Sat Oct 15 12:17:53 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 15 2011 at 12:17:53 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 = 2299 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: 0.6542915 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): -26.16000 26.96200 ymin,ymax (A): 7.918000 51.16100 zmin,zma (A): -13.03600 41.37400 x,y,z range (A): 53.12200 43.24300 54.41000 scale (grids/A): 0.6542915 object centre (A): 0.4010000 29.53950 14.16900 number of atom coordinates read : 2299 total number of charged atoms : 2165 net assigned charge : 11.50002 assigned positive charge : 332.5694 centred at (gu) : 89.72063 90.45013 91.61913 assigned negative charge : -321.0701 centred at (gu) : 89.79697 90.39790 91.64027 start vw surface at 0.1100000 fill in re-entrant regions at 0.1200000 boundary points on vw surface= 6838 nv = 96 ne = 84 npr = 46307 no. pairs analyzed = 46307 no. exposed pairs = 2996 no. arc points = 21043 no. surface atoms = 999 nbur = 1300 mkacc time = 0.1200000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 419 mr = 3684 m= 1 mr = 46 m= 0 mr = 0 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 51 time to turn everything in is 0.2900000 number of dielectric boundary points 3528 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2033 ## 190 charges are in solution ## iepsmp to db, and charging done at 0.4400000 number of grid points assigned charge 7856 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.0138909E-08 3.0471753E-08 midg,1,midg; midg,igrid,midg 1.6055081E-08 3.5376733E-08 1,midg,midg; igrid,midg,midg 3.7711011E-08 1.3359419E-08 gauss-seidel spectral radius is 0.9878743 estimated iterations to convergence 74 setup time was (sec) 0.6300000 now iterating at: 12:17:54 rms-change max change #iterations 0.1495387 23.32554 at 10iterations 1.5671086E-02 2.403974 at 20iterations 1.7593306E-03 0.2691288 at 30iterations 3.3240704E-04 5.6699753E-02 at 40iterations 1.1116463E-04 2.0333290E-02 at 50iterations finished qdiffx linear iterations at : 12:17:58 total time elapsed so far: 5.010000 # loops : 50 mean,max change (kT/e) : 1.1116463E-04 2.0333290E-02 energy calculations done at 5.010000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 5.180000 DelPhi exited at 12:17:59 5.186u 0.460s 0:05.94 94.9% 0+0k 0+0io 6pf+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 15 2011 at 12:17:59 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 = 2299 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: 1.962875 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): -26.16000 26.96200 ymin,ymax (A): 7.918000 51.16100 zmin,zma (A): -13.03600 41.37400 x,y,z range (A): 53.12200 43.24300 54.41000 scale (grids/A): 1.962875 object centre (A): 0.4010000 29.53950 14.16900 number of atom coordinates read : 2299 total number of charged atoms : 2165 net assigned charge : 11.50002 assigned positive charge : 332.5694 centred at (gu) : 89.16138 91.35000 94.85701 assigned negative charge : -321.0701 centred at (gu) : 89.39102 91.19372 94.92083 start vw surface at 0.1100000 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 72641 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21043 grid for indexing accessible points = 1.400000 m= 26736 mr = 49426 m= 4715 mr = 19496 m= 333 mr = 2953 m= 5 mr = 123 m= 0 mr = 0 time to grow re-entrant surface = 0.3200000 no. cavity mid-points inaccessible to solvent = 2156 time to turn everything in is 0.6200000 number of dielectric boundary points 32432 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 114 iepsmp to db, and charging done at 0.8100000 number of grid points assigned charge 17093 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) : 0.6542915 object centre at (A) : 0.4010000 29.53950 14.16900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 5.2066833E-02 2.5319137E-02 