Tue Oct 11 03:20:44 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 03:20:44 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 = 3336 !!! WARNING: ASN 165 has a net charge of -0.2720 !!! WARNING: GLU 499 has a net charge of -0.2720 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: 0.5443841 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): 4.083000 69.47800 ymin,ymax (A): 31.77200 91.59000 zmin,zma (A): 24.33800 78.45700 x,y,z range (A): 65.39500 59.81800 54.11900 scale (grids/A): 0.5443841 object centre (A): 36.78050 61.68100 51.39750 number of atom coordinates read : 3336 total number of charged atoms : 3196 net assigned charge : -6.543976 assigned positive charge : 501.5775 centred at (gu) : 87.64281 92.05906 87.96102 assigned negative charge : -508.1227 centred at (gu) : 87.60384 92.06360 87.98849 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1000000 boundary points on vw surface= 6322 nv = 96 ne = 84 npr = 68540 no. pairs analyzed = 68540 no. exposed pairs = 4140 no. arc points = 29100 no. surface atoms = 1402 nbur = 1934 mkacc time = 0.1200000 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 = 1.596000 m= 221 mr = 3291 m= 0 mr = 2 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2300000 number of dielectric boundary points 3250 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2956 ## 377 charges are in solution ## iepsmp to db, and charging done at 0.2900000 number of grid points assigned charge 8308 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -2.8800393E-10 -3.4571246E-10 midg,1,midg; midg,igrid,midg -2.0916438E-10 -6.6854389E-10 1,midg,midg; igrid,midg,midg -1.1644102E-09 -6.1343888E-11 gauss-seidel spectral radius is 0.9826270 estimated iterations to convergence 62 setup time was (sec) 0.4100000 now iterating at: 03:20:45 rms-change max change #iterations 7.7492811E-02 12.90106 at 10iterations 5.1895427E-03 0.9113636 at 20iterations 4.1719791E-04 6.0703278E-02 at 30iterations 6.3456770E-05 1.2258530E-02 at 40iterations 1.5417554E-05 3.3034086E-03 at 50iterations finished qdiffx linear iterations at : 03:20:48 total time elapsed so far: 3.250000 # loops : 50 mean,max change (kT/e) : 1.5417554E-05 3.3034086E-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) 3.390000 DelPhi exited at 03:20:48 3.392u 0.163s 0:03.88 91.4% 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 03:20:48 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 = 3336 !!! WARNING: ASN 165 has a net charge of -0.2720 !!! WARNING: GLU 499 has a net charge of -0.2720 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: 1.633152 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): 4.083000 69.47800 ymin,ymax (A): 31.77200 91.59000 zmin,zma (A): 24.33800 78.45700 x,y,z range (A): 65.39500 59.81800 54.11900 scale (grids/A): 1.633152 object centre (A): 36.78050 61.68100 51.39750 number of atom coordinates read : 3336 total number of charged atoms : 3196 net assigned charge : -6.543976 assigned positive charge : 501.5775 centred at (gu) : 82.92761 96.17640 83.88186 assigned negative charge : -508.1227 centred at (gu) : 82.81101 96.19025 83.96482 start vw surface at 0.1100000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 69761 reading accessible surface arcs data from file ARCDAT no. of arc points read = 29100 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 20830 mr = 47305 m= 1979 mr = 14321 m= 46 mr = 885 m= 0 mr = 3 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 638 time to turn everything in is 0.3500000 number of dielectric boundary points 30102 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 390 ## 4 charges are in solution ## iepsmp to db, and charging done at 0.4200000 number of grid points assigned charge 24398 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) : 0.5443841 object centre at (A) : 36.78050 61.68100 51.39750 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -4.0245824E-03 -3.1152528E-03 midg,1,midg; midg,igrid,midg -3.5972453E-03 -4.9135974E-03 