Sat Oct 15 15:28:26 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 15 2011 at 15:28:26 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 = 2748 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 0.6621777 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): -27.76600 24.00300 ymin,ymax (A): -38.54000 15.22200 zmin,zma (A): -43.24400 6.531000 x,y,z range (A): 51.76900 53.76200 49.77500 scale (grids/A): 0.6621777 object centre (A): -1.881499 -11.65900 -18.35650 number of atom coordinates read : 2748 total number of charged atoms : 2624 net assigned charge : 8.500015 assigned positive charge : 422.7916 centred at (gu) : 91.91193 89.49124 90.28792 assigned negative charge : -414.2922 centred at (gu) : 91.97531 89.33476 90.09277 start vw surface at 0.1700000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 8074 nv = 96 ne = 84 npr = 55293 no. pairs analyzed = 55293 no. exposed pairs = 3287 no. arc points = 23028 no. surface atoms = 1097 nbur = 1651 mkacc time = 0.1800000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 427 mr = 4598 m= 6 mr = 50 m= 0 mr = 0 time to grow re-entrant surface = 0.2200000 no. cavity mid-points inaccessible to solvent = 26 time to turn everything in is 0.4200000 number of dielectric boundary points 3859 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2291 ## 241 charges are in solution ## iepsmp to db, and charging done at 0.5900000 number of grid points assigned charge 9613 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.9706611E-08 6.9818903E-08 midg,1,midg; midg,igrid,midg -1.3639981E-08 5.1753695E-08 1,midg,midg; igrid,midg,midg 2.5317519E-08 1.2889911E-08 gauss-seidel spectral radius is 0.9881902 estimated iterations to convergence 75 setup time was (sec) 0.7700000 now iterating at: 15:28:27 rms-change max change #iterations 0.1748832 26.37567 at 10iterations 1.9160435E-02 2.589315 at 20iterations 2.0931549E-03 0.3185549 at 30iterations 2.4565085E-04 3.2405853E-02 at 40iterations 4.0854429E-05 6.7424774E-03 at 50iterations finished qdiffx linear iterations at : 15:28:36 total time elapsed so far: 4.710000 # loops : 50 mean,max change (kT/e) : 4.0854429E-05 6.7424774E-03 energy calculations done at 4.710000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.920000 DelPhi exited at 15:28:36 4.927u 0.438s 0:09.81 54.5% 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 15 2011 at 15:28:36 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 = 2748 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 1.986533 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): -27.76600 24.00300 ymin,ymax (A): -38.54000 15.22200 zmin,zma (A): -43.24400 6.531000 x,y,z range (A): 51.76900 53.76200 49.77500 scale (grids/A): 1.986533 object centre (A): -1.881499 -11.65900 -18.35650 number of atom coordinates read : 2748 total number of charged atoms : 2624 net assigned charge : 8.500015 assigned positive charge : 422.7916 centred at (gu) : 95.73520 88.47315 90.86353 assigned negative charge : -414.2922 centred at (gu) : 95.92568 88.00401 90.27793 start vw surface at 0.1500000 fill in re-entrant regions at 0.3400000 boundary points on vw surface= 86341 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23028 grid for indexing accessible points = 1.400000 m= 32203 mr = 60955 m= 5293 mr = 24218 m= 360 mr = 3379 m= 1 mr = 141 m= 0 mr = 0 time to grow re-entrant surface = 0.4700000 no. cavity mid-points inaccessible to solvent = 531 time to turn everything in is 0.8800000 number of dielectric boundary points 35505 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 153 iepsmp to db, and charging done at 1.010000 number of grid points assigned charge 20741 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) : 0.6621777 object centre at (A) : -1.881499 -11.65900 -18.35650 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.5779383E-03 7.1708888E-02 