Sat Oct 8 17:49:58 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 17:49:58 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 = 3065 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 0.5529410 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): -39.19000 10.08400 ymin,ymax (A): 8.046000 72.42900 zmin,zma (A): 62.93200 109.1800 x,y,z range (A): 49.27400 64.38300 46.24800 scale (grids/A): 0.5529410 object centre (A): -14.55300 40.23750 86.05600 number of atom coordinates read : 3065 total number of charged atoms : 2924 net assigned charge : 1.000005 assigned positive charge : 452.7431 centred at (gu) : 89.90012 89.01793 90.27585 assigned negative charge : -451.7443 centred at (gu) : 89.81287 88.98103 90.27959 start vw surface at 0.1700000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 6254 nv = 96 ne = 84 npr = 61829 no. pairs analyzed = 61829 no. exposed pairs = 3781 no. arc points = 25939 no. surface atoms = 1284 nbur = 1781 mkacc time = 0.1800000 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 = 1.540000 m= 259 mr = 3405 m= 1 mr = 8 m= 0 mr = 0 time to grow re-entrant surface = 0.2000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3800000 number of dielectric boundary points 3101 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2695 ## 366 charges are in solution ## iepsmp to db, and charging done at 0.5100000 number of grid points assigned charge 8050 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.1134545E-10 5.7136493E-11 midg,1,midg; midg,igrid,midg -3.0467689E-10 3.1984249E-10 1,midg,midg; igrid,midg,midg -7.0083378E-10 8.1905827E-10 gauss-seidel spectral radius is 0.9831391 estimated iterations to convergence 63 setup time was (sec) 0.6600000 now iterating at: 17:49:59 rms-change max change #iterations 7.6639272E-02 12.87662 at 10iterations 5.3819013E-03 0.8831062 at 20iterations 3.8528119E-04 7.1047619E-02 at 30iterations 3.5337824E-05 5.7420731E-03 at 40iterations 5.8122996E-06 1.2688637E-03 at 50iterations finished qdiffx linear iterations at : 17:50:02 total time elapsed so far: 4.040000 # loops : 50 mean,max change (kT/e) : 5.8122996E-06 1.2688637E-03 energy calculations done at 4.040000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.230000 DelPhi exited at 17:50:03 4.236u 0.281s 0:04.83 93.3% 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 8 2011 at 17:50:03 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 = 3065 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 1.658823 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): -39.19000 10.08400 ymin,ymax (A): 8.046000 72.42900 zmin,zma (A): 62.93200 109.1800 x,y,z range (A): 49.27400 64.38300 46.24800 scale (grids/A): 1.658823 object centre (A): -14.55300 40.23750 86.05600 number of atom coordinates read : 3065 total number of charged atoms : 2924 net assigned charge : 1.000005 assigned positive charge : 452.7431 centred at (gu) : 89.69960 87.05315 90.82697 assigned negative charge : -451.7443 centred at (gu) : 89.43837 86.94294 90.83824 start vw surface at 0.1600000 fill in re-entrant regions at 0.2800000 boundary points on vw surface= 69093 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25939 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 22927 mr = 48522 m= 2566 mr = 16129 m= 76 mr = 1295 m= 0 mr = 8 time to grow re-entrant surface = 0.3100000 no. cavity mid-points inaccessible to solvent = 196 time to turn everything in is 0.6200000 number of dielectric boundary points 28708 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 277 ## 4 charges are in solution ## iepsmp to db, and charging done at 0.7400000 number of grid points assigned charge 22449 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) : 0.5529410 object centre at (A) : -14.55300 40.23750 86.05600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -5.0646733E-03 -3.3919723E-03 midg,1,midg; midg,igrid,midg 