1,midg,midg; igrid,midg,midg -1.5930269E-02 2.7080100E-02 gauss-seidel spectral radius is 0.9982070 estimated iterations to convergence 188 setup time was (sec) 0.5600000 now iterating at: 03:20:49 rms-change max change #iterations 3.550027 154.6370 at 10iterations 1.485081 58.55051 at 20iterations 0.6221893 22.34677 at 30iterations 0.2600161 8.932573 at 40iterations 0.1095572 3.736143 at 50iterations 4.5807820E-02 1.765125 at 60iterations 1.9257691E-02 0.7275696 at 70iterations 8.0692628E-03 0.2791154 at 80iterations 3.4040171E-03 0.1116445 at 90iterations 1.4343746E-03 5.2436352E-02 at 100iterations 6.1021204E-04 1.9927979E-02 at 110iterations 2.6269039E-04 9.9732876E-03 at 120iterations finished qdiffx linear iterations at : 03:20:56 total time elapsed so far: 7.550000 # loops : 120 mean,max change (kT/e) : 2.6269039E-04 9.9732876E-03 energy calculations done at 7.550000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.690000 DelPhi exited at 03:20:56 7.692u 0.192s 0:08.22 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 Tue Oct 11 2011 at 03:20:56 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 = 3336 !!! WARNING: ASN 165 has a net charge of -0.2720 !!! WARNING: GLU 499 has a net charge of -0.2720 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 2.449728 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): 4.083000 69.47800 ymin,ymax (A): 31.77200 91.59000 zmin,zma (A): 24.33800 78.45700 x,y,z range (A): 65.39500 59.81800 54.11900 scale (grids/A): 2.449728 object centre (A): 36.78050 61.68100 51.39750 number of atom coordinates read : 3336 total number of charged atoms : 3196 net assigned charge : -6.543976 assigned positive charge : 501.5775 centred at (gu) : 79.39115 99.26439 80.82261 assigned negative charge : -508.1227 centred at (gu) : 79.21647 99.28529 80.94732 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.3000000 boundary points on vw surface= 162224 reading accessible surface arcs data from file ARCDAT no. of arc points read = 29100 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 73342 mr = 115809 m= 19515 mr = 57943 m= 2934 mr = 14537 m= 178 mr = 1852 m= 5 mr = 67 m= 0 mr = 0 time to grow re-entrant surface = 0.4600000 no. cavity mid-points inaccessible to solvent = 2255 time to turn everything in is 0.8500000 number of dielectric boundary points 67990 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 26 iepsmp to db, and charging done at 0.9400000 number of grid points assigned charge 25535 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) : 1.633152 object centre at (A) : 36.78050 61.68100 51.39750 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -4.3193676E-02 -6.2087186E-02 midg,1,midg; midg,igrid,midg -5.0981515E-03 -2.3406954E-03 1,midg,midg; igrid,midg,midg -0.3509211 0.5239485 gauss-seidel spectral radius is 0.9991495 estimated iterations to convergence 271 setup time was (sec) 1.080000 now iterating at: 03:20:58 rms-change max change #iterations 9.202229 315.1588 at 10iterations 5.197770 129.8519 at 20iterations 2.914261 82.88253 at 30iterations 1.627768 36.77432 at 40iterations 0.9059961 18.63355 at 50iterations 0.5037738 11.16871 at 60iterations 0.2793310 5.841476 at 70iterations 0.1546677 3.758443 at 80iterations 8.5684471E-02 1.672548 at 90iterations 4.7398712E-02 1.017235 at 100iterations 2.6148146E-02 0.5388794 at 110iterations 1.4456630E-02 0.2841301 at 120iterations 8.0344696E-03 0.1536620 at 130iterations 4.4475966E-03 9.5703125E-02 at 140iterations 2.4711343E-03 4.8376083E-02 at 150iterations 1.3763697E-03 3.0509949E-02 at 160iterations 7.7647157E-04 1.6029358E-02 at 170iterations 4.4458004E-04 1.0361195E-02 at 180iterations finished qdiffx linear iterations at : 03:21:09 total time elapsed so far: 12.25000 # loops : 180 mean,max change (kT/e) : 4.4458004E-04 1.0361195E-02 energy calculations done at 12.25000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.38000 DelPhi exited at 03:21:09 12.381u 0.217s 0:12.92 97.4% 0+0k 0+0io 0pf+0w