Sun Oct 9 23:49:43 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 Sun Oct 9 2011 at 23:49:43 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 = 3150 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: 0.5875654 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): -30.06900 30.52000 ymin,ymax (A): 7.915000 62.06600 zmin,zma (A): 24.87000 77.28800 x,y,z range (A): 60.58900 54.15100 52.41800 scale (grids/A): 0.5875654 object centre (A): 0.2255001 34.99050 51.07900 number of atom coordinates read : 3150 total number of charged atoms : 3005 net assigned charge : 0.5000069 assigned positive charge : 473.9809 centred at (gu) : 90.04128 88.98104 89.02033 assigned negative charge : -473.4822 centred at (gu) : 90.07288 89.01154 89.13244 start vw surface at 0.1000000 fill in re-entrant regions at 0.1000000 boundary points on vw surface= 7238 nv = 96 ne = 84 npr = 62504 no. pairs analyzed = 62504 no. exposed pairs = 4072 no. arc points = 29038 no. surface atoms = 1359 nbur = 1791 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= 322 mr = 3808 m= 2 mr = 14 m= 0 mr = 0 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 40 time to turn everything in is 0.2300000 number of dielectric boundary points 3740 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2890 ## 315 charges are in solution ## iepsmp to db, and charging done at 0.2900000 number of grid points assigned charge 9160 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 4.3057402E-09 -2.6304539E-09 midg,1,midg; midg,igrid,midg 1.2812799E-09 -6.4577743E-10 1,midg,midg; igrid,midg,midg 1.0311034E-09 -8.6368129E-10 gauss-seidel spectral radius is 0.9850666 estimated iterations to convergence 67 setup time was (sec) 0.4300000 now iterating at: 23:49:44 rms-change max change #iterations 0.1088160 18.36485 at 10iterations 8.8421935E-03 1.173540 at 20iterations 7.1185536E-04 9.9504471E-02 at 30iterations 5.8652531E-05 9.2506409E-03 at 40iterations 5.5329365E-06 8.4590912E-04 at 50iterations finished qdiffx linear iterations at : 23:49:47 total time elapsed so far: 3.350000 # loops : 50 mean,max change (kT/e) : 5.5329365E-06 8.4590912E-04 energy calculations done at 3.350000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.490000 DelPhi exited at 23:49:47 3.492u 0.169s 0:03.94 92.6% 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 23:49:47 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 = 3150 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: 1.762696 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): -30.06900 30.52000 ymin,ymax (A): 7.915000 62.06600 zmin,zma (A): 24.87000 77.28800 x,y,z range (A): 60.58900 54.15100 52.41800 scale (grids/A): 1.762696 object centre (A): 0.2255001 34.99050 51.07900 number of atom coordinates read : 3150 total number of charged atoms : 3005 net assigned charge : 0.5000069 assigned positive charge : 473.9809 centred at (gu) : 90.12292 86.94232 87.06023 assigned negative charge : -473.4822 centred at (gu) : 90.21841 87.03432 87.39718 start vw surface at 5.9999999E-02 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 79584 reading accessible surface arcs data from file ARCDAT no. of arc points read = 29038 grid for indexing accessible points = 1.400000 m= 25440 mr = 54092 m= 3122 mr = 17709 m= 112 mr = 1667 m= 3 mr = 14 m= 0 mr = 0 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 2437 time to turn everything in is 0.3500000 number of dielectric boundary points 34779 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 270 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.4200000 number of grid points assigned charge 23375 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) : 0.5875654 object centre at (A) : 0.2255001 34.99050 51.07900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.0155835E-02 -2.7525653E-03 midg,1,midg; midg,igrid,midg 9.0048062E-03 7.9034735E-03 