Tue Oct 11 08:33:39 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+sph.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 = amb.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 08:33:39 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2917 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 0.5891991 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): -13.71700 46.70400 ymin,ymax (A): 21.44800 78.88200 zmin,zma (A): -71.76900 -22.34700 x,y,z range (A): 60.42100 57.43400 49.42200 scale (grids/A): 0.5891991 object centre (A): 16.49350 50.16500 -47.05800 number of atom coordinates read : 2917 total number of charged atoms : 2778 net assigned charge : -4.999983 assigned positive charge : 425.7665 centred at (gu) : 87.80676 90.07401 89.49317 assigned negative charge : -430.7670 centred at (gu) : 87.79288 90.29971 89.45289 start vw surface at 0.1600000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 6661 nv = 96 ne = 84 npr = 60474 no. pairs analyzed = 60474 no. exposed pairs = 3781 no. arc points = 25729 no. surface atoms = 1275 nbur = 1642 mkacc time = 0.1400000 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 = 1.456000 m= 320 mr = 3564 m= 0 mr = 21 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3200000 number of dielectric boundary points 3396 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2572 ## 268 charges are in solution ## iepsmp to db, and charging done at 0.4200000 number of grid points assigned charge 8388 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -2.9400200E-09 -2.8392624E-10 midg,1,midg; midg,igrid,midg 4.7507691E-09 -8.2368485E-09 1,midg,midg; igrid,midg,midg -3.0664296E-09 -6.6136252E-10 gauss-seidel spectral radius is 0.9851245 estimated iterations to convergence 67 setup time was (sec) 0.5400000 now iterating at: 08:33:40 rms-change max change #iterations 0.1038956 18.74551 at 10iterations 8.4299920E-03 1.274622 at 20iterations 7.1301108E-04 0.1045303 at 30iterations 5.9471484E-05 9.5443726E-03 at 40iterations 5.5382438E-06 8.3732605E-04 at 50iterations finished qdiffx linear iterations at : 08:33:42 total time elapsed so far: 2.970000 # loops : 50 mean,max change (kT/e) : 5.5382438E-06 8.3732605E-04 energy calculations done at 2.970000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.130000 DelPhi exited at 08:33:43 3.138u 0.130s 0:03.73 87.3% 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 08:33:43 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2917 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 1.767597 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): -13.71700 46.70400 ymin,ymax (A): 21.44800 78.88200 zmin,zma (A): -71.76900 -22.34700 x,y,z range (A): 60.42100 57.43400 49.42200 scale (grids/A): 1.767597 object centre (A): 16.49350 50.16500 -47.05800 number of atom coordinates read : 2917 total number of charged atoms : 2778 net assigned charge : -4.999983 assigned positive charge : 425.7665 centred at (gu) : 83.41991 90.22158 88.47906 assigned negative charge : -430.7670 centred at (gu) : 83.37830 90.89876 88.35809 start vw surface at 0.1500000 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 72200 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25729 grid for indexing accessible points = 1.400000 m= 25462 mr = 49176 m= 3479 mr = 18392 m= 119 mr = 2023 m= 1 mr = 16 m= 0 mr = 0 time to grow re-entrant surface = 0.2300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5000000 number of dielectric boundary points 31654 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 208 ## 2 charges are in solution ## iepsmp to db, and charging done at 0.6000000 number of grid points assigned charge 21666 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) : 0.5891991 object centre at (A) : 16.49350 50.16500 -47.05800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 5.5921809E-03 1.4590221E-02 midg,1,midg; midg,igrid,midg 1.9632000E-04 -3.4985412E-02 1,midg,midg; igrid,midg,midg -3.5656735E-02 -2.8202739E-02 gauss-seidel spectral radius is 0.9984516 estimated iterations to convergence 202 setup time was (sec) 0.7500000 now iterating at: 08:33:44 rms-change max change #iterations 3.860997 158.0417 at 10iterations 1.720102 66.62864 at 20iterations 0.7628784 25.14570 at 30iterations 0.3384965 12.87828 at 40iterations 0.1509157 4.995794 at 50iterations 6.7415535E-02 2.314335 at 60iterations 2.9872041E-02 1.060923 at 70iterations 1.3356102E-02 0.4533684 at 80iterations 5.9535578E-03 0.2023706 at 90iterations 2.6622463E-03 9.0235710E-02 at 100iterations 1.1873281E-03 3.9806366E-02 at 110iterations 5.2955985E-04 1.6466141E-02 at 120iterations finished qdiffx linear iterations at : 08:33:50 total time elapsed so far: 6.630000 # loops : 120 mean,max change (kT/e) : 5.2955985E-04 1.6466141E-02 energy calculations done at 6.630000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 6.810000 DelPhi exited at 08:33:50 6.810u 0.173s 0:07.29 95.7% 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 08:33:50 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2917 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 2.651396 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): -13.71700 46.70400 ymin,ymax (A): 21.44800 78.88200 zmin,zma (A): -71.76900 -22.34700 x,y,z range (A): 60.42100 57.43400 49.42200 scale (grids/A): 2.651396 object centre (A): 16.49350 50.16500 -47.05800 number of atom coordinates read : 2917 total number of charged atoms : 2778 net assigned charge : -4.999983 assigned positive charge : 425.7665 centred at (gu) : 80.12970 90.33226 87.71842 assigned negative charge : -430.7670 centred at (gu) : 80.06749 91.34814 87.53706 start vw surface at 0.1500000 fill in re-entrant regions at 0.4200000 boundary points on vw surface= 167053 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25729 grid for indexing accessible points = 1.400000 m= 83271 mr = 119819 m= 29086 mr = 66993 m= 5891 mr = 23020 m= 515 mr = 4262 m= 14 mr = 239 m= 0 mr = 0 time to grow re-entrant surface = 0.7200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.220000 number of dielectric boundary points 71497 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3 iepsmp to db, and charging done at 1.340000 number of grid points assigned charge 22220 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) : 1.767597 object centre at (A) : 16.49350 50.16500 -47.05800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1122108 0.1867610 midg,1,midg; midg,igrid,midg -1.5508603E-02 -0.2985360 1,midg,midg; igrid,midg,midg -0.3822608 -0.6865441 gauss-seidel spectral radius is 0.9992254 estimated iterations to convergence 284 setup time was (sec) 1.500000 now iterating at: 08:33:52 rms-change max change #iterations 9.631756 245.1152 at 10iterations 5.610839 149.1676 at 20iterations 3.228377 88.63132 at 30iterations 1.852136 56.10415 at 40iterations 1.060683 22.19441 at 50iterations 0.6061360 13.29906 at 60iterations 0.3445918 8.053548 at 70iterations 0.1957799 3.966487 at 80iterations 0.1116008 2.145014 at 90iterations 6.3341662E-02 1.275444 at 100iterations 3.5955515E-02 0.7173920 at 110iterations 2.0378221E-02 0.3809261 at 120iterations 1.1562394E-02 0.2208405 at 130iterations 6.5570273E-03 0.1231651 at 140iterations 3.7216221E-03 6.4525604E-02 at 150iterations 2.1081762E-03 3.8982391E-02 at 160iterations 1.1950717E-03 2.2300720E-02 at 170iterations 6.7731779E-04 1.2855530E-02 at 180iterations finished qdiffx linear iterations at : 08:34:02 total time elapsed so far: 11.25000 # loops : 180 mean,max change (kT/e) : 6.7731779E-04 1.2855530E-02 energy calculations done at 11.25000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.43000 DelPhi exited at 08:34:02 11.437u 0.173s 0:12.05 96.2% 0+0k 0+0io 0pf+0w