midg,1,midg; midg,igrid,midg 1.9914142E-03 3.0626388E-02 1,midg,midg; igrid,midg,midg 5.5573314E-02 3.5376523E-02 gauss-seidel spectral radius is 0.9986899 estimated iterations to convergence 219 setup time was (sec) 1.040000 now iterating at: 12:18:00 rms-change max change #iterations 4.035042 198.1657 at 10iterations 1.920885 71.81223 at 20iterations 0.9081461 27.97281 at 30iterations 0.4343078 14.68518 at 40iterations 0.2059971 6.668930 at 50iterations 9.7441137E-02 3.236627 at 60iterations 4.6410073E-02 1.453078 at 70iterations 2.2115704E-02 0.6775503 at 80iterations 1.0568836E-02 0.3169289 at 90iterations 5.0611976E-03 0.1568215 at 100iterations 2.4627612E-03 7.9998016E-02 at 110iterations 1.2253285E-03 4.1206062E-02 at 120iterations finished qdiffx linear iterations at : 12:18:12 total time elapsed so far: 12.43000 # loops : 120 mean,max change (kT/e) : 1.2253285E-03 4.1206062E-02 energy calculations done at 12.43000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.61000 DelPhi exited at 12:18:12 12.618u 0.490s 0:13.53 96.8% 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 15 2011 at 12:18:12 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 = 2299 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: 2.944312 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): -26.16000 26.96200 ymin,ymax (A): 7.918000 51.16100 zmin,zma (A): -13.03600 41.37400 x,y,z range (A): 53.12200 43.24300 54.41000 scale (grids/A): 2.944312 object centre (A): 0.4010000 29.53950 14.16900 number of atom coordinates read : 2299 total number of charged atoms : 2165 net assigned charge : 11.50002 assigned positive charge : 332.5694 centred at (gu) : 88.74211 92.02494 97.28535 assigned negative charge : -321.0701 centred at (gu) : 89.08651 91.79060 97.38134 start vw surface at 0.1100000 fill in re-entrant regions at 0.5100000 boundary points on vw surface= 167848 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21043 grid for indexing accessible points = 1.400000 m= 85144 mr = 119946 m= 32280 mr = 69089 m= 8551 mr = 25683 m= 1338 mr = 6455 m= 97 mr = 912 m= 1 mr = 23 m= 0 mr = 0 time to grow re-entrant surface = 1.000000 no. cavity mid-points inaccessible to solvent = 7051 time to turn everything in is 1.630000 number of dielectric boundary points 73151 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.790000 number of grid points assigned charge 17319 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) : 1.962875 object centre at (A) : 0.4010000 29.53950 14.16900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.6977911 0.3100477 midg,1,midg; midg,igrid,midg -5.1779258E-03 0.2743018 1,midg,midg; igrid,midg,midg 0.5990790 0.3019544 gauss-seidel spectral radius is 0.9992759 estimated iterations to convergence 293 setup time was (sec) 2.020000 now iterating at: 12:18:15 rms-change max change #iterations 9.514672 343.5282 at 10iterations 5.627377 141.4005 at 20iterations 3.304093 85.44322 at 30iterations 1.935433 49.66111 at 40iterations 1.132131 21.45826 at 50iterations 0.6604001 13.18749 at 60iterations 0.3856324 9.116268 at 70iterations 0.2241412 4.908250 at 80iterations 0.1304384 2.702679 at 90iterations 7.5792164E-02 1.403028 at 100iterations 4.3930963E-02 0.8018064 at 110iterations 2.5536630E-02 0.4433298 at 120iterations 1.4803768E-02 0.2863536 at 130iterations 8.6217076E-03 0.1860657 at 140iterations 5.0373999E-03 9.3460083E-02 at 150iterations 2.9572800E-03 6.4744949E-02 at 160iterations 1.7631481E-03 3.3136368E-02 at 170iterations 1.0778300E-03 2.2993088E-02 at 180iterations finished qdiffx linear iterations at : 12:18:34 total time elapsed so far: 20.94000 # loops : 180 mean,max change (kT/e) : 1.0778300E-03 2.2993088E-02 energy calculations done at 20.94000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 21.10000 DelPhi exited at 12:18:34 21.108u 0.565s 0:21.99 98.4% 0+0k 0+0io 0pf+0w