Mon Oct 10 17:02:33 PDT 2011 #!/bin/csh -f # input: # $1 receptor coordinates file; # $2 grid size; # $3 # of iterations for the first run; # $4 # of iterations for the second run; # $5 # of iterations for the third run; # output: # delphi map: $1.phi # log file: delphi.out set RECCRG = rec+sph2.crg set GRID = 179 set n1 = 50 set n2 = 120 set n3 = 180 set DELPHI = $DOCK_BASE/private/delphi set VDW = vdw.siz #set VDW = vdw.hydren set CRG = amb2.crg.oxt set PRM = genric.prm # three step focussing calc. if (-e ARCDAT) /bin/rm ARCDAT cp $VDW fort.11 cp $CRG fort.12 cp $RECCRG fort.13 echo "gsize=$GRID, perfil=20, bndcon=2, linit=$n1\n" >! fort.10 cat $PRM >> fort.10 time $DELPHI if ($status != 0) exit(100) echo "gsize=$GRID, perfil=60, bndcon=3, linit=$n2\n" >! fort.10 cat $PRM >> fort.10 mv fort.14 fort.18 time $DELPHI if ($status != 0) exit(100) echo "gsize=$GRID, perfil=90, bndcon=3, linit=$n3\n" >! fort.10 cat $PRM >> fort.10 mv fort.14 fort.18 time $DELPHI if ($status != 0) exit(100) /bin/rm fort.1[0-3] fort.18 ARCDAT mv fort.14 $RECCRG:r.phi ___________________DelPhi II____________________ / | A program to solve the PB equation | | in 3D, using non-linear form, incorporating | | 2 dielectric regions, ionic strength, periodic | | and focussing boundary conditions, utilizing | | stripped optimum successive over-relaxation | | and an improved algorithm for mapping the | | Mol. Surface to the finite-Difference grid | __________________ ____________________/ DelPhi II program started on Mon Oct 10 2011 at 17:02:33 opening parameter file fort.10 atom radii read from file fort.11 ! default extended atom radii based loosely ! on mike connolly's MS program- note H's are 0 # of radius parameter records: 18 atomic charges read from file fort.12 # of charge parameter records: 312 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4843 !!! WARNING: GLM 169 has a net charge of -0.0940 !!! WARNING: HEM 819 has a net charge of 1.4000 !!! WARNING: FE 3 has a net charge of 1.4000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1300000 grid size : 179 scale,in grids/A, set to be: 0.5139310 object centred at (gu) : 0.0000000E+00 0.0000000E+00 0.0000000E+00 inner,outer dielectrics : 2.060000 78.50000 ionic strength (M) : 0.1450000 debye length (A) : 8.001814 ion exclusion radius (A) : 2.000000 probe radius (A) : 1.400000 boundary conditions : dipolar x,y,z periodic bc. flags : F F F # of linear iterations : 50 # of non-linear iterations : 0 concentration map output : F spherical charge distbn. : F INSIGHT format output : F site potential output : F modified atom file output : T map file label : qdiffxas: qdiffxs4 with an improved surfacing routine convergence graph turned off potential listings turned off box fill (%): 20.00000 xmin,xmax (A): -16.64400 37.27500 ymin,ymax (A): -31.22200 35.30100 zmin,zma (A): -3.942000 65.32800 x,y,z range (A): 53.91900 66.52300 69.27000 scale (grids/A): 0.5139310 object centre (A): 10.31550 2.039501 30.69300 number of atom coordinates read : 4843 total number of charged atoms : 4592 net assigned charge : 5.706026 assigned positive charge : 727.4482 centred at (gu) : 89.85841 90.46777 88.42950 assigned negative charge : -721.7468 centred at (gu) : 89.73676 90.46635 88.40775 start vw surface at 0.2200000 fill in re-entrant regions at 0.2300000 boundary points on vw surface= 8141 nv = 96 ne = 84 npr = 97418 no. pairs analyzed = 97418 no. exposed pairs = 6239 no. arc points = 43373 no. surface atoms = 2085 nbur = 2758 mkacc time = 0.2300000 writing accessible surface arcs data to file ARCDAT initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.652000 m= 306 mr = 4183 m= 0 mr = 13 time to grow re-entrant surface = 0.2600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4900000 number of dielectric boundary points 4251 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4173 ## 638 charges are in solution ## iepsmp to db, and charging done at 0.6000000 number of grid points assigned charge 10821 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 4.2807841E-11 1.0743558E-10 midg,1,midg; midg,igrid,midg 8.1029461E-11 1.1245609E-10 1,midg,midg; igrid,midg,midg -2.8759081E-10 4.3923234E-10 gauss-seidel spectral radius is 0.9806451 estimated iterations to convergence 59 setup time was (sec) 0.7200000 now iterating at: 17:02:34 rms-change max change #iterations 7.2901599E-02 11.99660 at 10iterations 5.2902014E-03 0.9697762 at 20iterations 9.5997349E-04 0.1763763 at 30iterations 3.1661533E-04 4.4189453E-02 at 40iterations 