Wed Dec 21 14:21:51 PST 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 Wed Dec 21 2011 at 14:21:54 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: 259 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1948 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 0.5687718 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): -34.52200 12.60100 ymin,ymax (A): 0.3030000 41.35100 zmin,zma (A): -1.518000 61.07300 x,y,z range (A): 47.12300 41.04800 62.59100 scale (grids/A): 0.5687718 object centre (A): -10.96050 20.82700 29.77750 number of atom coordinates read : 1948 total number of charged atoms : 1818 net assigned charge : 4.000004 assigned positive charge : 288.5840 centred at (gu) : 89.55447 89.79002 88.87866 assigned negative charge : -284.5843 centred at (gu) : 89.44252 89.97192 88.86067 start vw surface at 0.1500000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 4277 nv = 96 ne = 84 npr = 39540 no. pairs analyzed = 39540 no. exposed pairs = 2415 no. arc points = 17400 no. surface atoms = 823 nbur = 1125 mkacc time = 0.1200000 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 = 1.540000 m= 200 mr = 2299 m= 0 mr = 18 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2900000 number of dielectric boundary points 2160 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1808 ## 210 charges are in solution ## iepsmp to db, and charging done at 0.4200000 number of grid points assigned charge 5382 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 5.4024735E-10 5.8975541E-10 midg,1,midg; midg,igrid,midg 2.4251818E-09 -1.1380960E-09 1,midg,midg; igrid,midg,midg -5.6168337E-10 1.4894291E-09 gauss-seidel spectral radius is 0.9839686 estimated iterations to convergence 65 setup time was (sec) 0.6100000 now iterating at: 14:21:57 rms-change max change #iterations 7.2178684E-02 12.72634 at 10iterations 5.5371504E-03 0.9014766 at 20iterations 3.9876634E-04 7.2916031E-02 at 30iterations 2.9508110E-05 5.4512024E-03 at 40iterations 2.1979060E-06 3.8528442E-04 at 50iterations finished qdiffx linear iterations at : 14:22:01 total time elapsed so far: 4.820000 # loops : 50 mean,max change (kT/e) : 2.1979060E-06 3.8528442E-04 energy calculations done at 4.820000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 5.000000 DelPhi exited at 14:22:12 5.006u 0.406s 0:19.12 28.2% 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 Wed Dec 21 2011 at 14:22:14 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: 259 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1948 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 1.706316 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): -34.52200 12.60100 ymin,ymax (A): 0.3030000 41.35100 zmin,zma (A): -1.518000 61.07300 x,y,z range (A): 47.12300 41.04800 62.59100 scale (grids/A): 1.706316 object centre (A): -10.96050 20.82700 29.77750 number of atom coordinates read : 1948 total number of charged atoms : 1818 net assigned charge : 4.000004 assigned positive charge : 288.5840 centred at (gu) : 88.66344 89.37018 86.63594 assigned negative charge : -284.5843 centred at (gu) : 88.32780 89.91577 86.58234 start vw surface at 0.1500000 fill in re-entrant regions at 0.2300000 boundary points on vw surface= 46827 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17400 grid for indexing accessible points = 1.400000 m= 16033 mr = 32006 m= 2056 mr = 11909 m= 90 mr = 1229 m= 1 mr = 15 m= 0 mr = 0 time to grow re-entrant surface = 0.2000000 no. cavity mid-points inaccessible to solvent = 248 time to turn everything in is 0.4700000 number of dielectric boundary points 19848 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 150 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.6100000 number of grid points assigned charge 14064 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) : 0.5687718 object centre at (A) : -10.96050 20.82700 29.77750 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.3193022E-02 1.6936969E-02 midg,1,midg; midg,igrid,midg 