Mon Oct 10 00:55:50 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 00:55:50 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: 280 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2240 !!! WARNING: HIR 127 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: 0.6900696 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): -9.304000 42.28500 ymin,ymax (A): -52.29900 -3.393000 zmin,zma (A): -22.73500 25.21900 x,y,z range (A): 51.58900 48.90600 47.95400 scale (grids/A): 0.6900696 object centre (A): 16.49050 -27.84600 1.242001 number of atom coordinates read : 2240 total number of charged atoms : 2098 net assigned charge : 5.014012 assigned positive charge : 334.2104 centred at (gu) : 88.66264 89.00871 89.72650 assigned negative charge : -329.1968 centred at (gu) : 88.54694 89.00427 89.72031 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 7470 nv = 96 ne = 84 npr = 44273 no. pairs analyzed = 44273 no. exposed pairs = 3145 no. arc points = 21309 no. surface atoms = 1051 nbur = 1189 mkacc time = 9.9999994E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 490 mr = 3961 m= 5 mr = 80 m= 0 mr = 0 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2800000 number of dielectric boundary points 3924 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1904 ## 159 charges are in solution ## iepsmp to db, and charging done at 0.3900000 number of grid points assigned charge 8250 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.7605742E-08 2.8951533E-08 midg,1,midg; midg,igrid,midg 3.2458757E-08 2.4726148E-08 1,midg,midg; igrid,midg,midg -1.7157491E-08 5.2464205E-08 gauss-seidel spectral radius is 0.9890876 estimated iterations to convergence 78 setup time was (sec) 0.5300000 now iterating at: 00:55:51 rms-change max change #iterations 0.1926664 28.56370 at 10iterations 2.2310257E-02 3.218460 at 20iterations 2.6385635E-03 0.3663940 at 30iterations 3.0488704E-04 3.8031578E-02 at 40iterations 3.6948699E-05 5.6924820E-03 at 50iterations finished qdiffx linear iterations at : 00:55:53 total time elapsed so far: 3.220000 # loops : 50 mean,max change (kT/e) : 3.6948699E-05 5.6924820E-03 energy calculations done at 3.220000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.380000 DelPhi exited at 00:55:54 3.386u 0.199s 0:03.86 92.4% 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 Mon Oct 10 2011 at 00:55:54 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: 280 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2240 !!! WARNING: HIR 127 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: 2.070209 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): -9.304000 42.28500 ymin,ymax (A): -52.29900 -3.393000 zmin,zma (A): -22.73500 25.21900 x,y,z range (A): 51.58900 48.90600 47.95400 scale (grids/A): 2.070209 object centre (A): 16.49050 -27.84600 1.242001 number of atom coordinates read : 2240 total number of charged atoms : 2098 net assigned charge : 5.014012 assigned positive charge : 334.2104 centred at (gu) : 85.98791 87.02596 89.17923 assigned negative charge : -329.1968 centred at (gu) : 85.64073 87.01263 89.16097 start vw surface at 0.1400000 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 79044 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21309 grid for indexing accessible points = 1.400000 m= 29823 mr = 53382 m= 5890 mr = 21732 m= 523 mr = 3864 m= 15 mr = 236 m= 0 mr = 0 time to grow re-entrant surface = 0.2800000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5700000 number of dielectric boundary points 36081 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 66 iepsmp to db, and charging done at 0.6900000 number of grid points assigned charge 16644 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) : 0.6900696 object centre at (A) : 16.49050 -27.84600 1.242001 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 6.1459240E-02 2.5828904E-02 