1.2051468E-04 1.4413595E-02 at 50iterations finished qdiffx linear iterations at : 17:02:37 total time elapsed so far: 3.320000 # loops : 50 mean,max change (kT/e) : 1.2051468E-04 1.4413595E-02 energy calculations done at 3.320000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.520000 DelPhi exited at 17:02:37 3.520u 0.136s 0:04.00 91.2% 0+0k 0+0io 0pf+0w ___________________DelPhi II____________________ / | A program to solve the PB equation | | in 3D, using non-linear form, incorporating | | 2 dielectric regions, ionic strength, periodic | | and focussing boundary conditions, utilizing | | stripped optimum successive over-relaxation | | and an improved algorithm for mapping the | | Mol. Surface to the finite-Difference grid | __________________ ____________________/ DelPhi II program started on Mon Oct 10 2011 at 17:02:37 opening parameter file fort.10 atom radii read from file fort.11 ! default extended atom radii based loosely ! on mike connolly's MS program- note H's are 0 # of radius parameter records: 18 atomic charges read from file fort.12 # of charge parameter records: 312 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4843 !!! WARNING: GLM 169 has a net charge of -0.0940 !!! WARNING: HEM 819 has a net charge of 1.4000 !!! WARNING: FE 3 has a net charge of 1.4000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1400000 grid size : 179 scale,in grids/A, set to be: 1.541793 object centred at (gu) : 0.0000000E+00 0.0000000E+00 0.0000000E+00 inner,outer dielectrics : 2.060000 78.50000 ionic strength (M) : 0.1450000 debye length (A) : 8.001814 ion exclusion radius (A) : 2.000000 probe radius (A) : 1.400000 boundary conditions : focussing x,y,z periodic bc. flags : F F F # of linear iterations : 120 # of non-linear iterations : 0 concentration map output : F spherical charge distbn. : F INSIGHT format output : F site potential output : F modified atom file output : T map file label : qdiffxas: qdiffxs4 with an improved surfacing routine convergence graph turned off potential listings turned off box fill (%): 60.00000 xmin,xmax (A): -16.64400 37.27500 ymin,ymax (A): -31.22200 35.30100 zmin,zma (A): -3.942000 65.32800 x,y,z range (A): 53.91900 66.52300 69.27000 scale (grids/A): 1.541793 object centre (A): 10.31550 2.039501 30.69300 number of atom coordinates read : 4843 total number of charged atoms : 4592 net assigned charge : 5.706026 assigned positive charge : 727.4482 centred at (gu) : 89.57402 91.40208 85.28684 assigned negative charge : -721.7468 centred at (gu) : 89.21029 91.39867 85.22303 start vw surface at 0.2200000 fill in re-entrant regions at 0.3400000 boundary points on vw surface= 92765 reading accessible surface arcs data from file ARCDAT no. of arc points read = 43373 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.568000 m= 26875 mr = 63609 m= 2240 mr = 17474 m= 46 mr = 870 m= 0 mr = 0 time to grow re-entrant surface = 0.3100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.7000000 number of dielectric boundary points 39973 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 585 ## 7 charges are in solution ## iepsmp to db, and charging done at 0.8200000 number of grid points assigned charge 34608 setting boundary conditions focussing boundary condition read from file fort.18 focussing potential map: qdiffxas: qdiffxs4 with an improved surfacing routine original scale (grids/A) : 0.5139310 object centre at (A) : 10.31550 2.039501 30.69300 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.7324505E-03 1.9367995E-02 midg,1,midg; midg,igrid,midg -2.3095615E-03 -9.9943150E-03 1,midg,midg; igrid,midg,midg -1.8407813E-03 1.1821932E-02 gauss-seidel spectral radius is 0.9981518 estimated iterations to convergence 185 setup time was (sec) 0.9900000 now iterating at: 17:02:39 rms-change max change #iterations 3.919180 160.0347 at 10iterations 1.612615 55.23898 at 20iterations 0.6675375 20.63011 at 30iterations 0.2767932 8.635948 at 40iterations 0.1148505 3.693184 at 50iterations 4.7541790E-02 1.449692 at 60iterations 1.9790752E-02 0.6459247 at 70iterations 8.2828756E-03 0.2765961 at 80iterations 3.5317901E-03 0.1155624 at 90iterations 1.5407035E-03 5.0483704E-02 at 100iterations 7.3394686E-04 2.8349400E-02 at 110iterations 3.9380213E-04 1.1962891E-02 at 120iterations finished qdiffx linear iterations at : 17:02:45 total time elapsed so far: 7.630000 # loops : 120 mean,max change (kT/e) : 3.9380213E-04 1.1962891E-02 energy calculations done at 7.630000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.830000 