1.9712338E-02 -2.3956627E-02 1,midg,midg; igrid,midg,midg 4.1702087E-03 1.2333713E-02 gauss-seidel spectral radius is 0.9982520 estimated iterations to convergence 190 setup time was (sec) 0.8900000 now iterating at: 17:50:04 rms-change max change #iterations 3.451761 148.5434 at 10iterations 1.461824 51.26536 at 20iterations 0.6202846 22.69300 at 30iterations 0.2635893 9.203568 at 40iterations 0.1116122 4.021638 at 50iterations 4.7545776E-02 1.582014 at 60iterations 2.0162266E-02 0.6928902 at 70iterations 8.5824085E-03 0.2896357 at 80iterations 3.6457465E-03 0.1447301 at 90iterations 1.5600474E-03 5.2679062E-02 at 100iterations 6.6516054E-04 2.4087429E-02 at 110iterations 2.8658935E-04 9.9678040E-03 at 120iterations finished qdiffx linear iterations at : 17:50:12 total time elapsed so far: 9.350000 # loops : 120 mean,max change (kT/e) : 2.8658935E-04 9.9678040E-03 energy calculations done at 9.350000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.530000 DelPhi exited at 17:50:13 9.532u 0.359s 0:10.15 97.3% 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 17:50:13 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 = 3065 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 2.488234 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): -39.19000 10.08400 ymin,ymax (A): 8.046000 72.42900 zmin,zma (A): 62.93200 109.1800 x,y,z range (A): 49.27400 64.38300 46.24800 scale (grids/A): 2.488234 object centre (A): -14.55300 40.23750 86.05600 number of atom coordinates read : 3065 total number of charged atoms : 2924 net assigned charge : 1.000005 assigned positive charge : 452.7431 centred at (gu) : 89.54936 85.57941 91.24026 assigned negative charge : -451.7443 centred at (gu) : 89.15739 85.41428 91.25746 start vw surface at 0.1700000 fill in re-entrant regions at 0.5100000 boundary points on vw surface= 160472 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25939 grid for indexing accessible points = 1.400000 m= 78522 mr = 118214 m= 23354 mr = 63153 m= 4052 mr = 17563 m= 337 mr = 2711 m= 4 mr = 183 m= 0 mr = 0 time to grow re-entrant surface = 0.9200000 no. cavity mid-points inaccessible to solvent = 702 time to turn everything in is 1.530000 number of dielectric boundary points 64917 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 20 iepsmp to db, and charging done at 1.680000 number of grid points assigned charge 23354 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) : 1.658823 object centre at (A) : -14.55300 40.23750 86.05600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -8.2917228E-02 -3.9511755E-02 midg,1,midg; midg,igrid,midg 0.4875358 -0.4211001 1,midg,midg; igrid,midg,midg 9.3419023E-02 0.1732391 gauss-seidel spectral radius is 0.9991589 estimated iterations to convergence 272 setup time was (sec) 1.860000 now iterating at: 17:50:15 rms-change max change #iterations 8.825804 310.5031 at 10iterations 4.980392 123.3055 at 20iterations 2.793677 58.21054 at 30iterations 1.558678 35.63354 at 40iterations 0.8701182 18.17275 at 50iterations 0.4836056 9.656492 at 60iterations 0.2683955 5.310471 at 70iterations 0.1489965 2.944134 at 80iterations 8.2742468E-02 1.679497 at 90iterations 4.5822386E-02 0.9375153 at 100iterations 2.5384240E-02 0.4994287 at 110iterations 1.4075033E-02 0.2970390 at 120iterations 7.8132628E-03 0.1683254 at 130iterations 4.3187425E-03 8.3385468E-02 at 140iterations 2.4007361E-03 4.5436859E-02 at 150iterations 1.3313245E-03 2.6507854E-02 at 160iterations 7.4305956E-04 1.4951706E-02 at 170iterations 4.1544824E-04 7.9382062E-03 at 180iterations finished qdiffx linear iterations at : 17:50:29 total time elapsed so far: 15.67000 # loops : 180 mean,max change (kT/e) : 4.1544824E-04 7.9382062E-03 energy calculations done at 15.67000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.85000 DelPhi exited at 17:50:29 15.849u 0.326s 0:16.49 97.9% 0+0k 0+0io 0pf+0w