Thu Mar 1 19:29:40 PST 2012 #!/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 Thu Mar 1 2012 at 19:29:40 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: 232 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3246 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: 0.5983897 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): -2.483000 57.01000 ymin,ymax (A): -23.57600 26.93400 zmin,zma (A): -9.933001 45.28400 x,y,z range (A): 59.49300 50.51000 55.21700 scale (grids/A): 0.5983897 object centre (A): 27.26350 1.679000 17.67550 number of atom coordinates read : 3246 total number of charged atoms : 3101 net assigned charge : 4.500019 assigned positive charge : 486.4337 centred at (gu) : 91.92618 88.89387 90.13855 assigned negative charge : -481.9352 centred at (gu) : 91.94933 88.92176 90.13419 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1000000 boundary points on vw surface= 7513 nv = 96 ne = 84 npr = 67473 no. pairs analyzed = 67473 no. exposed pairs = 3670 no. arc points = 25852 no. surface atoms = 1245 nbur = 2001 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 = 1.456000 m= 339 mr = 4282 m= 2 mr = 20 m= 0 mr = 0 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 6 time to turn everything in is 0.2300000 number of dielectric boundary points 3552 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2678 ## 296 charges are in solution ## iepsmp to db, and charging done at 0.3000000 number of grid points assigned charge 9684 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.5891983E-09 2.0747093E-09 midg,1,midg; midg,igrid,midg 3.8744732E-09 5.0339810E-10 1,midg,midg; igrid,midg,midg 1.8366908E-09 1.2390419E-09 gauss-seidel spectral radius is 0.9855935 estimated iterations to convergence 68 setup time was (sec) 0.4200000 now iterating at: 19:29:41 rms-change max change #iterations 0.1185170 19.56540 at 10iterations 1.0179468E-02 1.445892 at 20iterations 8.9588331E-04 0.1254883 at 30iterations 9.1696515E-05 1.3834953E-02 at 40iterations 1.3833436E-05 2.0494461E-03 at 50iterations finished qdiffx linear iterations at : 19:29:44 total time elapsed so far: 3.340000 # loops : 50 mean,max change (kT/e) : 1.3833436E-05 2.0494461E-03 energy calculations done at 3.340000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.470000 DelPhi exited at 19:29:44 3.477u 0.179s 0:03.91 93.0% 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 Thu Mar 1 2012 at 19:29:44 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: 232 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3246 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: 1.795169 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): -2.483000 57.01000 ymin,ymax (A): -23.57600 26.93400 zmin,zma (A): -9.933001 45.28400 x,y,z range (A): 59.49300 50.51000 55.21700 scale (grids/A): 1.795169 object centre (A): 27.26350 1.679000 17.67550 number of atom coordinates read : 3246 total number of charged atoms : 3101 net assigned charge : 4.500019 assigned positive charge : 486.4337 centred at (gu) : 95.77748 86.68049 90.41444 assigned negative charge : -481.9352 centred at (gu) : 95.84776 86.76504 90.40222 start vw surface at 0.1000000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 83580 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25852 grid for indexing accessible points = 1.400000 m= 28361 mr = 60041 m= 3523 mr = 20626 m= 137 mr = 2037 m= 1 mr = 30 m= 0 mr = 0 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 1554 time to turn everything in is 0.4000000 number of dielectric boundary points 32868 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 192 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.4700000 number of grid points assigned charge 24185 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) : 0.5983897 object centre at (A) : 27.26350 1.679000 17.67550 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.1492753E-03 -1.1470379E-02 midg,1,midg; midg,igrid,midg 