midg,1,midg; midg,igrid,midg -3.0257044E-02 3.1999961E-02 1,midg,midg; igrid,midg,midg 5.8549013E-02 3.4981683E-02 gauss-seidel spectral radius is 0.9987531 estimated iterations to convergence 224 setup time was (sec) 1.210000 now iterating at: 15:28:38 rms-change max change #iterations 4.772213 225.1649 at 10iterations 2.297769 78.97551 at 20iterations 1.118356 36.24271 at 30iterations 0.5425116 16.01876 at 40iterations 0.2611764 8.721411 at 50iterations 0.1272449 3.637047 at 60iterations 6.1527420E-02 1.924733 at 70iterations 2.9825311E-02 0.9439163 at 80iterations 1.4455592E-02 0.4028540 at 90iterations 7.0113055E-03 0.2144451 at 100iterations 3.4058434E-03 0.1075926 at 110iterations 1.6616038E-03 4.9213409E-02 at 120iterations finished qdiffx linear iterations at : 15:28:54 total time elapsed so far: 11.46000 # loops : 120 mean,max change (kT/e) : 1.6616038E-03 4.9213409E-02 energy calculations done at 11.47000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.67000 DelPhi exited at 15:28:54 11.672u 0.555s 0:18.29 66.8% 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 15 2011 at 15:28:54 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2748 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 2.979800 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): -27.76600 24.00300 ymin,ymax (A): -38.54000 15.22200 zmin,zma (A): -43.24400 6.531000 x,y,z range (A): 51.76900 53.76200 49.77500 scale (grids/A): 2.979800 object centre (A): -1.881499 -11.65900 -18.35650 number of atom coordinates read : 2748 total number of charged atoms : 2624 net assigned charge : 8.500015 assigned positive charge : 422.7916 centred at (gu) : 98.60274 87.70966 91.29507 assigned negative charge : -414.2922 centred at (gu) : 98.88851 87.00586 90.41690 start vw surface at 0.1700000 fill in re-entrant regions at 0.7600000 boundary points on vw surface= 199880 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23028 grid for indexing accessible points = 1.400000 m= 103399 mr = 147332 m= 38400 mr = 85925 m= 9754 mr = 31264 m= 1534 mr = 7355 m= 131 mr = 1052 m= 1 mr = 64 m= 0 mr = 0 time to grow re-entrant surface = 1.420000 no. cavity mid-points inaccessible to solvent = 1636 time to turn everything in is 2.350000 number of dielectric boundary points 80107 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 2.530000 number of grid points assigned charge 20992 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) : 1.986533 object centre at (A) : -1.881499 -11.65900 -18.35650 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -4.6528831E-02 0.7736844 midg,1,midg; midg,igrid,midg -0.4269596 0.6899109 1,midg,midg; igrid,midg,midg 0.5173523 0.4827002 gauss-seidel spectral radius is 0.9992875 estimated iterations to convergence 296 setup time was (sec) 2.760000 now iterating at: 15:28:58 rms-change max change #iterations 10.91417 405.8821 at 10iterations 6.395498 141.4970 at 20iterations 3.750304 71.45357 at 30iterations 2.190830 44.78540 at 40iterations 1.282345 24.97219 at 50iterations 0.7470862 12.94103 at 60iterations 0.4361503 7.500534 at 70iterations 0.2540185 4.268214 at 80iterations 0.1479671 2.495283 at 90iterations 8.6223505E-02 1.511253 at 100iterations 5.0066374E-02 0.9098549 at 110iterations 2.9137000E-02 0.4872513 at 120iterations 1.6954646E-02 0.2926102 at 130iterations 9.8691201E-03 0.1562519 at 140iterations 5.7667629E-03 9.3545914E-02 at 150iterations 3.3713880E-03 5.6693077E-02 at 160iterations 1.9829343E-03 3.2112122E-02 at 170iterations 1.1776859E-03 2.2032738E-02 at 180iterations finished qdiffx linear iterations at : 15:29:26 total time elapsed so far: 23.56000 # loops : 180 mean,max change (kT/e) : 1.1776859E-03 2.2032738E-02 energy calculations done at 23.56000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 23.78000 DelPhi exited at 15:29:26 23.787u 0.568s 0:32.04 75.9% 0+0k 0+0io 0pf+0w