Sat Oct 8 16:45:44 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 Sat Oct 8 2011 at 16:45:44 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: 274 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4459 !!! WARNING: GLM 204 has a net charge of -0.0940 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1000000 grid size : 179 scale,in grids/A, set to be: 0.5450926 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): 15.97600 79.54100 ymin,ymax (A): 119.3750 184.6850 zmin,zma (A): -1.110000 59.87800 x,y,z range (A): 63.56500 65.31000 60.98800 scale (grids/A): 0.5450926 object centre (A): 47.75850 152.0300 29.38400 number of atom coordinates read : 4459 total number of charged atoms : 4285 net assigned charge : 3.406051 assigned positive charge : 682.1057 centred at (gu) : 92.09948 89.74250 87.54136 assigned negative charge : -678.7030 centred at (gu) : 92.11066 89.67001 87.56496 start vw surface at 0.1700000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 8583 nv = 96 ne = 84 npr = 89277 no. pairs analyzed = 89277 no. exposed pairs = 5581 no. arc points = 38408 no. surface atoms = 1871 nbur = 2588 mkacc time = 0.2300000 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 = 1.568000 m= 364 mr = 4565 m= 1 mr = 14 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 0.4700000 number of dielectric boundary points 4369 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4019 ## 546 charges are in solution ## iepsmp to db, and charging done at 0.5500000 number of grid points assigned charge 11429 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 7.9245055E-10 -1.2376292E-11 midg,1,midg; midg,igrid,midg -5.4242227E-10 8.4019075E-10 1,midg,midg; igrid,midg,midg 1.8586363E-10 1.4893511E-10 gauss-seidel spectral radius is 0.9827595 estimated iterations to convergence 63 setup time was (sec) 0.7200000 now iterating at: 16:45:46 rms-change max change #iterations 9.0537012E-02 13.38792 at 10iterations 6.4512058E-03 0.9501925 at 20iterations 9.8595687E-04 0.1447315 at 30iterations 3.1929000E-04 4.1282654E-02 at 40iterations 1.1524700E-04 1.4306664E-02 at 50iterations finished qdiffx linear iterations at : 16:45:49 total time elapsed so far: 4.640000 # loops : 50 mean,max change (kT/e) : 1.1524700E-04 1.4306664E-02 energy calculations done at 4.640000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.800000 DelPhi exited at 16:45:50 4.809u 0.396s 0:05.49 94.5% 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 Sat Oct 8 2011 at 16:45:50 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: 274 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4459 !!! WARNING: GLM 204 has a net charge of -0.0940 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1000000 grid size : 179 scale,in grids/A, set to be: 1.635278 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): 15.97600 79.54100 ymin,ymax (A): 119.3750 184.6850 zmin,zma (A): -1.110000 59.87800 x,y,z range (A): 63.56500 65.31000 60.98800 scale (grids/A): 1.635278 object centre (A): 47.75850 152.0300 29.38400 number of atom coordinates read : 4459 total number of charged atoms : 4285 net assigned charge : 3.406051 assigned positive charge : 682.1057 centred at (gu) : 96.29781 89.22643 82.62276 assigned negative charge : -678.7030 centred at (gu) : 96.33157 89.00970 82.69452 start vw surface at 0.1600000 fill in re-entrant regions at 0.3000000 boundary points on vw surface= 96000 reading accessible surface arcs data from file ARCDAT no. of arc points read = 38408 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 30583 mr = 66778 m= 3537 mr = 20943 m= 123 mr = 1866 m= 1 mr = 23 m= 0 mr = 0 time to grow re-entrant surface = 0.4200000 no. cavity mid-points inaccessible to solvent = 1107 time to turn everything in is 0.7900000 number of dielectric boundary points 40634 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 530 ## 8 charges are in solution ## iepsmp to db, and charging done at 0.9100000 number of grid points assigned charge 32827 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) : 0.5450926 object centre at (A) : 47.75850 152.0300 29.38400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 