7.9595307E-03 -7.8837108E-03 1,midg,midg; igrid,midg,midg -2.3605330E-03 1.1168804E-03 gauss-seidel spectral radius is 0.9982229 estimated iterations to convergence 188 setup time was (sec) 0.8300000 now iterating at: 14:22:16 rms-change max change #iterations 2.878895 167.7493 at 10iterations 1.207476 63.00650 at 20iterations 0.5083773 24.51003 at 30iterations 0.2141902 8.809212 at 40iterations 9.0123408E-02 4.014326 at 50iterations 3.7845436E-02 1.518976 at 60iterations 1.5903261E-02 0.6627960 at 70iterations 6.6778320E-03 0.2833557 at 80iterations 2.8201439E-03 0.1124840 at 90iterations 1.1858937E-03 4.9772263E-02 at 100iterations 4.9738114E-04 1.9433975E-02 at 110iterations 2.1032558E-04 8.6555481E-03 at 120iterations finished qdiffx linear iterations at : 14:22:27 total time elapsed so far: 11.85000 # loops : 120 mean,max change (kT/e) : 2.1032558E-04 8.6555481E-03 energy calculations done at 11.85000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.05000 DelPhi exited at 14:22:32 12.051u 0.465s 0:17.91 69.8% 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 Wed Dec 21 2011 at 14:22:35 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: 259 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1948 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 2.559473 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): -34.52200 12.60100 ymin,ymax (A): 0.3030000 41.35100 zmin,zma (A): -1.518000 61.07300 x,y,z range (A): 47.12300 41.04800 62.59100 scale (grids/A): 2.559473 object centre (A): -10.96050 20.82700 29.77750 number of atom coordinates read : 1948 total number of charged atoms : 1818 net assigned charge : 4.000004 assigned positive charge : 288.5840 centred at (gu) : 87.99503 89.05526 84.95396 assigned negative charge : -284.5843 centred at (gu) : 87.49177 89.87381 84.87360 start vw surface at 0.1500000 fill in re-entrant regions at 0.3800000 boundary points on vw surface= 108290 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17400 grid for indexing accessible points = 1.400000 m= 53504 mr = 77384 m= 17573 mr = 43925 m= 3357 mr = 14257 m= 354 mr = 2455 m= 8 mr = 229 m= 0 mr = 0 time to grow re-entrant surface = 0.6000000 no. cavity mid-points inaccessible to solvent = 837 time to turn everything in is 1.060000 number of dielectric boundary points 44836 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 7 iepsmp to db, and charging done at 1.210000 number of grid points assigned charge 14538 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) : 1.706316 object centre at (A) : -10.96050 20.82700 29.77750 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2559136 0.1712103 midg,1,midg; midg,igrid,midg 7.7568732E-02 -0.1190250 1,midg,midg; igrid,midg,midg -3.9146584E-02 1.9849218E-02 gauss-seidel spectral radius is 0.9991149 estimated iterations to convergence 266 setup time was (sec) 1.380000 now iterating at: 14:22:37 rms-change max change #iterations 7.035133 321.9778 at 10iterations 3.867537 92.94196 at 20iterations 2.104327 57.57561 at 30iterations 1.143508 27.74843 at 40iterations 0.6215346 15.07511 at 50iterations 0.3388734 8.375854 at 60iterations 0.1846275 5.133698 at 70iterations 9.9987917E-02 2.570051 at 80iterations 5.4443561E-02 1.227045 at 90iterations 2.9580785E-02 0.6868806 at 100iterations 1.6108805E-02 0.3652358 at 110iterations 8.7317331E-03 0.2111434 at 120iterations 4.7515212E-03 0.1043172 at 130iterations 2.5804422E-03 6.0020447E-02 at 140iterations 1.4056830E-03 3.2761812E-02 at 150iterations 7.6460670E-04 1.8218040E-02 at 160iterations 4.1665992E-04 9.8829269E-03 at 170iterations 2.2513619E-04 5.5516958E-03 at 180iterations finished qdiffx linear iterations at : 14:22:52 total time elapsed so far: 16.38000 # loops : 180 mean,max change (kT/e) : 2.2513619E-04 5.5516958E-03 energy calculations done at 16.38000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 16.56000 DelPhi exited at 14:22:57 16.557u 0.335s 0:22.72 74.2% 0+0k 0+0io 0pf+0w