Sun Oct 9 11:47:25 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 Sun Oct 9 2011 at 11:47:25 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: 262 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2742 !!! WARNING: HIR 203 has a net charge of 0.5140 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: 0.6651222 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): -5.104000 47.36600 ymin,ymax (A): 8.745001 59.89600 zmin,zma (A): 5.613000 59.13700 x,y,z range (A): 52.47000 51.15100 53.52400 scale (grids/A): 0.6651222 object centre (A): 21.13100 34.32050 32.37500 number of atom coordinates read : 2742 total number of charged atoms : 2664 net assigned charge : 3.014008 assigned positive charge : 410.1260 centred at (gu) : 90.77233 90.07264 90.72153 assigned negative charge : -407.1136 centred at (gu) : 90.89593 90.02901 90.68961 start vw surface at 0.1600000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 8667 nv = 96 ne = 84 npr = 52752 no. pairs analyzed = 52752 no. exposed pairs = 3814 no. arc points = 27378 no. surface atoms = 1275 nbur = 1467 mkacc time = 0.1200000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 593 mr = 4466 m= 6 mr = 88 m= 0 mr = 0 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3100000 number of dielectric boundary points 4712 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2538 ## 170 charges are in solution ## iepsmp to db, and charging done at 0.4200000 number of grid points assigned charge 9959 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.2876393E-09 1.9140019E-08 midg,1,midg; midg,igrid,midg -1.3364075E-09 1.9535527E-08 1,midg,midg; igrid,midg,midg 3.2218832E-08 -2.4355829E-08 gauss-seidel spectral radius is 0.9883180 estimated iterations to convergence 75 setup time was (sec) 0.5300000 now iterating at: 11:47:26 rms-change max change #iterations 0.1753371 25.70428 at 10iterations 1.8715268E-02 2.728159 at 20iterations 2.0783492E-03 0.2946119 at 30iterations 2.2964967E-04 2.9501915E-02 at 40iterations 3.8685521E-05 5.8488846E-03 at 50iterations finished qdiffx linear iterations at : 11:47:28 total time elapsed so far: 3.020000 # loops : 50 mean,max change (kT/e) : 3.8685521E-05 5.8488846E-03 energy calculations done at 3.020000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.190000 DelPhi exited at 11:47:29 3.190u 0.161s 0:03.63 92.2% 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 Sun Oct 9 2011 at 11:47:29 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: 262 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2742 !!! WARNING: HIR 203 has a net charge of 0.5140 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: 1.995366 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): -5.104000 47.36600 ymin,ymax (A): 8.745001 59.89600 zmin,zma (A): 5.613000 59.13700 x,y,z range (A): 52.47000 51.15100 53.52400 scale (grids/A): 1.995366 object centre (A): 21.13100 34.32050 32.37500 number of atom coordinates read : 2742 total number of charged atoms : 2664 net assigned charge : 3.014008 assigned positive charge : 410.1260 centred at (gu) : 92.31641 90.21690 92.16351 assigned negative charge : -407.1136 centred at (gu) : 92.68780 90.08701 92.06862 start vw surface at 0.1500000 fill in re-entrant regions at 0.2700000 boundary points on vw surface= 91680 reading accessible surface arcs data from file ARCDAT no. of arc points read = 27378 grid for indexing accessible points = 1.400000 m= 34687 mr = 61112 m= 7029 mr = 24747 m= 571 mr = 4446 m= 10 mr = 210 m= 0 mr = 0 time to grow re-entrant surface = 0.3200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.6300000 number of dielectric boundary points 43462 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 123 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.7500000 number of grid points assigned charge 21080 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) : 0.6651222 object centre at (A) : 21.13100 34.32050 32.37500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 