Mon Oct 10 19:33:50 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+sph2.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 = amb2.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 Mon Oct 10 2011 at 19:33:50 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: 276 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2764 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 0.6381301 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): -5.138000 47.10000 ymin,ymax (A): -32.17000 23.61800 zmin,zma (A): -17.46300 37.06600 x,y,z range (A): 52.23800 55.78800 54.52900 scale (grids/A): 0.6381301 object centre (A): 20.98100 -4.276001 9.801501 number of atom coordinates read : 2764 total number of charged atoms : 2625 net assigned charge : 1.000027 assigned positive charge : 415.1565 centred at (gu) : 88.95525 91.44081 87.94917 assigned negative charge : -414.1577 centred at (gu) : 88.91335 91.50186 88.00880 start vw surface at 0.1700000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 7658 nv = 96 ne = 84 npr = 55183 no. pairs analyzed = 55183 no. exposed pairs = 3851 no. arc points = 26572 no. surface atoms = 1292 nbur = 1472 mkacc time = 0.1300000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 442 mr = 3897 m= 0 mr = 50 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3400000 number of dielectric boundary points 4153 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2569 ## 211 charges are in solution ## iepsmp to db, and charging done at 0.4600000 number of grid points assigned charge 9080 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.3075343E-08 -3.6081242E-09 midg,1,midg; midg,igrid,midg 6.2353300E-09 -8.0385494E-09 1,midg,midg; igrid,midg,midg -4.4927484E-09 5.0157647E-09 gauss-seidel spectral radius is 0.9872993 estimated iterations to convergence 73 setup time was (sec) 0.6000000 now iterating at: 19:33:51 rms-change max change #iterations 0.1464448 20.27696 at 10iterations 1.4893973E-02 2.016573 at 20iterations 1.8832209E-03 0.2409172 at 30iterations 5.2359438E-04 6.1727524E-02 at 40iterations 2.0262164E-04 2.4026871E-02 at 50iterations finished qdiffx linear iterations at : 19:33:54 total time elapsed so far: 3.470000 # loops : 50 mean,max change (kT/e) : 2.0262164E-04 2.4026871E-02 energy calculations done at 3.470000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.660000 DelPhi exited at 19:33:54 3.668u 0.206s 0:04.19 92.1% 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 Mon Oct 10 2011 at 19:33:54 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: 276 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2764 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 1.914390 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): -5.138000 47.10000 ymin,ymax (A): -32.17000 23.61800 zmin,zma (A): -17.46300 37.06600 x,y,z range (A): 52.23800 55.78800 54.52900 scale (grids/A): 1.914390 object centre (A): 20.98100 -4.276001 9.801501 number of atom coordinates read : 2764 total number of charged atoms : 2625 net assigned charge : 1.000027 assigned positive charge : 415.1565 centred at (gu) : 86.86536 94.32185 83.84686 assigned negative charge : -414.1577 centred at (gu) : 86.73980 94.50547 84.02608 start vw surface at 0.2000000 fill in re-entrant regions at 0.3200000 boundary points on vw surface= 82219 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26572 grid for indexing accessible points = 1.400000 m= 29140 mr = 55098 m= 4717 mr = 20448 m= 270 mr = 2724 m= 3 mr = 70 m= 0 mr = 0 time to grow re-entrant surface = 0.3000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.6600000 number of dielectric boundary points 38009 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 145 iepsmp to db, and charging done at 0.7900000 number of grid points assigned charge 20664 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) : 0.6381301 object centre at (A) : 20.98100 -4.276001 9.801501 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 