29126.1140 1-4 EEL = 23905.1567 RESTRAINT = 0.0000
 EAMBER = *************

   NSTEP ENERGY RMS GMAX NAME NUMBER
      9 1.2074E+13 2.1752E+12 5.9383E+14 O 17223

 BOND = 149935.3146 ANGLE = 46211.6910 DIHED = 9161.8452
 VDWAALS = ************* EEL = -246200.1611 HBOND = 0.0000
 1-4 VDW = 29126.1076 1-4 EEL = 23905.1528 RESTRAINT = 0.0000
 EAMBER = *************

   NSTEP ENERGY RMS GMAX NAME NUMBER
     10 1.8860E+12 2.8967E+11 7.9077E+13 O 17223

 BOND = 149936.6064 ANGLE = 46211.7479 DIHED = 9161.8474
 VDWAALS = ************* EEL = -246180.8298 HBOND = 0.0000
 1-4 VDW = 29126.1006 1-4 EEL = 23905.1483 RESTRAINT = 0.0000
 EAMBER = *************

   NSTEP ENERGY RMS GMAX NAME NUMBER
     11 2.8815E+11 3.6643E+10 1.0002E+13 O 17223

 BOND = 149938.5018 ANGLE = 46211.8441 DIHED = 9161.8506
 VDWAALS = ************* EEL = -246163.7303 HBOND = 0.0000
 1-4 VDW = 29126.0930 1-4 EEL = 23905.1432 RESTRAINT = 0.0000
 EAMBER = *************

   NSTEP ENERGY RMS GMAX NAME NUMBER
     12 2.8815E+11 3.6643E+10 1.0002E+13 O 17223

 BOND = 149938.5018 ANGLE = 46211.8441 DIHED = 9161.8506
 VDWAALS = ************* EEL = -246163.7303 HBOND = 0.0000
 1-4 VDW = 29126.0930 1-4 EEL = 23905.1432 RESTRAINT = 0.0000
 EAMBER = *************

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