midg,1,midg; midg,igrid,midg 1.1618108E-02 -2.0815557E-02 1,midg,midg; igrid,midg,midg 2.0920301E-02 4.1027404E-02 gauss-seidel spectral radius is 0.9988170 estimated iterations to convergence 230 setup time was (sec) 0.8600000 now iterating at: 00:55:55 rms-change max change #iterations 4.575303 191.6810 at 10iterations 2.254592 77.94964 at 20iterations 1.115114 40.45775 at 30iterations 0.5497902 20.54365 at 40iterations 0.2704341 8.462339 at 50iterations 0.1335529 3.946347 at 60iterations 6.5604232E-02 1.946874 at 70iterations 3.2622203E-02 0.9599781 at 80iterations 1.6045857E-02 0.4773636 at 90iterations 7.9427296E-03 0.2280884 at 100iterations 3.9055611E-03 0.1286049 at 110iterations 1.9356605E-03 6.2475204E-02 at 120iterations finished qdiffx linear iterations at : 00:56:02 total time elapsed so far: 7.590000 # loops : 120 mean,max change (kT/e) : 1.9356605E-03 6.2475204E-02 energy calculations done at 7.590000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.790000 DelPhi exited at 00:56:02 7.792u 0.232s 0:08.38 95.7% 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 00:56:02 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: 280 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2240 !!! WARNING: HIR 127 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: 3.105313 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): -9.304000 42.28500 ymin,ymax (A): -52.29900 -3.393000 zmin,zma (A): -22.73500 25.21900 x,y,z range (A): 51.58900 48.90600 47.95400 scale (grids/A): 3.105313 object centre (A): 16.49050 -27.84600 1.242001 number of atom coordinates read : 2240 total number of charged atoms : 2098 net assigned charge : 5.014012 assigned positive charge : 334.2104 centred at (gu) : 83.98176 85.53893 88.76884 assigned negative charge : -329.1968 centred at (gu) : 83.46101 85.51894 88.74148 start vw surface at 0.1400000 fill in re-entrant regions at 0.7900000 boundary points on vw surface= 182432 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21309 grid for indexing accessible points = 1.400000 m= 92939 mr = 129649 m= 37771 mr = 74898 m= 11261 mr = 30372 m= 2165 mr = 8709 m= 234 mr = 1489 m= 5 mr = 123 m= 0 mr = 0 time to grow re-entrant surface = 0.8600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.760000 number of dielectric boundary points 81567 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.890000 number of grid points assigned charge 16784 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) : 2.070209 object centre at (A) : 16.49050 -27.84600 1.242001 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.8930740 0.2051925 midg,1,midg; midg,igrid,midg 7.1450680E-02 -0.3676059 1,midg,midg; igrid,midg,midg 0.3560825 0.3689939 gauss-seidel spectral radius is 0.9993107 estimated iterations to convergence 300 setup time was (sec) 2.050000 now iterating at: 00:56:05 rms-change max change #iterations 10.44552 378.0677 at 10iterations 6.264117 141.7732 at 20iterations 3.723781 84.99780 at 30iterations 2.208046 44.40892 at 40iterations 1.310498 22.25236 at 50iterations 0.7753003 15.77029 at 60iterations 0.4572556 8.684720 at 70iterations 0.2685211 5.402988 at 80iterations 0.1582533 3.017675 at 90iterations 9.2970647E-02 1.636452 at 100iterations 5.4660473E-02 1.005687 at 110iterations 3.2067209E-02 0.5819530 at 120iterations 1.8844539E-02 0.3121681 at 130iterations 1.1057447E-02 0.2054482 at 140iterations 6.4697005E-03 0.1096497 at 150iterations 3.7957656E-03 6.3947678E-02 at 160iterations 2.2335642E-03 3.9415359E-02 at 170iterations 1.3076906E-03 2.6587993E-02 at 180iterations finished qdiffx linear iterations at : 00:56:14 total time elapsed so far: 11.74000 # loops : 180 mean,max change (kT/e) : 1.3076906E-03 2.6587993E-02 energy calculations done at 11.74000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.91000 DelPhi exited at 00:56:15 11.916u 0.147s 0:12.34 97.6% 0+0k 0+0io 0pf+0w