Sat Oct 8 13:38:14 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 Sat Oct 8 2011 at 13:38:14 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: 284 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3046 !!! WARNING: NAP 318 has a net charge of -2.0000 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: 0.6117469 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): -12.98400 33.81700 ymin,ymax (A): -12.82000 45.37400 zmin,zma (A): -41.14300 11.54200 x,y,z range (A): 46.80100 58.19400 52.68500 scale (grids/A): 0.6117469 object centre (A): 10.41650 16.27700 -14.80050 number of atom coordinates read : 3046 total number of charged atoms : 2899 net assigned charge : 7.1674585E-06 assigned positive charge : 456.1106 centred at (gu) : 91.01639 92.14189 91.09286 assigned negative charge : -456.1113 centred at (gu) : 91.06885 92.05170 91.16947 start vw surface at 0.1800000 fill in re-entrant regions at 0.1900000 boundary points on vw surface= 7421 nv = 96 ne = 84 npr = 64082 no. pairs analyzed = 64082 no. exposed pairs = 3480 no. arc points = 24519 no. surface atoms = 1186 nbur = 1860 mkacc time = 0.1800000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 345 mr = 4239 m= 3 mr = 37 m= 0 mr = 0 time to grow re-entrant surface = 0.2000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4000000 number of dielectric boundary points 3493 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2391 ## 263 charges are in solution ## iepsmp to db, and charging done at 0.5300000 number of grid points assigned charge 9318 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 3.5833181E-09 -6.0776371E-09 midg,1,midg; midg,igrid,midg -3.4468313E-09 8.8344176E-09 1,midg,midg; igrid,midg,midg 2.4947497E-09 -4.0910200E-09 gauss-seidel spectral radius is 0.9861949 estimated iterations to convergence 70 setup time was (sec) 0.6900000 now iterating at: 13:38:15 rms-change max change #iterations 0.1316937 21.45848 at 10iterations 1.2130021E-02 1.601555 at 20iterations 1.2106164E-03 0.1710472 at 30iterations 1.5081489E-04 2.1049500E-02 at 40iterations 2.5629901E-05 4.1027069E-03 at 50iterations finished qdiffx linear iterations at : 13:38:18 total time elapsed so far: 4.030000 # loops : 50 mean,max change (kT/e) : 2.5629901E-05 4.1027069E-03 energy calculations done at 4.030000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.210000 DelPhi exited at 13:38:19 4.214u 0.252s 0:04.81 92.7% 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 Sat Oct 8 2011 at 13:38:19 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: 284 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3046 !!! WARNING: NAP 318 has a net charge of -2.0000 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: 1.835241 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): -12.98400 33.81700 ymin,ymax (A): -12.82000 45.37400 zmin,zma (A): -41.14300 11.54200 x,y,z range (A): 46.80100 58.19400 52.68500 scale (grids/A): 1.835241 object centre (A): 10.41650 16.27700 -14.80050 number of atom coordinates read : 3046 total number of charged atoms : 2899 net assigned charge : 7.1674585E-06 assigned positive charge : 456.1106 centred at (gu) : 93.04855 96.42487 93.27815 assigned negative charge : -456.1113 centred at (gu) : 93.20627 96.15479 93.50808 start vw surface at 0.1600000 fill in re-entrant regions at 0.3100000 boundary points on vw surface= 81586 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24519 grid for indexing accessible points = 1.400000 m= 27862 mr = 58607 m= 3596 mr = 20414 m= 152 mr = 2066 m= 2 mr = 17 m= 0 mr = 0 time to grow re-entrant surface = 0.3500000 no. cavity mid-points inaccessible to solvent = 121 time to turn everything in is 0.7000000 number of dielectric boundary points 32094 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 202 iepsmp to db, and charging done at 0.8400000 number of grid points assigned charge 22737 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) : 0.6117469 object centre at (A) : 10.41650 16.27700 -14.80050 