DelPhi exited at 17:02:46 7.837u 0.213s 0:08.41 95.6% 0+0k 0+0io 0pf+0w ___________________DelPhi II____________________ / | A program to solve the PB equation | | in 3D, using non-linear form, incorporating | | 2 dielectric regions, ionic strength, periodic | | and focussing boundary conditions, utilizing | | stripped optimum successive over-relaxation | | and an improved algorithm for mapping the | | Mol. Surface to the finite-Difference grid | __________________ ____________________/ DelPhi II program started on Mon Oct 10 2011 at 17:02:46 opening parameter file fort.10 atom radii read from file fort.11 ! default extended atom radii based loosely ! on mike connolly's MS program- note H's are 0 # of radius parameter records: 18 atomic charges read from file fort.12 # of charge parameter records: 312 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4843 !!! WARNING: GLM 169 has a net charge of -0.0940 !!! WARNING: HEM 819 has a net charge of 1.4000 !!! WARNING: FE 3 has a net charge of 1.4000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1700000 grid size : 179 scale,in grids/A, set to be: 2.312689 object centred at (gu) : 0.0000000E+00 0.0000000E+00 0.0000000E+00 inner,outer dielectrics : 2.060000 78.50000 ionic strength (M) : 0.1450000 debye length (A) : 8.001814 ion exclusion radius (A) : 2.000000 probe radius (A) : 1.400000 boundary conditions : focussing x,y,z periodic bc. flags : F F F # of linear iterations : 180 # of non-linear iterations : 0 concentration map output : F spherical charge distbn. : F INSIGHT format output : F site potential output : F modified atom file output : T map file label : qdiffxas: qdiffxs4 with an improved surfacing routine convergence graph turned off potential listings turned off box fill (%): 90.00000 xmin,xmax (A): -16.64400 37.27500 ymin,ymax (A): -31.22200 35.30100 zmin,zma (A): -3.942000 65.32800 x,y,z range (A): 53.91900 66.52300 69.27000 scale (grids/A): 2.312689 object centre (A): 10.31550 2.039501 30.69300 number of atom coordinates read : 4843 total number of charged atoms : 4592 net assigned charge : 5.706026 assigned positive charge : 727.4482 centred at (gu) : 89.36076 92.10286 82.92996 assigned negative charge : -721.7468 centred at (gu) : 88.81544 92.09798 82.83452 start vw surface at 0.2800000 fill in re-entrant regions at 0.6200000 boundary points on vw surface= 216733 reading accessible surface arcs data from file ARCDAT no. of arc points read = 43373 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.540000 m= 96562 mr = 156853 m= 23923 mr = 74924 m= 3134 mr = 16674 m= 183 mr = 1762 m= 3 mr = 74 m= 0 mr = 0 time to grow re-entrant surface = 1.000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.760000 number of dielectric boundary points 90251 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 69 iepsmp to db, and charging done at 1.920000 number of grid points assigned charge 36668 setting boundary conditions focussing boundary condition read from file fort.18 focussing potential map: qdiffxas: qdiffxs4 with an improved surfacing routine original scale (grids/A) : 1.541793 object centre at (A) : 10.31550 2.039501 30.69300 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1359621 0.4827621 midg,1,midg; midg,igrid,midg -0.1582121 -0.2636385 1,midg,midg; igrid,midg,midg -2.3520201E-02 0.1651701 gauss-seidel spectral radius is 0.9991788 estimated iterations to convergence 276 setup time was (sec) 2.090000 now iterating at: 17:02:48 rms-change max change #iterations 10.55947 317.0063 at 10iterations 6.104448 138.1714 at 20iterations 3.505995 89.11824 at 30iterations 1.994957 44.21582 at 40iterations 1.132745 22.40870 at 50iterations 0.6416809 14.59580 at 60iterations 0.3614158 6.740852 at 70iterations 0.2036438 4.109349 at 80iterations 0.1145135 2.254921 at 90iterations 6.4322323E-02 1.287581 at 100iterations 3.6011141E-02 0.7597637 at 110iterations 2.0141950E-02 0.3891735 at 120iterations 1.1305469E-02 0.2146912 at 130iterations 6.3407249E-03 0.1257424 at 140iterations 3.5465660E-03 6.9344997E-02 at 150iterations 1.9903276E-03 3.8825989E-02 at 160iterations 1.1182179E-03 1.9970894E-02 at 170iterations 6.3194754E-04 1.2651443E-02 at 180iterations finished qdiffx linear iterations at : 17:02:59 total time elapsed so far: 12.67000 # loops : 180 mean,max change (kT/e) : 6.3194754E-04 1.2651443E-02 energy calculations done at 12.67000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.88000 DelPhi exited at 17:03:00 12.882u 0.244s 0:14.10 93.0% 0+0k 0+0io 0pf+0w