6.0228009E-02 -9.8827248E-03 midg,1,midg; midg,igrid,midg 1.8109689E-02 -2.9805558E-02 1,midg,midg; igrid,midg,midg 6.9857072E-03 -4.0288935E-03 gauss-seidel spectral radius is 0.9986759 estimated iterations to convergence 218 setup time was (sec) 0.9500000 now iterating at: 19:33:55 rms-change max change #iterations 4.514547 204.8088 at 10iterations 2.133380 70.39665 at 20iterations 1.010875 35.06851 at 30iterations 0.4795239 13.96369 at 40iterations 0.2271201 6.985099 at 50iterations 0.1079747 3.216023 at 60iterations 5.0967291E-02 1.488225 at 70iterations 2.4349775E-02 0.7277050 at 80iterations 1.1609599E-02 0.3258438 at 90iterations 5.5617504E-03 0.1807728 at 100iterations 2.7349840E-03 8.1984520E-02 at 110iterations 1.3743599E-03 3.9710999E-02 at 120iterations finished qdiffx linear iterations at : 19:34:02 total time elapsed so far: 7.630000 # loops : 120 mean,max change (kT/e) : 1.3743599E-03 3.9710999E-02 energy calculations done at 7.630000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.810000 DelPhi exited at 19:34:03 7.816u 0.179s 0:08.29 96.2% 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 Mon Oct 10 2011 at 19:34:03 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: 276 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2764 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: 2.871585 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): -5.138000 47.10000 ymin,ymax (A): -32.17000 23.61800 zmin,zma (A): -17.46300 37.06600 x,y,z range (A): 52.23800 55.78800 54.52900 scale (grids/A): 2.871585 object centre (A): 20.98100 -4.276001 9.801501 number of atom coordinates read : 2764 total number of charged atoms : 2625 net assigned charge : 1.000027 assigned positive charge : 415.1565 centred at (gu) : 85.29783 96.48268 80.77033 assigned negative charge : -414.1577 centred at (gu) : 85.10971 96.75816 81.03905 start vw surface at 0.1500000 fill in re-entrant regions at 0.5100000 boundary points on vw surface= 190232 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26572 grid for indexing accessible points = 1.400000 m= 93705 mr = 134687 m= 34432 mr = 74317 m= 8289 mr = 26600 m= 1115 mr = 5824 m= 51 mr = 627 m= 2 mr = 14 m= 0 mr = 0 time to grow re-entrant surface = 0.9800000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.620000 number of dielectric boundary points 85757 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.770000 number of grid points assigned charge 21000 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) : 1.914390 object centre at (A) : 20.98100 -4.276001 9.801501 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.4998953 -0.2011309 midg,1,midg; midg,igrid,midg 0.3508644 -0.2855586 1,midg,midg; igrid,midg,midg 0.1868489 -0.1600858 gauss-seidel spectral radius is 0.9992850 estimated iterations to convergence 295 setup time was (sec) 1.970000 now iterating at: 19:34:05 rms-change max change #iterations 10.67135 358.9690 at 10iterations 6.354900 139.1259 at 20iterations 3.762169 83.07343 at 30iterations 2.216240 42.92129 at 40iterations 1.303154 24.66014 at 50iterations 0.7630181 13.82998 at 60iterations 0.4468026 7.965458 at 70iterations 0.2611889 4.756981 at 80iterations 0.1522417 2.943064 at 90iterations 8.8864528E-02 1.615562 at 100iterations 5.1754165E-02 1.062571 at 110iterations 3.0167388E-02 0.5321026 at 120iterations 1.7611206E-02 0.2996057 at 130iterations 1.0321787E-02 0.2081470 at 140iterations 6.0649971E-03 0.1092281 at 150iterations 3.6121472E-03 6.5996170E-02 at 160iterations 2.1967336E-03 4.6698779E-02 at 170iterations 1.3861753E-03 2.6159286E-02 at 180iterations finished qdiffx linear iterations at : 19:34:17 total time elapsed so far: 13.97000 # loops : 180 mean,max change (kT/e) : 1.3861753E-03 2.6159286E-02 energy calculations done at 13.97000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 14.16000 DelPhi exited at 19:34:17 14.161u 0.278s 0:14.76 97.7% 0+0k 0+0io 0pf+0w