Tue Oct 11 08:26:04 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 Tue Oct 11 2011 at 08:26:04 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: 309 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2725 !!! WARNING: HIR 57 has a net charge of 0.5140 !!! WARNING: GLV 97 has a net charge of -0.5880 !!! WARNING: TYS 1 has a net charge of -0.3380 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6402302 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): -12.74400 37.04700 ymin,ymax (A): -26.91000 21.57700 zmin,zma (A): -10.01300 45.59200 x,y,z range (A): 49.79100 48.48700 55.60500 scale (grids/A): 0.6402302 object centre (A): 12.15150 -2.666500 17.78950 number of atom coordinates read : 2725 total number of charged atoms : 2588 net assigned charge : 2.588015 assigned positive charge : 417.3368 centred at (gu) : 90.28358 90.49680 91.84687 assigned negative charge : -414.7493 centred at (gu) : 90.05708 90.32614 91.83336 start vw surface at 0.1200000 fill in re-entrant regions at 0.1300000 boundary points on vw surface= 7518 nv = 96 ne = 84 npr = 53786 no. pairs analyzed = 53786 no. exposed pairs = 3509 no. arc points = 24170 no. surface atoms = 1178 nbur = 1547 mkacc time = 0.1400000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 433 mr = 4188 m= 1 mr = 37 m= 0 mr = 0 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 28 time to turn everything in is 0.3200000 number of dielectric boundary points 3727 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2332 ## 238 charges are in solution ## iepsmp to db, and charging done at 0.4500000 number of grid points assigned charge 9016 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.3291700E-09 7.8072349E-09 midg,1,midg; midg,igrid,midg -1.6264858E-08 2.7321770E-08 1,midg,midg; igrid,midg,midg -2.3897849E-08 3.3195985E-08 gauss-seidel spectral radius is 0.9873715 estimated iterations to convergence 73 setup time was (sec) 0.6200000 now iterating at: 08:26:05 rms-change max change #iterations 0.1529828 20.70024 at 10iterations 1.5269123E-02 2.093286 at 20iterations 1.5692479E-03 0.2242098 at 30iterations 1.7208915E-04 3.0614853E-02 at 40iterations 2.3050343E-05 3.0593872E-03 at 50iterations finished qdiffx linear iterations at : 08:26:09 total time elapsed so far: 4.820000 # loops : 50 mean,max change (kT/e) : 2.3050343E-05 3.0593872E-03 energy calculations done at 4.820000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.980000 DelPhi exited at 08:26:10 4.982u 0.384s 0:05.66 94.6% 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 Tue Oct 11 2011 at 08:26:10 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: 309 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2725 !!! WARNING: HIR 57 has a net charge of 0.5140 !!! WARNING: GLV 97 has a net charge of -0.5880 !!! WARNING: TYS 1 has a net charge of -0.3380 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.920690 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): -12.74400 37.04700 ymin,ymax (A): -26.91000 21.57700 zmin,zma (A): -10.01300 45.59200 x,y,z range (A): 49.79100 48.48700 55.60500 scale (grids/A): 1.920690 object centre (A): 12.15150 -2.666500 17.78950 number of atom coordinates read : 2725 total number of charged atoms : 2588 net assigned charge : 2.588015 assigned positive charge : 417.3368 centred at (gu) : 90.85024 91.49005 95.54001 assigned negative charge : -414.7493 centred at (gu) : 90.17090 90.97804 95.49975 start vw surface at 0.1300000 fill in re-entrant regions at 0.2700000 boundary points on vw surface= 80514 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24170 grid for indexing accessible points = 1.400000 m= 29611 mr = 55796 m= 4614 mr = 21773 m= 259 mr = 2764 m= 4 mr = 92 m= 0 mr = 0 time to grow re-entrant surface = 0.3500000 no. cavity mid-points inaccessible to solvent = 327 time to turn everything in is 0.6700000 number of dielectric boundary points 34577 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 168 iepsmp to db, and charging done at 0.7700000 number of grid points assigned charge 20391 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) : 0.6402302 object centre at (A) : 12.15150 -2.666500 