9.6886251E-03 3.3037145E-02 midg,1,midg; midg,igrid,midg -1.3344443E-02 2.5041072E-02 1,midg,midg; igrid,midg,midg 3.5411190E-02 -9.0559209E-03 gauss-seidel spectral radius is 0.9987985 estimated iterations to convergence 228 setup time was (sec) 0.9000000 now iterating at: 11:47:30 rms-change max change #iterations 4.818017 181.1228 at 10iterations 2.358815 70.81961 at 20iterations 1.153524 31.46958 at 30iterations 0.5666013 17.06580 at 40iterations 0.2775102 7.729802 at 50iterations 0.1363064 3.856090 at 60iterations 6.6791020E-02 2.088612 at 70iterations 3.2849099E-02 0.9698792 at 80iterations 1.6068295E-02 0.4381409 at 90iterations 7.8874305E-03 0.2129192 at 100iterations 3.8654578E-03 0.1113319 at 110iterations 1.9038451E-03 5.9892654E-02 at 120iterations finished qdiffx linear iterations at : 11:47:36 total time elapsed so far: 7.260000 # loops : 120 mean,max change (kT/e) : 1.9038451E-03 5.9892654E-02 energy calculations done at 7.260000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.430000 DelPhi exited at 11:47:37 7.432u 0.212s 0:07.92 96.4% 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 Sun Oct 9 2011 at 11:47:37 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: 262 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2742 !!! WARNING: HIR 203 has a net charge of 0.5140 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: 2.993050 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): -5.104000 47.36600 ymin,ymax (A): 8.745001 59.89600 zmin,zma (A): 5.613000 59.13700 x,y,z range (A): 52.47000 51.15100 53.52400 scale (grids/A): 2.993050 object centre (A): 21.13100 34.32050 32.37500 number of atom coordinates read : 2742 total number of charged atoms : 2664 net assigned charge : 3.014008 assigned positive charge : 410.1260 centred at (gu) : 93.47446 90.32513 93.24518 assigned negative charge : -407.1136 centred at (gu) : 94.03165 90.13051 93.10312 start vw surface at 0.1500000 fill in re-entrant regions at 0.5100000 boundary points on vw surface= 211492 reading accessible surface arcs data from file ARCDAT no. of arc points read = 27378 grid for indexing accessible points = 1.400000 m= 107441 mr = 148672 m= 43856 mr = 85609 m= 13226 mr = 34836 m= 2405 mr = 9850 m= 212 mr = 1591 m= 3 mr = 94 m= 0 mr = 0 time to grow re-entrant surface = 1.010000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.650000 number of dielectric boundary points 97983 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.790000 number of grid points assigned charge 21312 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) : 1.995366 object centre at (A) : 21.13100 34.32050 32.37500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.8249003E-02 0.3752421 midg,1,midg; midg,igrid,midg -6.5852180E-02 0.2835118 1,midg,midg; igrid,midg,midg 0.3134284 0.1375425 gauss-seidel spectral radius is 0.9993263 estimated iterations to convergence 304 setup time was (sec) 1.950000 now iterating at: 11:47:39 rms-change max change #iterations 11.34064 464.6511 at 10iterations 6.914415 179.5627 at 20iterations 4.180745 84.75627 at 30iterations 2.520149 51.46844 at 40iterations 1.510905 34.27918 at 50iterations 0.9030387 20.87442 at 60iterations 0.5372816 10.46648 at 70iterations 0.3199826 5.837067 at 80iterations 0.1900458 3.131392 at 90iterations 0.1128611 1.907049 at 100iterations 6.6910602E-02 1.104917 at 110iterations 3.9594844E-02 0.7462566 at 120iterations 2.3434935E-02 0.4055634 at 130iterations 1.3861278E-02 0.2412090 at 140iterations 8.1895897E-03 0.1621017 at 150iterations 4.8419293E-03 7.7522278E-02 at 160iterations 2.8623615E-03 4.7359467E-02 at 170iterations 1.6882307E-03 2.6880264E-02 at 180iterations finished qdiffx linear iterations at : 11:47:50 total time elapsed so far: 12.88000 # loops : 180 mean,max change (kT/e) : 1.6882307E-03 2.6880264E-02 energy calculations done at 12.88000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.05000 DelPhi exited at 11:47:50 13.053u 0.186s 0:13.54 97.7% 0+0k 0+0io 0pf+0w