Tue Nov 22 14:16:34 PST 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 Nov 22 2011 at 14:16:37 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1952 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6502758 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): -6.106000 30.77500 ymin,ymax (A): -46.52900 7.714000 zmin,zma (A): -54.44900 0.2969999 x,y,z range (A): 36.88100 54.24300 54.74600 scale (grids/A): 0.6502758 object centre (A): 12.33450 -19.40750 -27.07600 number of atom coordinates read : 1952 total number of charged atoms : 1820 net assigned charge : 3.000004 assigned positive charge : 286.6140 centred at (gu) : 90.03756 92.07520 89.85827 assigned negative charge : -283.6143 centred at (gu) : 89.94807 92.19774 89.93871 start vw surface at 0.1100000 fill in re-entrant regions at 0.1100000 boundary points on vw surface= 5712 nv = 96 ne = 84 npr = 39385 no. pairs analyzed = 39385 no. exposed pairs = 2550 no. arc points = 17697 no. surface atoms = 867 nbur = 1085 mkacc time = 8.0000006E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 339 mr = 3106 m= 1 mr = 54 m= 0 mr = 0 time to grow re-entrant surface = 0.1000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2200000 number of dielectric boundary points 2892 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1755 ## 158 charges are in solution ## iepsmp to db, and charging done at 0.3200000 number of grid points assigned charge 6611 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.5498264E-08 -2.8343563E-09 midg,1,midg; midg,igrid,midg 1.2732380E-08 -1.2400938E-08 1,midg,midg; igrid,midg,midg -3.9267904E-09 1.6162229E-08 gauss-seidel spectral radius is 0.9876911 estimated iterations to convergence 74 setup time was (sec) 0.4300000 now iterating at: 14:16:40 rms-change max change #iterations 0.1318292 20.43296 at 10iterations 1.3407029E-02 1.842262 at 20iterations 1.3933327E-03 0.2174160 at 30iterations 1.4306093E-04 2.2198677E-02 at 40iterations 1.4530047E-05 2.1400452E-03 at 50iterations finished qdiffx linear iterations at : 14:16:48 total time elapsed so far: 2.850000 # loops : 50 mean,max change (kT/e) : 1.4530047E-05 2.1400452E-03 energy calculations done at 2.850000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.020000 DelPhi exited at 14:16:50 3.023u 0.127s 0:13.50 23.2% 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 Tue Nov 22 2011 at 14:16:52 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 = 1952 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.950827 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): -6.106000 30.77500 ymin,ymax (A): -46.52900 7.714000 zmin,zma (A): -54.44900 0.2969999 x,y,z range (A): 36.88100 54.24300 54.74600 scale (grids/A): 1.950827 object centre (A): 12.33450 -19.40750 -27.07600 number of atom coordinates read : 1952 total number of charged atoms : 1820 net assigned charge : 3.000004 assigned positive charge : 286.6140 centred at (gu) : 90.11253 96.22567 89.57481 assigned negative charge : -283.6143 centred at (gu) : 89.84451 96.59345 89.81634 start vw surface at 0.1100000 fill in re-entrant regions at 0.1900000 boundary points on vw surface= 61116 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17697 grid for indexing accessible points = 1.400000 m= 22814 mr = 41716 m= 3827 mr = 17131 m= 245 mr = 2533 m= 3 mr = 90 m= 0 mr = 0 time to grow re-entrant surface = 0.2000000 no. cavity mid-points inaccessible to solvent = 745 time to turn everything in is 0.4200000 number of dielectric boundary points 26535 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 135 iepsmp to db, and charging done at 0.5300000 number of grid points assigned charge 14378 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) : 0.6502758 object centre at (A) : 12.33450 -19.40750 -27.07600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 9.5637571E-03 4.7425888E-02 midg,1,midg; midg,igrid,midg 