Tue Oct 11 03:25:43 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 03:25:43 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 = 3393 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.5257174 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): -20.59300 34.79000 ymin,ymax (A): -14.64400 53.07300 zmin,zma (A): -11.38200 56.05000 x,y,z range (A): 55.38300 67.71700 67.43201 scale (grids/A): 0.5257174 object centre (A): 7.098500 19.21450 22.33400 number of atom coordinates read : 3393 total number of charged atoms : 3233 net assigned charge : -4.499990 assigned positive charge : 503.1185 centred at (gu) : 89.00114 91.48367 89.42265 assigned negative charge : -507.6201 centred at (gu) : 88.93382 91.53362 89.41219 start vw surface at 0.1000000 fill in re-entrant regions at 0.1100000 boundary points on vw surface= 6134 nv = 96 ne = 84 npr = 65827 no. pairs analyzed = 65827 no. exposed pairs = 4850 no. arc points = 34076 no. surface atoms = 1614 nbur = 1779 mkacc time = 0.1100000 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 = 1.624000 m= 212 mr = 2822 m= 1 mr = 9 m= 0 mr = 0 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2400000 number of dielectric boundary points 3516 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3357 ## 476 charges are in solution ## iepsmp to db, and charging done at 0.3100000 number of grid points assigned charge 8102 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.7672348E-10 -7.0255073E-11 midg,1,midg; midg,igrid,midg 3.5336248E-11 -4.2478188E-10 1,midg,midg; igrid,midg,midg -4.5334042E-10 8.5957123E-11 gauss-seidel spectral radius is 0.9814041 estimated iterations to convergence 61 setup time was (sec) 0.4400000 now iterating at: 03:25:44 rms-change max change #iterations 6.2446486E-02 13.91809 at 10iterations 3.7109635E-03 0.7419281 at 20iterations 2.5079810E-04 4.3441772E-02 at 30iterations 2.7955120E-05 5.2614212E-03 at 40iterations 5.2225905E-06 1.0685921E-03 at 50iterations finished qdiffx linear iterations at : 03:25:47 total time elapsed so far: 3.380000 # loops : 50 mean,max change (kT/e) : 5.2225905E-06 1.0685921E-03 energy calculations done at 3.380000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.510000 DelPhi exited at 03:25:47 3.517u 0.207s 0:04.48 82.8% 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 Tue Oct 11 2011 at 03:25:48 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 = 3393 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: 1.577152 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): -20.59300 34.79000 ymin,ymax (A): -14.64400 53.07300 zmin,zma (A): -11.38200 56.05000 x,y,z range (A): 55.38300 67.71700 67.43201 scale (grids/A): 1.577152 object centre (A): 7.098500 19.21450 22.33400 number of atom coordinates read : 3393 total number of charged atoms : 3233 net assigned charge : -4.499990 assigned positive charge : 503.1185 centred at (gu) : 87.00248 94.44999 88.26717 assigned negative charge : -507.6201 centred at (gu) : 86.80119 94.60072 88.23598 start vw surface at 0.1000000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 68184 reading accessible surface arcs data from file ARCDAT no. of arc points read = 34076 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.512000 m= 18405 mr = 43512 m= 1531 mr = 11442 m= 48 mr = 538 m= 1 mr = 0 m= 0 mr = 0 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 337 time to turn everything in is 0.3400000 number of dielectric boundary points 32677 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 436 ## 3 charges are in solution ## iepsmp to db, and charging done at 0.4100000 number of grid points assigned charge 24591 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) : 0.5257174 object centre at (A) : 7.098500 19.21450 22.33400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -6.8382933E-03 -2.0099558E-02 midg,1,midg; midg,igrid,midg 1.9012960E-02 -1.7276186E-02 