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.5510287E-02 7.6776836E-03 midg,1,midg; midg,igrid,midg -1.7622247E-02 3.2743655E-02 1,midg,midg; igrid,midg,midg 7.4081193E-03 -4.5508416E-03 gauss-seidel spectral radius is 0.9985670 estimated iterations to convergence 209 setup time was (sec) 1.000000 now iterating at: 13:38:20 rms-change max change #iterations 4.323925 171.6075 at 10iterations 1.996724 71.44429 at 20iterations 0.9205658 30.06848 at 30iterations 0.4228720 12.84036 at 40iterations 0.1954999 5.739291 at 50iterations 9.0001777E-02 2.529242 at 60iterations 4.1343432E-02 1.265509 at 70iterations 1.9129487E-02 0.5788612 at 80iterations 8.8285692E-03 0.2947156 at 90iterations 4.0591368E-03 0.1201706 at 100iterations 1.8704443E-03 5.7601929E-02 at 110iterations 8.6879841E-04 3.0378342E-02 at 120iterations finished qdiffx linear iterations at : 13:38:29 total time elapsed so far: 9.520000 # loops : 120 mean,max change (kT/e) : 8.6879841E-04 3.0378342E-02 energy calculations done at 9.520000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.680000 DelPhi exited at 13:38:29 9.685u 0.344s 0:10.35 96.8% 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 Sat Oct 8 2011 at 13:38:30 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: 284 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3046 !!! WARNING: NAP 318 has a net charge of -2.0000 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: 2.752861 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): -12.98400 33.81700 ymin,ymax (A): -12.82000 45.37400 zmin,zma (A): -41.14300 11.54200 x,y,z range (A): 46.80100 58.19400 52.68500 scale (grids/A): 2.752861 object centre (A): 10.41650 16.27700 -14.80050 number of atom coordinates read : 3046 total number of charged atoms : 2899 net assigned charge : 7.1674585E-06 assigned positive charge : 456.1106 centred at (gu) : 94.57272 99.63730 94.91704 assigned negative charge : -456.1113 centred at (gu) : 94.80934 99.23218 95.26206 start vw surface at 0.1700000 fill in re-entrant regions at 0.6200000 boundary points on vw surface= 189633 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24519 grid for indexing accessible points = 1.400000 m= 93600 mr = 142288 m= 30396 mr = 77032 m= 6189 mr = 23983 m= 646 mr = 4461 m= 19 mr = 356 m= 1 mr = 2 m= 0 mr = 0 time to grow re-entrant surface = 1.090000 no. cavity mid-points inaccessible to solvent = 423 time to turn everything in is 1.820000 number of dielectric boundary points 72362 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.980000 number of grid points assigned charge 23191 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) : 1.835241 object centre at (A) : 10.41650 16.27700 -14.80050 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1565442 0.2094374 midg,1,midg; midg,igrid,midg -0.1240101 0.5315514 1,midg,midg; igrid,midg,midg 0.1003546 -2.4377229E-02 gauss-seidel spectral radius is 0.9992439 estimated iterations to convergence 287 setup time was (sec) 2.150000 now iterating at: 13:38:32 rms-change max change #iterations 10.26088 325.5649 at 10iterations 5.979427 150.3154 at 20iterations 3.455545 78.51019 at 30iterations 1.992051 44.19396 at 40iterations 1.144874 22.65605 at 50iterations 0.6582901 12.93494 at 60iterations 0.3770874 7.977359 at 70iterations 0.2166551 4.028697 at 80iterations 0.1240169 2.232723 at 90iterations 7.1152166E-02 1.264587 at 100iterations 4.0712286E-02 0.6979980 at 110iterations 2.3291770E-02 0.4113770 at 120iterations 1.3347639E-02 0.2397537 at 130iterations 7.6327887E-03 0.1331997 at 140iterations 4.3717516E-03 7.5947464E-02 at 150iterations 2.5130769E-03 4.2304993E-02 at 160iterations 1.4445549E-03 2.5547028E-02 at 170iterations 8.3172676E-04 1.4858723E-02 at 180iterations finished qdiffx linear iterations at : 13:38:46 total time elapsed so far: 16.29000 # loops : 180 mean,max change (kT/e) : 8.3172676E-04 1.4858723E-02 energy calculations done at 16.29000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 16.47000 DelPhi exited at 13:38:47 16.469u 0.337s 0:17.11 98.1% 0+0k 0+0io 0pf+0w