17.78950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.0963517E-02 3.1975273E-03 midg,1,midg; midg,igrid,midg -2.0240091E-02 6.9181095E-03 1,midg,midg; igrid,midg,midg -6.4000953E-03 5.9006523E-02 gauss-seidel spectral radius is 0.9986745 estimated iterations to convergence 218 setup time was (sec) 0.9600000 now iterating at: 08:26:11 rms-change max change #iterations 4.514980 191.9296 at 10iterations 2.138063 71.50745 at 20iterations 1.014240 29.90168 at 30iterations 0.4814854 15.00136 at 40iterations 0.2281464 6.898514 at 50iterations 0.1083048 3.799580 at 60iterations 5.1491819E-02 1.638816 at 70iterations 2.4438508E-02 0.7378623 at 80iterations 1.1533778E-02 0.3451767 at 90iterations 5.4841689E-03 0.1633101 at 100iterations 2.6010727E-03 8.4829330E-02 at 110iterations 1.2336823E-03 3.6380291E-02 at 120iterations finished qdiffx linear iterations at : 08:26:22 total time elapsed so far: 11.58000 # loops : 120 mean,max change (kT/e) : 1.2336823E-03 3.6380291E-02 energy calculations done at 11.58000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.74000 DelPhi exited at 08:26:23 11.741u 0.456s 0:12.56 97.0% 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 Tue Oct 11 2011 at 08:26:23 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: 309 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2725 !!! WARNING: HIR 57 has a net charge of 0.5140 !!! WARNING: GLV 97 has a net charge of -0.5880 !!! WARNING: TYS 1 has a net charge of -0.3380 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.881036 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): -12.74400 37.04700 ymin,ymax (A): -26.91000 21.57700 zmin,zma (A): -10.01300 45.59200 x,y,z range (A): 49.79100 48.48700 55.60500 scale (grids/A): 2.881036 object centre (A): 12.15150 -2.666500 17.78950 number of atom coordinates read : 2725 total number of charged atoms : 2588 net assigned charge : 2.588015 assigned positive charge : 417.3368 centred at (gu) : 91.27530 92.23496 98.30979 assigned negative charge : -414.7493 centred at (gu) : 90.25634 91.46692 98.24957 start vw surface at 0.1200000 fill in re-entrant regions at 0.5500000 boundary points on vw surface= 185955 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24170 grid for indexing accessible points = 1.400000 m= 95625 mr = 134968 m= 34507 mr = 78291 m= 8148 mr = 27418 m= 1175 mr = 5977 m= 88 mr = 776 m= 4 mr = 55 m= 0 mr = 0 time to grow re-entrant surface = 1.070000 no. cavity mid-points inaccessible to solvent = 1297 time to turn everything in is 1.730000 number of dielectric boundary points 78017 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.870000 number of grid points assigned charge 20704 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) : 1.920690 object centre at (A) : 12.15150 -2.666500 17.78950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.3146733 0.1557140 midg,1,midg; midg,igrid,midg -0.2282138 -3.2096840E-02 1,midg,midg; igrid,midg,midg -3.5400208E-02 0.5232012 gauss-seidel spectral radius is 0.9992710 estimated iterations to convergence 292 setup time was (sec) 2.080000 now iterating at: 08:26:25 rms-change max change #iterations 10.53683 294.9365 at 10iterations 6.201411 141.7308 at 20iterations 3.636472 73.17618 at 30iterations 2.125040 44.36623 at 40iterations 1.239417 25.06712 at 50iterations 0.7201673 13.92337 at 60iterations 0.4184679 7.484734 at 70iterations 0.2430312 4.572939 at 80iterations 0.1408971 2.766609 at 90iterations 8.1824258E-02 1.422211 at 100iterations 4.7259603E-02 0.8135715 at 110iterations 2.7370822E-02 0.4610157 at 120iterations 1.5844062E-02 0.2981796 at 130iterations 9.1939531E-03 0.1725769 at 140iterations 5.3286646E-03 9.9449158E-02 at 150iterations 3.0991728E-03 5.8654785E-02 at 160iterations 1.8066755E-03 3.0120850E-02 at 170iterations 1.0601735E-03 1.8882751E-02 at 180iterations finished qdiffx linear iterations at : 08:26:43 total time elapsed so far: 20.40000 # loops : 180 mean,max change (kT/e) : 1.0601735E-03 1.8882751E-02 energy calculations done at 20.40000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 20.58000 DelPhi exited at 08:26:44 20.585u 0.450s 0:21.62 97.2% 0+0k 0+0io 0pf+0w