1,midg,midg; igrid,midg,midg -7.6074130E-03 3.8487562E-03 gauss-seidel spectral radius is 0.9981025 estimated iterations to convergence 182 setup time was (sec) 0.5500000 now iterating at: 03:25:48 rms-change max change #iterations 3.281940 151.0215 at 10iterations 1.341346 48.06377 at 20iterations 0.5447379 18.82208 at 30iterations 0.2224017 9.347696 at 40iterations 9.0506293E-02 3.580781 at 50iterations 3.6967203E-02 1.421017 at 60iterations 1.5095054E-02 0.5160725 at 70iterations 6.1762375E-03 0.2438660 at 80iterations 2.5176075E-03 9.2154980E-02 at 90iterations 1.0303892E-03 3.6153793E-02 at 100iterations 4.2504020E-04 1.4873028E-02 at 110iterations 1.7541344E-04 6.3018799E-03 at 120iterations finished qdiffx linear iterations at : 03:25:55 total time elapsed so far: 7.640000 # loops : 120 mean,max change (kT/e) : 1.7541344E-04 6.3018799E-03 energy calculations done at 7.640000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.780000 DelPhi exited at 03:25:56 7.779u 0.203s 0:08.27 96.3% 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 03:25:56 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 = 3393 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.365728 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): -20.59300 34.79000 ymin,ymax (A): -14.64400 53.07300 zmin,zma (A): -11.38200 56.05000 x,y,z range (A): 55.38300 67.71700 67.43201 scale (grids/A): 2.365728 object centre (A): 7.098500 19.21450 22.33400 number of atom coordinates read : 3393 total number of charged atoms : 3233 net assigned charge : -4.499990 assigned positive charge : 503.1185 centred at (gu) : 85.50344 96.67462 87.40044 assigned negative charge : -507.6201 centred at (gu) : 85.20180 96.90103 87.35411 start vw surface at 0.1000000 fill in re-entrant regions at 0.2900000 boundary points on vw surface= 159162 reading accessible surface arcs data from file ARCDAT no. of arc points read = 34076 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.512000 m= 66116 mr = 108309 m= 15985 mr = 49287 m= 2066 mr = 10895 m= 126 mr = 1087 m= 3 mr = 37 m= 0 mr = 0 time to grow re-entrant surface = 0.4300000 no. cavity mid-points inaccessible to solvent = 1168 time to turn everything in is 0.8100000 number of dielectric boundary points 73843 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 50 iepsmp to db, and charging done at 0.9100000 number of grid points assigned charge 25804 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) : 1.577152 object centre at (A) : 7.098500 19.21450 22.33400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -5.0837055E-02 -0.4463327 midg,1,midg; midg,igrid,midg 0.3554322 -0.5362022 1,midg,midg; igrid,midg,midg -0.1582204 4.8254639E-02 gauss-seidel spectral radius is 0.9991327 estimated iterations to convergence 268 setup time was (sec) 1.050000 now iterating at: 03:25:57 rms-change max change #iterations 8.972740 290.6352 at 10iterations 5.095639 147.6094 at 20iterations 2.869949 73.76080 at 30iterations 1.602670 37.60064 at 40iterations 0.8922603 22.62474 at 50iterations 0.4944824 11.63552 at 60iterations 0.2725706 6.058517 at 70iterations 0.1505808 3.350082 at 80iterations 8.3084129E-02 1.699219 at 90iterations 4.5715563E-02 0.9150243 at 100iterations 2.5151312E-02 0.5377882 at 110iterations 1.3835776E-02 0.3058414 at 120iterations 7.5829197E-03 0.1563272 at 130iterations 4.1647335E-03 8.5376740E-02 at 140iterations 2.2874933E-03 4.3679237E-02 at 150iterations 1.2557311E-03 2.7854919E-02 at 160iterations 6.8916375E-04 1.3753414E-02 at 170iterations 3.7848306E-04 8.5792542E-03 at 180iterations finished qdiffx linear iterations at : 03:26:08 total time elapsed so far: 12.41000 # loops : 180 mean,max change (kT/e) : 3.7848306E-04 8.5792542E-03 energy calculations done at 12.41000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.54000 DelPhi exited at 03:26:09 12.547u 0.213s 0:13.13 97.1% 0+0k 0+0io 0pf+0w