Sat Oct 8 20:55:32 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 Sat Oct 8 2011 at 20:55:33 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: 300 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2613 !!! WARNING: GLM 92 has a net charge of -0.0940 !!! WARNING: HIZ 94 has a net charge of 0.2000 !!! WARNING: HIZ 96 has a net charge of 0.2000 !!! WARNING: HIY 119 has a net charge of 0.2000 !!! WARNING: ZN5 504 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= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6155868 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): -31.73900 17.49200 ymin,ymax (A): -23.67500 24.21100 zmin,zma (A): -12.52300 45.30800 x,y,z range (A): 49.23100 47.88600 57.83100 scale (grids/A): 0.6155868 object centre (A): -7.123500 0.2680006 16.39250 number of atom coordinates read : 2613 total number of charged atoms : 2470 net assigned charge : 4.406007 assigned positive charge : 395.4050 centred at (gu) : 88.68973 88.78874 89.54430 assigned negative charge : -390.9995 centred at (gu) : 88.58643 88.82382 89.43483 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1000000 boundary points on vw surface= 6353 nv = 96 ne = 84 npr = 55062 no. pairs analyzed = 55062 no. exposed pairs = 3009 no. arc points = 21811 no. surface atoms = 1014 nbur = 1599 mkacc time = 8.9999996E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 305 mr = 3526 m= 1 mr = 33 m= 0 mr = 0 time to grow re-entrant surface = 0.1000000 no. cavity mid-points inaccessible to solvent = 108 time to turn everything in is 0.2000000 number of dielectric boundary points 3100 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2221 ## 243 charges are in solution ## iepsmp to db, and charging done at 0.2700000 number of grid points assigned charge 8068 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -3.6905572E-09 8.6131022E-09 midg,1,midg; midg,igrid,midg 6.8410517E-09 8.8879609E-10 1,midg,midg; igrid,midg,midg -4.0302748E-09 6.8751191E-09 gauss-seidel spectral radius is 0.9863321 estimated iterations to convergence 70 setup time was (sec) 0.3900000 now iterating at: 20:55:33 rms-change max change #iterations 0.1225861 20.25536 at 10iterations 1.0990628E-02 1.794139 at 20iterations 1.0243270E-03 0.1500626 at 30iterations 9.3762559E-05 1.3966084E-02 at 40iterations 8.7294966E-06 1.2950897E-03 at 50iterations finished qdiffx linear iterations at : 20:55:36 total time elapsed so far: 3.250000 # loops : 50 mean,max change (kT/e) : 8.7294966E-06 1.2950897E-03 energy calculations done at 3.250000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.380000 DelPhi exited at 20:55:36 3.387u 0.157s 0:03.85 91.6% 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 Sat Oct 8 2011 at 20:55:36 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: 300 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2613 !!! WARNING: GLM 92 has a net charge of -0.0940 !!! WARNING: HIZ 94 has a net charge of 0.2000 !!! WARNING: HIZ 96 has a net charge of 0.2000 !!! WARNING: HIY 119 has a net charge of 0.2000 !!! WARNING: ZN5 504 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= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.846760 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): -31.73900 17.49200 ymin,ymax (A): -23.67500 24.21100 zmin,zma (A): -12.52300 45.30800 x,y,z range (A): 49.23100 47.88600 57.83100 scale (grids/A): 1.846760 object centre (A): -7.123500 0.2680006 16.39250 number of atom coordinates read : 2613 total number of charged atoms : 2470 net assigned charge : 4.406007 assigned positive charge : 395.4050 centred at (gu) : 86.06905 86.36576 88.63232 assigned negative charge : -390.9995 centred at (gu) : 85.75906 86.47142 88.30435 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 69769 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21811 grid for indexing accessible points = 1.400000 m= 23092 mr = 48631 m= 2926 mr = 16816 m= 84 mr = 1690 m= 0 mr = 15 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 4389 time to turn everything in is 0.3400000 number of dielectric boundary points 28719 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 147 iepsmp to db, and charging done at 0.4200000 number of grid points assigned charge 19336 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) : 0.6155868 object centre at (A) : -7.123500 