6.7446665E-03 4.0507410E-03 1,midg,midg; igrid,midg,midg 3.0517045E-02 1.5976731E-02 gauss-seidel spectral radius is 0.9985207 estimated iterations to convergence 206 setup time was (sec) 0.6100000 now iterating at: 19:29:45 rms-change max change #iterations 4.219980 183.0925 at 10iterations 1.915839 97.79214 at 20iterations 0.8671836 27.72249 at 30iterations 0.3958579 12.53688 at 40iterations 0.1798479 5.623419 at 50iterations 8.1933953E-02 3.069373 at 60iterations 3.7179928E-02 1.242783 at 70iterations 1.6903348E-02 0.5549297 at 80iterations 7.7010202E-03 0.2356033 at 90iterations 3.5065436E-03 0.1040974 at 100iterations 1.6006266E-03 5.1508427E-02 at 110iterations 7.2866603E-04 2.1581650E-02 at 120iterations finished qdiffx linear iterations at : 19:29:53 total time elapsed so far: 7.930000 # loops : 120 mean,max change (kT/e) : 7.2866603E-04 2.1581650E-02 energy calculations done at 7.930000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.060000 DelPhi exited at 19:29:53 8.066u 0.238s 0:08.59 96.5% 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 Thu Mar 1 2012 at 19:29:53 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: 232 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3246 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: 2.692754 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): -2.483000 57.01000 ymin,ymax (A): -23.57600 26.93400 zmin,zma (A): -9.933001 45.28400 x,y,z range (A): 59.49300 50.51000 55.21700 scale (grids/A): 2.692754 object centre (A): 27.26350 1.679000 17.67550 number of atom coordinates read : 3246 total number of charged atoms : 3101 net assigned charge : 4.500019 assigned positive charge : 486.4337 centred at (gu) : 98.66622 85.02072 90.62141 assigned negative charge : -481.9352 centred at (gu) : 98.77148 85.14742 90.60321 start vw surface at 0.1000000 fill in re-entrant regions at 0.3600000 boundary points on vw surface= 193843 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25852 grid for indexing accessible points = 1.400000 m= 95462 mr = 145169 m= 30718 mr = 78240 m= 6105 mr = 24419 m= 558 mr = 4357 m= 16 mr = 270 m= 0 mr = 1 time to grow re-entrant surface = 0.5800000 no. cavity mid-points inaccessible to solvent = 5070 time to turn everything in is 1.030000 number of dielectric boundary points 74246 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 7 iepsmp to db, and charging done at 1.120000 number of grid points assigned charge 24799 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) : 1.795169 object centre at (A) : 27.26350 1.679000 17.67550 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -3.5162926E-02 -0.1926595 midg,1,midg; midg,igrid,midg 7.2229598E-03 6.2928587E-02 1,midg,midg; igrid,midg,midg 0.3604270 0.2996906 gauss-seidel spectral radius is 0.9992349 estimated iterations to convergence 285 setup time was (sec) 1.270000 now iterating at: 19:29:54 rms-change max change #iterations 10.11585 362.5876 at 10iterations 5.822264 111.0407 at 20iterations 3.329735 63.74281 at 30iterations 1.906920 33.74806 at 40iterations 1.087733 19.72066 at 50iterations 0.6207551 10.76648 at 60iterations 0.3544606 6.181457 at 70iterations 0.2018936 3.539002 at 80iterations 0.1148860 1.943512 at 90iterations 6.5496072E-02 1.099506 at 100iterations 3.7340034E-02 0.6274910 at 110iterations 2.1238128E-02 0.4296875 at 120iterations 1.2110320E-02 0.2068577 at 130iterations 6.8999459E-03 0.1289845 at 140iterations 3.9492762E-03 6.8485260E-02 at 150iterations 2.2617579E-03 3.8711071E-02 at 160iterations 1.2946369E-03 2.2441149E-02 at 170iterations 7.4739393E-04 1.3450623E-02 at 180iterations finished qdiffx linear iterations at : 19:30:06 total time elapsed so far: 12.91000 # loops : 180 mean,max change (kT/e) : 7.4739393E-04 1.3450623E-02 energy calculations done at 12.91000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.04000 DelPhi exited at 19:30:07 13.041u 0.250s 0:13.69 97.0% 0+0k 0+0io 0pf+0w