Sat Oct 8 20:55:06 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 Sat Oct 8 2011 at 20:55:06 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: 262 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2613 !!! 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 : 2474 net assigned charge : 4.500007 assigned positive charge : 394.9650 centred at (gu) : 88.67979 88.79266 89.53707 assigned negative charge : -390.4655 centred at (gu) : 88.57375 88.82810 89.42789 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 0.2600000 number of grid points assigned charge 8071 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -3.5916901E-09 8.6392644E-09 midg,1,midg; midg,igrid,midg 6.9489481E-09 9.2869135E-10 1,midg,midg; igrid,midg,midg -4.1584989E-09 7.0226291E-09 gauss-seidel spectral radius is 0.9863321 estimated iterations to convergence 70 setup time was (sec) 0.3900000 now iterating at: 20:55:07 rms-change max change #iterations 0.1215642 20.30704 at 10iterations 1.0905570E-02 1.745522 at 20iterations 1.0187458E-03 0.1509647 at 30iterations 9.3130257E-05 1.3788700E-02 at 40iterations 8.6854980E-06 1.3427734E-03 at 50iterations finished qdiffx linear iterations at : 20:55:09 total time elapsed so far: 3.220000 # loops : 50 mean,max change (kT/e) : 8.6854980E-06 1.3427734E-03 energy calculations done at 3.220000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.350000 DelPhi exited at 20:55:10 3.358u 0.164s 0:03.80 92.3% 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 Sat Oct 8 2011 at 20:55:10 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: 262 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2613 !!! 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= 5.0000001E-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 : 2474 net assigned charge : 4.500007 assigned positive charge : 394.9650 centred at (gu) : 86.03917 86.37756 88.61059 assigned negative charge : -390.4655 centred at (gu) : 85.72099 86.48425 88.28352 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1700000 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 19366 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 -1.5275130E-02 2.6013399E-02 midg,1,midg; midg,igrid,midg 1.3266277E-02 5.9016300E-03 1,midg,midg; igrid,midg,midg -3.7022426E-03 2.9432198E-02 gauss-seidel spectral radius is 0.9985462 estimated iterations to convergence 208 setup time was (sec) 0.5500000 now iterating at: 20:55:11 rms-change max change #iterations 3.975113 180.7973 at 10iterations 1.819873 66.83846 at 20iterations 0.8300357 28.95308 at 30iterations 0.3801066 12.52819 at 40iterations 0.1742644 6.019180 at 50iterations 7.9554029E-02 2.558262 at 60iterations 3.6261272E-02 1.154655 at 70iterations 1.6616078E-02 0.5756073 at 80iterations 7.6109180E-03 0.2528830 at 90iterations 3.4773259E-03 0.1265259 at 100iterations 1.5866063E-03 5.6900978E-02 at 110iterations 7.2646234E-04 2.5588989E-02 at 120iterations finished qdiffx linear iterations at : 20:55:18 total time elapsed so far: 7.710000 # loops : 120 mean,max change (kT/e) : 7.2646234E-04 2.5588989E-02 energy calculations done at 7.710000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.840000 DelPhi exited at 20:55:18 7.842u 0.210s 0:08.40 95.8% 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 20:55:18 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: 262 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2613 !!! 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 : 2474 net assigned charge : 4.500007 assigned positive charge : 394.9650 centred at (gu) : 84.05858 84.56622 87.91582 assigned negative charge : -390.4655 centred at (gu) : 83.58147 84.72629 87.42515 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.3000000 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 = 0.4600000 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 19789 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 -8.3889991E-02 0.3441292 midg,1,midg; midg,igrid,midg 0.1586983 0.1297359 1,midg,midg; igrid,midg,midg -3.0227186E-02 0.3569271 gauss-seidel spectral radius is 0.9992279 estimated iterations to convergence 284 setup time was (sec) 1.070000 now iterating at: 20:55:20 rms-change max change #iterations 9.388955 335.4295 at 10iterations 5.383315 114.0629 at 20iterations 3.059318 83.42157 at 30iterations 1.741159 38.84063 at 40iterations 0.9889212 19.45126 at 50iterations 0.5611942 10.40645 at 60iterations 0.3188279 6.669140 at 70iterations 0.1804156 3.889074 at 80iterations 0.1023969 2.015661 at 90iterations 5.8125891E-02 1.222399 at 100iterations 3.3053104E-02 0.6193695 at 110iterations 1.8749945E-02 0.3369062 at 120iterations 1.0614810E-02 0.2073021 at 130iterations 6.0265744E-03 0.1137733 at 140iterations 3.4090432E-03 6.3854218E-02 at 150iterations 1.9412016E-03 3.8692474E-02 at 160iterations 1.0970451E-03 2.1438599E-02 at 170iterations 6.2375027E-04 1.1672020E-02 at 180iterations finished qdiffx linear iterations at : 20:55:32 total time elapsed so far: 13.37000 # loops : 180 mean,max change (kT/e) : 6.2375027E-04 1.1672020E-02 energy calculations done at 13.37000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.50000 DelPhi exited at 20:55:32 13.501u 0.212s 0:14.04 97.6% 0+0k 0+0io 0pf+0w