Mon Oct 10 17:12:43 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 17:12:43 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: 285 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2783 !!! WARNING: HIT 107 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= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6192166 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): -9.015000 48.47700 ymin,ymax (A): -7.549000 39.28300 zmin,zma (A): 0.9320000 56.14300 x,y,z range (A): 57.49200 46.83200 55.21100 scale (grids/A): 0.6192166 object centre (A): 19.73100 15.86700 28.53750 number of atom coordinates read : 2783 total number of charged atoms : 2643 net assigned charge : -2.485971 assigned positive charge : 419.3333 centred at (gu) : 89.28500 89.60654 88.69379 assigned negative charge : -421.8202 centred at (gu) : 89.22416 89.49574 88.59171 start vw surface at 0.1200000 fill in re-entrant regions at 0.1300000 boundary points on vw surface= 7266 nv = 96 ne = 84 npr = 55067 no. pairs analyzed = 55067 no. exposed pairs = 3752 no. arc points = 26407 no. surface atoms = 1265 nbur = 1518 mkacc time = 0.1500000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 340 mr = 3735 m= 2 mr = 22 m= 0 mr = 0 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 15 time to turn everything in is 0.3200000 number of dielectric boundary points 3851 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2655 ## 254 charges are in solution ## iepsmp to db, and charging done at 0.4600000 number of grid points assigned charge 8827 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.2113588E-08 3.9704262E-09 midg,1,midg; midg,igrid,midg -1.0554468E-08 5.4323226E-09 1,midg,midg; igrid,midg,midg -7.1256649E-09 2.1079603E-09 gauss-seidel spectral radius is 0.9865187 estimated iterations to convergence 71 setup time was (sec) 0.6300000 now iterating at: 17:12:44 rms-change max change #iterations 0.1286014 18.29054 at 10iterations 1.1786908E-02 1.985352 at 20iterations 1.0818965E-03 0.1661816 at 30iterations 1.0156708E-04 1.7452240E-02 at 40iterations 9.8025621E-06 1.3246536E-03 at 50iterations finished qdiffx linear iterations at : 17:12:47 total time elapsed so far: 4.310000 # loops : 50 mean,max change (kT/e) : 9.8025621E-06 1.3246536E-03 energy calculations done at 4.310000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.460000 DelPhi exited at 17:12:48 4.469u 0.380s 0:05.35 90.4% 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 17:12:48 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: 285 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2783 !!! WARNING: HIT 107 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= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 1.857650 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): -9.015000 48.47700 ymin,ymax (A): -7.549000 39.28300 zmin,zma (A): 0.9320000 56.14300 x,y,z range (A): 57.49200 46.83200 55.21100 scale (grids/A): 1.857650 object centre (A): 19.73100 15.86700 28.53750 number of atom coordinates read : 2783 total number of charged atoms : 2643 net assigned charge : -2.485971 assigned positive charge : 419.3333 centred at (gu) : 87.85426 88.81882 86.08067 assigned negative charge : -421.8202 centred at (gu) : 87.67223 88.48671 85.77468 start vw surface at 0.1200000 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 78372 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26407 grid for indexing accessible points = 1.400000 m= 26283 mr = 52597 m= 3549 mr = 18400 m= 173 mr = 1971 m= 1 mr = 37 m= 0 mr = 0 time to grow re-entrant surface = 0.3300000 no. cavity mid-points inaccessible to solvent = 867 time to turn everything in is 0.6200000 number of dielectric boundary points 35373 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 162 iepsmp to db, and charging done at 0.7700000 number of grid points assigned charge 20714 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) : 0.6192166 object centre at (A) : 19.73100 15.86700 28.53750 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -7.5967642E-03 -1.6105418E-03 midg,1,midg; midg,igrid,midg -2.3846364E-02 -4.7071106E-04 1,midg,midg; igrid,midg,midg -4.3594945E-02 2.7643433E-02 gauss-seidel spectral radius is 0.9985945 estimated iterations to convergence 211 setup time was (sec) 0.9600000 now iterating at: 17:12:49 rms-change max change #iterations 4.241271 205.9609 at 10iterations 1.953987 65.88255 at 20iterations 0.9041613 30.62153 at 30iterations 0.4187613 12.39796 at 40iterations 0.1934673 6.632477 at 50iterations 8.9289621E-02 3.117329 at 60iterations 4.1227028E-02 1.261590 at 70iterations 1.9133572E-02 0.5990458 at 80iterations 8.8513000E-03 0.2691054 at 90iterations 4.0935902E-03 0.1525800 at 100iterations 1.8906896E-03 6.0026646E-02 at 110iterations 8.7817211E-04 2.7702332E-02 at 120iterations finished qdiffx linear iterations at : 17:12:59 total time elapsed so far: 10.38000 # loops : 120 mean,max change (kT/e) : 8.7817211E-04 2.7702332E-02 energy calculations done at 10.38000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.54000 DelPhi exited at 17:12:59 10.542u 0.459s 0:11.38 96.5% 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 Mon Oct 10 2011 at 17:13:00 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: 285 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2783 !!! WARNING: HIT 107 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= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.786475 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): -9.015000 48.47700 ymin,ymax (A): -7.549000 39.28300 zmin,zma (A): 0.9320000 56.14300 x,y,z range (A): 57.49200 46.83200 55.21100 scale (grids/A): 2.786475 object centre (A): 19.73100 15.86700 28.53750 number of atom coordinates read : 2783 total number of charged atoms : 2643 net assigned charge : -2.485971 assigned positive charge : 419.3333 centred at (gu) : 86.78116 88.22811 84.12102 assigned negative charge : -421.8202 centred at (gu) : 86.50824 87.73005 83.66201 start vw surface at 0.1200000 fill in re-entrant regions at 0.5100000 boundary points on vw surface= 181468 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26407 grid for indexing accessible points = 1.400000 m= 86807 mr = 128478 m= 29012 mr = 69044 m= 6025 mr = 22213 m= 677 mr = 4100 m= 37 mr = 382 m= 0 mr = 12 time to grow re-entrant surface = 0.9900001 no. cavity mid-points inaccessible to solvent = 2891 time to turn everything in is 1.620000 number of dielectric boundary points 79797 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.740000 number of grid points assigned charge 21142 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) : 1.857650 object centre at (A) : 19.73100 15.86700 28.53750 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 7.1658798E-02 -0.2420949 midg,1,midg; midg,igrid,midg -0.2470782 -3.1119971E-02 1,midg,midg; igrid,midg,midg -0.6120882 0.3632206 gauss-seidel spectral radius is 0.9992706 estimated iterations to convergence 292 setup time was (sec) 1.930000 now iterating at: 17:13:02 rms-change max change #iterations 10.26080 298.2772 at 10iterations 6.088063 139.4028 at 20iterations 3.579075 75.31701 at 30iterations 2.102303 48.97916 at 40iterations 1.225976 31.74360 at 50iterations 0.7129098 16.01856 at 60iterations 0.4139098 7.515117 at 70iterations 0.2402322 4.467031 at 80iterations 0.1389916 2.766621 at 90iterations 8.0336928E-02 1.573723 at 100iterations 4.6581466E-02 0.8620605 at 110iterations 2.6934767E-02 0.5155706 at 120iterations 1.5562902E-02 0.2860236 at 130iterations 8.9883087E-03 0.1866617 at 140iterations 5.1815985E-03 9.7293854E-02 at 150iterations 2.9980405E-03 5.6507111E-02 at 160iterations 1.7275569E-03 3.1959534E-02 at 170iterations 9.9793158E-04 1.9692779E-02 at 180iterations finished qdiffx linear iterations at : 17:13:18 total time elapsed so far: 17.94000 # loops : 180 mean,max change (kT/e) : 9.9793158E-04 1.9692779E-02 energy calculations done at 17.94000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 18.11000 DelPhi exited at 17:13:18 18.111u 0.496s 0:18.89 98.4% 0+0k 0+0io 0pf+0w