Mon Oct 10 14:18:36 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 14:18:36 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: 326 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2646 !!! WARNING: HIT 133 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= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 0.5717223 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): -16.12900 38.81200 ymin,ymax (A): 28.70500 75.27600 zmin,zma (A): -10.73800 51.53000 x,y,z range (A): 54.94100 46.57100 62.26800 scale (grids/A): 0.5717223 object centre (A): 11.34150 51.99050 20.39600 number of atom coordinates read : 2646 total number of charged atoms : 2496 net assigned charge : -1.985993 assigned positive charge : 390.5685 centred at (gu) : 90.31367 91.12999 90.62280 assigned negative charge : -392.5553 centred at (gu) : 90.34060 91.11655 90.61713 start vw surface at 0.1600000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 5598 nv = 96 ne = 84 npr = 53971 no. pairs analyzed = 53971 no. exposed pairs = 3464 no. arc points = 24007 no. surface atoms = 1172 nbur = 1474 mkacc time = 0.1800000 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 = 1.484000 m= 255 mr = 2819 m= 3 mr = 12 m= 0 mr = 0 time to grow re-entrant surface = 0.2100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3900000 number of dielectric boundary points 3025 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2469 ## 270 charges are in solution ## iepsmp to db, and charging done at 0.5100000 number of grid points assigned charge 7236 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -3.5392175E-10 -2.7862487E-10 midg,1,midg; midg,igrid,midg -4.0216766E-10 -1.6303033E-10 1,midg,midg; igrid,midg,midg 6.3079625E-11 -7.7814621E-10 gauss-seidel spectral radius is 0.9841876 estimated iterations to convergence 65 setup time was (sec) 0.6900000 now iterating at: 14:18:37 rms-change max change #iterations 8.9480177E-02 14.38045 at 10iterations 6.5641622E-03 1.192793 at 20iterations 5.5983139E-04 8.9321136E-02 at 30iterations 9.4240306E-05 2.2334099E-02 at 40iterations 3.0421586E-05 7.6732635E-03 at 50iterations finished qdiffx linear iterations at : 14:18:41 total time elapsed so far: 4.260000 # loops : 50 mean,max change (kT/e) : 3.0421586E-05 7.6732635E-03 energy calculations done at 4.260000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.480000 DelPhi exited at 14:18:42 4.487u 0.420s 0:05.40 90.7% 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 14:18:42 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: 326 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2646 !!! WARNING: HIT 133 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= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 1.715167 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): -16.12900 38.81200 ymin,ymax (A): 28.70500 75.27600 zmin,zma (A): -10.73800 51.53000 x,y,z range (A): 54.94100 46.57100 62.26800 scale (grids/A): 1.715167 object centre (A): 11.34150 51.99050 20.39600 number of atom coordinates read : 2646 total number of charged atoms : 2496 net assigned charge : -1.985993 assigned positive charge : 390.5685 centred at (gu) : 90.94041 93.38932 91.86785 assigned negative charge : -392.5553 centred at (gu) : 91.02137 93.34913 91.85112 start vw surface at 0.1500000 fill in re-entrant regions at 0.2800000 boundary points on vw surface= 61551 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24007 grid for indexing accessible points = 1.400000 m= 19133 mr = 40939 m= 2116 mr = 12998 m= 67 mr = 1008 m= 2 mr = 15 m= 0 mr = 0 time to grow re-entrant surface = 0.3000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.6300000 number of dielectric boundary points 27909 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 208 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.7600000 number of grid points assigned charge 19291 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) : 0.5717223 object centre at (A) : 11.34150 51.99050 20.39600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -3.0641675E-03 -2.2263454E-02 midg,1,midg; midg,igrid,midg 7.8503095E-04 -3.3303900E-03 1,midg,midg; igrid,midg,midg -3.3432664E-03 -4.9333572E-03 gauss-seidel spectral radius is 0.9983228 estimated iterations to convergence 194 setup time was (sec) 0.9500000 now iterating at: 14:18:43 rms-change max change #iterations 3.433659 153.9689 at 10iterations 1.472150 53.32169 at 20iterations 0.6361662 23.08331 at 30iterations 0.2728565 9.441286 at 40iterations 0.1179947 4.311081 at 50iterations 5.0601646E-02 2.049160 at 60iterations 2.1959838E-02 0.8116884 at 70iterations 9.4757574E-03 0.3735733 at 80iterations 4.1490025E-03 0.1521301 at 90iterations 1.8414560E-03 7.4588776E-02 at 100iterations 8.5145771E-04 3.8078547E-02 at 110iterations 4.2917088E-04 1.9896150E-02 at 120iterations finished qdiffx linear iterations at : 14:18:52 total time elapsed so far: 9.850000 # loops : 120 mean,max change (kT/e) : 4.2917088E-04 1.9896150E-02 energy calculations done at 9.850000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.07000 DelPhi exited at 14:18:53 10.076u 0.462s 0:11.08 95.0% 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 14:18:53 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: 326 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2646 !!! WARNING: HIT 133 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= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 2.572750 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): -16.12900 38.81200 ymin,ymax (A): 28.70500 75.27600 zmin,zma (A): -10.73800 51.53000 x,y,z range (A): 54.94100 46.57100 62.26800 scale (grids/A): 2.572750 object centre (A): 11.34150 51.99050 20.39600 number of atom coordinates read : 2646 total number of charged atoms : 2496 net assigned charge : -1.985993 assigned positive charge : 390.5685 centred at (gu) : 91.41035 95.08373 92.80151 assigned negative charge : -392.5553 centred at (gu) : 91.53212 95.02377 92.77664 start vw surface at 0.1600000 fill in re-entrant regions at 0.5400000 boundary points on vw surface= 143026 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24007 grid for indexing accessible points = 1.400000 m= 65200 mr = 100642 m= 19320 mr = 51147 m= 3326 mr = 14185 m= 274 mr = 2103 m= 7 mr = 127 m= 0 mr = 0 time to grow re-entrant surface = 0.9100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.560000 number of dielectric boundary points 62949 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 6 iepsmp to db, and charging done at 1.710000 number of grid points assigned charge 19958 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) : 1.715167 object centre at (A) : 11.34150 51.99050 20.39600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1016704 -0.1719243 midg,1,midg; midg,igrid,midg 2.2006115E-02 -9.3107879E-02 1,midg,midg; igrid,midg,midg -8.9834601E-02 -9.4526052E-02 gauss-seidel spectral radius is 0.9991728 estimated iterations to convergence 275 setup time was (sec) 1.920000 now iterating at: 14:18:55 rms-change max change #iterations 8.631886 296.6080 at 10iterations 4.884870 131.0922 at 20iterations 2.747517 69.88722 at 30iterations 1.540912 33.08357 at 40iterations 0.8613672 20.25195 at 50iterations 0.4811360 11.10140 at 60iterations 0.2685841 6.031139 at 70iterations 0.1500583 3.328004 at 80iterations 8.3683163E-02 2.134258 at 90iterations 4.6442948E-02 1.093364 at 100iterations 2.5878718E-02 0.6186330 at 110iterations 1.4421526E-02 0.2890134 at 120iterations 8.0187973E-03 0.1677036 at 130iterations 4.4713924E-03 9.9217892E-02 at 140iterations 2.4809777E-03 4.9616337E-02 at 150iterations 1.3815054E-03 2.8993607E-02 at 160iterations 7.6726667E-04 1.6553402E-02 at 170iterations 4.2729027E-04 8.8233948E-03 at 180iterations finished qdiffx linear iterations at : 14:19:10 total time elapsed so far: 16.76000 # loops : 180 mean,max change (kT/e) : 4.2729027E-04 8.8233948E-03 energy calculations done at 16.76000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 16.98000 DelPhi exited at 14:19:11 16.980u 0.472s 0:17.94 97.2% 0+0k 0+0io 0pf+0w