1,midg,midg; igrid,midg,midg 1.4428956E-02 -5.5093677E-03 gauss-seidel spectral radius is 0.9984802 estimated iterations to convergence 203 setup time was (sec) 0.5500000 now iterating at: 23:49:48 rms-change max change #iterations 4.057182 175.4269 at 10iterations 1.819703 60.77145 at 20iterations 0.8103684 28.86418 at 30iterations 0.3641850 12.31586 at 40iterations 0.1634274 5.406925 at 50iterations 7.3420502E-02 2.362404 at 60iterations 3.2955579E-02 1.043897 at 70iterations 1.4767363E-02 0.4633904 at 80iterations 6.6323713E-03 0.2141681 at 90iterations 2.9734466E-03 0.1002655 at 100iterations 1.3376412E-03 4.4954300E-02 at 110iterations 6.0132350E-04 2.0278931E-02 at 120iterations finished qdiffx linear iterations at : 23:49:55 total time elapsed so far: 7.750000 # loops : 120 mean,max change (kT/e) : 6.0132350E-04 2.0278931E-02 energy calculations done at 7.750000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.880000 DelPhi exited at 23:49:56 7.880u 0.257s 0:08.51 95.5% 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 Sun Oct 9 2011 at 23:49:56 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 = 3150 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: 2.644044 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): -30.06900 30.52000 ymin,ymax (A): 7.915000 62.06600 zmin,zma (A): 24.87000 77.28800 x,y,z range (A): 60.58900 54.15100 52.41800 scale (grids/A): 2.644044 object centre (A): 0.2255001 34.99050 51.07900 number of atom coordinates read : 3150 total number of charged atoms : 3005 net assigned charge : 0.5000069 assigned positive charge : 473.9809 centred at (gu) : 90.18419 85.41322 85.59006 assigned negative charge : -473.4822 centred at (gu) : 90.32751 85.55128 86.09556 start vw surface at 0.1000000 fill in re-entrant regions at 0.3400000 boundary points on vw surface= 184565 reading accessible surface arcs data from file ARCDAT no. of arc points read = 29038 grid for indexing accessible points = 1.400000 m= 86208 mr = 131823 m= 26555 mr = 68597 m= 5104 mr = 20290 m= 421 mr = 3515 m= 6 mr = 206 m= 0 mr = 0 time to grow re-entrant surface = 0.5500000 no. cavity mid-points inaccessible to solvent = 8309 time to turn everything in is 0.9700000 number of dielectric boundary points 78428 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4 iepsmp to db, and charging done at 1.060000 number of grid points assigned charge 24028 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) : 1.762696 object centre at (A) : 0.2255001 34.99050 51.07900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1428779 1.2254269E-02 midg,1,midg; midg,igrid,midg 8.2245007E-02 0.1613404 1,midg,midg; igrid,midg,midg 0.1584078 -8.2168348E-02 gauss-seidel spectral radius is 0.9992394 estimated iterations to convergence 286 setup time was (sec) 1.210000 now iterating at: 23:49:57 rms-change max change #iterations 10.11221 305.5943 at 10iterations 5.935702 166.7996 at 20iterations 3.461163 78.73714 at 30iterations 2.008172 39.59524 at 40iterations 1.156641 24.33498 at 50iterations 0.6686206 13.65551 at 60iterations 0.3844551 7.863162 at 70iterations 0.2207064 4.249144 at 80iterations 0.1266286 2.306389 at 90iterations 7.2649837E-02 1.470490 at 100iterations 4.1552149E-02 0.8288670 at 110iterations 2.3769679E-02 0.4825354 at 120iterations 1.3594832E-02 0.2436452 at 130iterations 7.7722566E-03 0.1407089 at 140iterations 4.4266717E-03 8.4090471E-02 at 150iterations 2.5336077E-03 4.7262281E-02 at 160iterations 1.4501039E-03 2.8703213E-02 at 170iterations 8.2980271E-04 1.9748211E-02 at 180iterations finished qdiffx linear iterations at : 23:50:09 total time elapsed so far: 12.68000 # loops : 180 mean,max change (kT/e) : 8.2980271E-04 1.9748211E-02 energy calculations done at 12.68000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.81000 DelPhi exited at 23:50:09 12.812u 0.205s 0:13.28 97.9% 0+0k 0+0io 0pf+0w