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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Received on Sun Dec 02 2007 - 06:07:49 PST
