Mon Oct 10 14:08:10 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 14:08:10 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: 245 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2289 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: 0.6897220 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): -20.10600 31.50900 ymin,ymax (A): -62.32200 -12.37100 zmin,zma (A): -8.168000 42.03300 x,y,z range (A): 51.61500 49.95100 50.20100 scale (grids/A): 0.6897220 object centre (A): 5.701500 -37.34650 16.93250 number of atom coordinates read : 2289 total number of charged atoms : 2154 net assigned charge : -4.499990 assigned positive charge : 342.5693 centred at (gu) : 89.15277 90.57937 89.61461 assigned negative charge : -347.0699 centred at (gu) : 89.35327 90.55556 89.55088 start vw surface at 0.1700000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 7626 nv = 96 ne = 84 npr = 45834 no. pairs analyzed = 45834 no. exposed pairs = 3069 no. arc points = 21459 no. surface atoms = 1043 nbur = 1246 mkacc time = 0.1400000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 504 mr = 4091 m= 1 mr = 87 m= 0 mr = 0 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3500000 number of dielectric boundary points 3953 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1894 ## 144 charges are in solution ## iepsmp to db, and charging done at 0.4800000 number of grid points assigned charge 8435 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -5.2656375E-08 -1.9985942E-09 midg,1,midg; midg,igrid,midg -3.0373627E-08 -1.8451184E-08 1,midg,midg; igrid,midg,midg 5.5919742E-08 -8.4615742E-08 gauss-seidel spectral radius is 0.9890816 estimated iterations to convergence 78 setup time was (sec) 0.6400000 now iterating at: 14:08:11 rms-change max change #iterations 0.1889699 24.62431 at 10iterations 2.1963410E-02 3.081099 at 20iterations 2.5614982E-03 0.3831940 at 30iterations 3.0176534E-04 4.1915894E-02 at 40iterations 3.7062546E-05 5.0334930E-03 at 50iterations finished qdiffx linear iterations at : 14:08:14 total time elapsed so far: 4.070000 # loops : 50 mean,max change (kT/e) : 3.7062546E-05 5.0334930E-03 energy calculations done at 4.070000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.310000 DelPhi exited at 14:08:15 4.314u 0.246s 0:05.27 86.3% 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 Mon Oct 10 2011 at 14:08:15 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: 245 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2289 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: 2.069166 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): -20.10600 31.50900 ymin,ymax (A): -62.32200 -12.37100 zmin,zma (A): -8.168000 42.03300 x,y,z range (A): 51.61500 49.95100 50.20100 scale (grids/A): 2.069166 object centre (A): 5.701500 -37.34650 16.93250 number of atom coordinates read : 2289 total number of charged atoms : 2154 net assigned charge : -4.499990 assigned positive charge : 342.5693 centred at (gu) : 87.45811 91.73784 88.84348 assigned negative charge : -347.0699 centred at (gu) : 88.05981 91.66643 88.65258 start vw surface at 0.1900000 fill in re-entrant regions at 0.3400000 boundary points on vw surface= 80635 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21459 grid for indexing accessible points = 1.400000 m= 30928 mr = 54996 m= 5999 mr = 22810 m= 509 mr = 3887 m= 8 mr = 244 m= 0 mr = 0 time to grow re-entrant surface = 0.3800000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.7800000 number of dielectric boundary points 36142 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 76 iepsmp to db, and charging done at 0.9300000 number of grid points assigned charge 17118 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) : 0.6897220 object centre at (A) : 5.701500 -37.34650 16.93250 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -4.5583174E-02 -2.7675308E-02 midg,1,midg; midg,igrid,midg -9.5324283E-03 -1.3017338E-02 1,midg,midg; igrid,midg,midg -9.6657639E-03 -1.4615470E-02 gauss-seidel spectral radius is 0.9988157 estimated iterations to convergence 230 setup time was (sec) 1.140000 now iterating at: 14:08:17 rms-change max change #iterations 4.684726 260.0017 at 10iterations 2.289741 90.10124 at 20iterations 1.128230 36.70043 at 30iterations 0.5550858 18.84796 at 40iterations 0.2729380 8.829374 at 50iterations 0.1348376 4.170772 at 60iterations 6.6581927E-02 2.021848 at 70iterations 3.2773264E-02 0.9749947 at 80iterations 1.6108664E-02 0.4663162 at 90iterations 7.9605868E-03 0.2317705 at 100iterations 3.9324150E-03 0.1228638 at 110iterations 1.9380399E-03 5.4430962E-02 at 120iterations finished qdiffx linear iterations at : 14:08:25 total time elapsed so far: 9.670000 # loops : 120 mean,max change (kT/e) : 1.9380399E-03 5.4430962E-02 energy calculations done at 9.670000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.910000 DelPhi exited at 14:08:26 9.910u 0.265s 0:10.90 93.3% 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 Mon Oct 10 2011 at 14:08:26 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: 245 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2289 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: 3.103749 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): -20.10600 31.50900 ymin,ymax (A): -62.32200 -12.37100 zmin,zma (A): -8.168000 42.03300 x,y,z range (A): 51.61500 49.95100 50.20100 scale (grids/A): 3.103749 object centre (A): 5.701500 -37.34650 16.93250 number of atom coordinates read : 2289 total number of charged atoms : 2154 net assigned charge : -4.499990 assigned positive charge : 342.5693 centred at (gu) : 86.18709 92.60676 88.26516 assigned negative charge : -347.0699 centred at (gu) : 87.08980 92.49969 87.97891 start vw surface at 0.1800000 fill in re-entrant regions at 1.080000 boundary points on vw surface= 186014 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21459 grid for indexing accessible points = 1.400000 m= 96396 mr = 133293 m= 39049 mr = 78600 m= 11221 mr = 31521 m= 2165 mr = 8535 m= 202 mr = 1530 m= 10 mr = 100 m= 0 mr = 0 time to grow re-entrant surface = 1.210000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 2.450000 number of dielectric boundary points 81478 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.630000 number of grid points assigned charge 17232 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) : 2.069166 object centre at (A) : 5.701500 -37.34650 16.93250 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1466645 -0.5283282 midg,1,midg; midg,igrid,midg 1.0070495E-03 6.2110503E-03 1,midg,midg; igrid,midg,midg -0.5987438 -3.7999459E-02 gauss-seidel spectral radius is 0.9993063 estimated iterations to convergence 300 setup time was (sec) 2.840000 now iterating at: 14:08:29 rms-change max change #iterations 10.73799 382.7980 at 10iterations 6.419488 134.0137 at 20iterations 3.832336 85.60965 at 30iterations 2.281573 46.47433 at 40iterations 1.351519 25.19391 at 50iterations 0.7998723 13.90623 at 60iterations 0.4724785 8.556052 at 70iterations 0.2780982 5.141036 at 80iterations 0.1636110 2.749527 at 90iterations 9.6191160E-02 1.625642 at 100iterations 5.6573268E-02 1.039363 at 110iterations 3.3125266E-02 0.6142788 at 120iterations 1.9468177E-02 0.3405104 at 130iterations 1.1419527E-02 0.1829529 at 140iterations 6.6985418E-03 0.1264038 at 150iterations 3.9400505E-03 6.9227219E-02 at 160iterations 2.3140656E-03 3.9339066E-02 at 170iterations 1.3617261E-03 2.3492336E-02 at 180iterations finished qdiffx linear iterations at : 14:08:44 total time elapsed so far: 17.60000 # loops : 180 mean,max change (kT/e) : 1.3617261E-03 2.3492336E-02 energy calculations done at 17.60000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 17.84000 DelPhi exited at 14:08:45 17.846u 0.264s 0:18.97 95.4% 0+0k 0+0io 0pf+0w