7.7012046E-03 7.7743204E-03 midg,1,midg; midg,igrid,midg 1.1849252E-02 2.8451931E-02 1,midg,midg; igrid,midg,midg -1.1379001E-02 -2.0067273E-02 gauss-seidel spectral radius is 0.9983364 estimated iterations to convergence 195 setup time was (sec) 1.090000 now iterating at: 16:45:51 rms-change max change #iterations 4.261477 164.6752 at 10iterations 1.837273 56.36916 at 20iterations 0.7940089 26.09690 at 30iterations 0.3443288 10.68070 at 40iterations 0.1492818 4.632148 at 50iterations 6.4629517E-02 2.179947 at 60iterations 2.8116761E-02 0.8225670 at 70iterations 1.2304001E-02 0.3684797 at 80iterations 5.3977570E-03 0.1676998 at 90iterations 2.4336288E-03 7.3867798E-02 at 100iterations 1.1442007E-03 3.8400650E-02 at 110iterations 5.7520572E-04 1.7604828E-02 at 120iterations finished qdiffx linear iterations at : 16:46:01 total time elapsed so far: 10.97000 # loops : 120 mean,max change (kT/e) : 5.7520572E-04 1.7604828E-02 energy calculations done at 10.97000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.15000 DelPhi exited at 16:46:02 11.154u 0.432s 0:11.96 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 16:46:02 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: 274 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4459 !!! WARNING: GLM 204 has a net charge of -0.0940 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1000000 grid size : 179 scale,in grids/A, set to be: 2.452917 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): 15.97600 79.54100 ymin,ymax (A): 119.3750 184.6850 zmin,zma (A): -1.110000 59.87800 x,y,z range (A): 63.56500 65.31000 60.98800 scale (grids/A): 2.452917 object centre (A): 47.75850 152.0300 29.38400 number of atom coordinates read : 4459 total number of charged atoms : 4285 net assigned charge : 3.406051 assigned positive charge : 682.1057 centred at (gu) : 99.44634 88.83920 78.93390 assigned negative charge : -678.7030 centred at (gu) : 99.49731 88.51442 79.04169 start vw surface at 0.1700000 fill in re-entrant regions at 0.6000000 boundary points on vw surface= 223281 reading accessible surface arcs data from file ARCDAT no. of arc points read = 38408 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 105550 mr = 163489 m= 31226 mr = 83510 m= 5736 mr = 23348 m= 502 mr = 3962 m= 12 mr = 273 m= 0 mr = 0 time to grow re-entrant surface = 1.230000 no. cavity mid-points inaccessible to solvent = 3603 time to turn everything in is 1.970000 number of dielectric boundary points 91725 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 36 iepsmp to db, and charging done at 2.140000 number of grid points assigned charge 34228 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) : 1.635278 object centre at (A) : 47.75850 152.0300 29.38400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 7.0621334E-03 0.1727895 midg,1,midg; midg,igrid,midg 0.2057417 0.4808823 1,midg,midg; igrid,midg,midg -0.1602816 -0.3223654 gauss-seidel spectral radius is 0.9992178 estimated iterations to convergence 282 setup time was (sec) 2.340000 now iterating at: 16:46:05 rms-change max change #iterations 11.01319 325.8907 at 10iterations 6.416973 144.5386 at 20iterations 3.711943 72.05487 at 30iterations 2.138630 39.91927 at 40iterations 1.226947 23.38403 at 50iterations 0.7019359 13.07704 at 60iterations 0.4002161 7.200360 at 70iterations 0.2277353 3.903738 at 80iterations 0.1295418 2.480235 at 90iterations 7.3560715E-02 1.299419 at 100iterations 4.1812945E-02 0.8849621 at 110iterations 2.3773393E-02 0.4311113 at 120iterations 1.3509650E-02 0.2417867 at 130iterations 7.6496527E-03 0.1366906 at 140iterations 4.3577719E-03 7.3288083E-02 at 150iterations 2.4901880E-03 4.5305144E-02 at 160iterations 1.4355547E-03 2.4602890E-02 at 170iterations 8.3715073E-04 1.4587402E-02 at 180iterations finished qdiffx linear iterations at : 16:46:23 total time elapsed so far: 20.38000 # loops : 180 mean,max change (kT/e) : 8.3715073E-04 1.4587402E-02 energy calculations done at 20.38000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 20.55000 DelPhi exited at 16:46:23 20.556u 0.474s 0:21.36 98.4% 0+0k 0+0io 0pf+0w