4.1163076E-02 -9.2038866E-03 1,midg,midg; igrid,midg,midg -3.8675840E-03 5.4708105E-03 gauss-seidel spectral radius is 0.9986254 estimated iterations to convergence 214 setup time was (sec) 0.6800000 now iterating at: 14:16:56 rms-change max change #iterations 3.708542 181.8694 at 10iterations 1.734167 69.50523 at 20iterations 0.8085844 30.86438 at 30iterations 0.3777519 15.31491 at 40iterations 0.1764968 5.821615 at 50iterations 8.2018241E-02 2.886831 at 60iterations 3.8337510E-02 1.313363 at 70iterations 1.7890189E-02 0.6074715 at 80iterations 8.3592245E-03 0.3006773 at 90iterations 3.8950634E-03 0.1331997 at 100iterations 1.8128236E-03 7.1110606E-02 at 110iterations 8.4890780E-04 2.8816223E-02 at 120iterations finished qdiffx linear iterations at : 14:17:14 total time elapsed so far: 6.650000 # loops : 120 mean,max change (kT/e) : 8.4890780E-04 2.8816223E-02 energy calculations done at 6.650000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 6.810000 DelPhi exited at 14:17:17 6.813u 0.163s 0:25.90 26.9% 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 Nov 22 2011 at 14:17:19 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 = 1952 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.926241 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): -6.106000 30.77500 ymin,ymax (A): -46.52900 7.714000 zmin,zma (A): -54.44900 0.2969999 x,y,z range (A): 36.88100 54.24300 54.74600 scale (grids/A): 2.926241 object centre (A): 12.33450 -19.40750 -27.07600 number of atom coordinates read : 1952 total number of charged atoms : 1820 net assigned charge : 3.000004 assigned positive charge : 286.6140 centred at (gu) : 90.16890 99.33847 89.36214 assigned negative charge : -283.6143 centred at (gu) : 89.76682 99.89029 89.72463 start vw surface at 0.1100000 fill in re-entrant regions at 0.3500000 boundary points on vw surface= 140999 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17697 grid for indexing accessible points = 1.400000 m= 72602 mr = 100852 m= 27746 mr = 59756 m= 7067 mr = 22801 m= 1126 mr = 5515 m= 77 mr = 802 m= 3 mr = 46 m= 0 mr = 0 time to grow re-entrant surface = 0.6299999 no. cavity mid-points inaccessible to solvent = 2510 time to turn everything in is 1.080000 number of dielectric boundary points 59848 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.200000 number of grid points assigned charge 14560 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) : 1.950827 object centre at (A) : 12.33450 -19.40750 -27.07600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -5.9538361E-02 0.8523887 midg,1,midg; midg,igrid,midg 0.4108401 -0.1709830 1,midg,midg; igrid,midg,midg -3.7155826E-02 1.7827848E-02 gauss-seidel spectral radius is 0.9992465 estimated iterations to convergence 288 setup time was (sec) 1.360000 now iterating at: 14:17:26 rms-change max change #iterations 8.684840 398.4597 at 10iterations 4.994856 121.8318 at 20iterations 2.859462 59.42194 at 30iterations 1.639165 32.41808 at 40iterations 0.9355146 18.44608 at 50iterations 0.5340802 11.40891 at 60iterations 0.3049241 6.282082 at 70iterations 0.1736011 4.001129 at 80iterations 9.9209607E-02 1.904938 at 90iterations 5.6596857E-02 1.292500 at 100iterations 3.2313164E-02 0.6628380 at 110iterations 1.8462591E-02 0.3712444 at 120iterations 1.0498150E-02 0.2074060 at 130iterations 5.9958356E-03 0.1235962 at 140iterations 3.4201345E-03 6.7466736E-02 at 150iterations 1.9475017E-03 3.8432121E-02 at 160iterations 1.1139319E-03 2.1440506E-02 at 170iterations 6.3590088E-04 1.3370514E-02 at 180iterations finished qdiffx linear iterations at : 14:17:54 total time elapsed so far: 10.82000 # loops : 180 mean,max change (kT/e) : 6.3590088E-04 1.3370514E-02 energy calculations done at 10.82000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.99000 DelPhi exited at 14:17:56 10.994u 0.154s 0:37.62 29.6% 0+0k 0+0io 0pf+0w