0.2680006 16.39250 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.5388796E-02 2.6090261E-02 midg,1,midg; midg,igrid,midg 1.3100086E-02 5.8473800E-03 1,midg,midg; igrid,midg,midg -3.6725444E-03 2.8884947E-02 gauss-seidel spectral radius is 0.9985462 estimated iterations to convergence 208 setup time was (sec) 0.5500000 now iterating at: 20:55:37 rms-change max change #iterations 3.984459 180.7973 at 10iterations 1.824795 66.83846 at 20iterations 0.8323147 28.85680 at 30iterations 0.3810568 12.48525 at 40iterations 0.1746823 6.028870 at 50iterations 7.9753391E-02 2.585608 at 60iterations 3.6357231E-02 1.157804 at 70iterations 1.6659904E-02 0.5821533 at 80iterations 7.6309801E-03 0.2546253 at 90iterations 3.4863108E-03 0.1259346 at 100iterations 1.5904336E-03 5.6677818E-02 at 110iterations 7.2844315E-04 2.6128769E-02 at 120iterations finished qdiffx linear iterations at : 20:55:44 total time elapsed so far: 7.550000 # loops : 120 mean,max change (kT/e) : 7.2844315E-04 2.6128769E-02 energy calculations done at 7.550000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.680000 DelPhi exited at 20:55:45 7.685u 0.181s 0:08.13 96.6% 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 Sat Oct 8 2011 at 20:55:45 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: 300 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2613 !!! WARNING: GLM 92 has a net charge of -0.0940 !!! WARNING: HIZ 94 has a net charge of 0.2000 !!! WARNING: HIZ 96 has a net charge of 0.2000 !!! WARNING: HIY 119 has a net charge of 0.2000 !!! WARNING: ZN5 504 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= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.770140 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): -31.73900 17.49200 ymin,ymax (A): -23.67500 24.21100 zmin,zma (A): -12.52300 45.30800 x,y,z range (A): 49.23100 47.88600 57.83100 scale (grids/A): 2.770140 object centre (A): -7.123500 0.2680006 16.39250 number of atom coordinates read : 2613 total number of charged atoms : 2470 net assigned charge : 4.406007 assigned positive charge : 395.4050 centred at (gu) : 84.10339 84.54854 87.94842 assigned negative charge : -390.9995 centred at (gu) : 83.63857 84.70703 87.45638 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.3100000 boundary points on vw surface= 161666 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21811 grid for indexing accessible points = 1.400000 m= 77624 mr = 117773 m= 24736 mr = 63491 m= 5040 mr = 19501 m= 503 mr = 3718 m= 16 mr = 316 m= 0 mr = 5 time to grow re-entrant surface = 0.4700000 no. cavity mid-points inaccessible to solvent = 14966 time to turn everything in is 0.8400000 number of dielectric boundary points 64781 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3 iepsmp to db, and charging done at 0.9300000 number of grid points assigned charge 19757 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) : 1.846760 object centre at (A) : -7.123500 0.2680006 16.39250 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -8.4997430E-02 0.3454123 midg,1,midg; midg,igrid,midg 0.1572190 0.1291117 1,midg,midg; igrid,midg,midg -2.9825147E-02 0.3502275 gauss-seidel spectral radius is 0.9992279 estimated iterations to convergence 284 setup time was (sec) 1.060000 now iterating at: 20:55:46 rms-change max change #iterations 9.418812 335.4296 at 10iterations 5.399851 114.0641 at 20iterations 3.068254 83.42110 at 30iterations 1.746380 38.82375 at 40iterations 0.9916877 19.38176 at 50iterations 0.5626983 10.39813 at 60iterations 0.3197111 6.563038 at 70iterations 0.1808904 3.916275 at 80iterations 0.1026778 2.035484 at 90iterations 5.8295798E-02 1.209191 at 100iterations 3.3139177E-02 0.6162033 at 110iterations 1.8803867E-02 0.3381348 at 120iterations 1.0644039E-02 0.2037354 at 130iterations 6.0427999E-03 0.1124783 at 140iterations 3.4190277E-03 6.5139771E-02 at 150iterations 1.9464645E-03 3.8776398E-02 at 160iterations 1.0997792E-03 2.0740509E-02 at 170iterations 6.2538113E-04 1.1672020E-02 at 180iterations finished qdiffx linear iterations at : 20:55:57 total time elapsed so far: 12.20000 # loops : 180 mean,max change (kT/e) : 6.2538113E-04 1.1672020E-02 energy calculations done at 12.20000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.33000 DelPhi exited at 20:55:57 12.333u 0.217s 0:12.81 97.8% 0+0k 0+0io 0pf+0w