Sat Oct 8 23:13:22 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 8 2011 at 23:13:22 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 = 2453 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6432030 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): 0.3140000 54.79700 ymin,ymax (A): 19.97300 63.45700 zmin,zma (A): -11.96600 43.38200 x,y,z range (A): 54.48300 43.48400 55.34800 scale (grids/A): 0.6432030 object centre (A): 27.55550 41.71500 15.70800 number of atom coordinates read : 2453 total number of charged atoms : 2317 net assigned charge : 11.50002 assigned positive charge : 358.2842 centred at (gu) : 89.56798 89.54761 90.64679 assigned negative charge : -346.7850 centred at (gu) : 89.59221 89.62767 90.61677 start vw surface at 7.9999998E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 6928 nv = 96 ne = 84 npr = 48946 no. pairs analyzed = 48946 no. exposed pairs = 3339 no. arc points = 23785 no. surface atoms = 1112 nbur = 1341 mkacc time = 7.9999998E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 433 mr = 3544 m= 2 mr = 58 m= 0 mr = 0 time to grow re-entrant surface = 8.9999989E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.1900000 number of dielectric boundary points 3761 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2323 ## 202 charges are in solution ## iepsmp to db, and charging done at 0.2600000 number of grid points assigned charge 8188 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.3018045E-08 2.4781359E-08 midg,1,midg; midg,igrid,midg 2.9999082E-08 8.3190228E-09 1,midg,midg; igrid,midg,midg 2.2976536E-08 1.4196642E-08 gauss-seidel spectral radius is 0.9874726 estimated iterations to convergence 73 setup time was (sec) 0.3800000 now iterating at: 23:13:22 rms-change max change #iterations 0.1398462 25.30857 at 10iterations 1.3737019E-02 2.071495 at 20iterations 1.4732451E-03 0.2409859 at 30iterations 2.2624347E-04 4.0462494E-02 at 40iterations 6.2194020E-05 1.3069153E-02 at 50iterations finished qdiffx linear iterations at : 23:13:25 total time elapsed so far: 3.390000 # loops : 50 mean,max change (kT/e) : 6.2194020E-05 1.3069153E-02 energy calculations done at 3.390000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.520000 DelPhi exited at 23:13:26 3.525u 0.192s 0:04.03 92.0% 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 Sat Oct 8 2011 at 23:13:26 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 = 2453 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.929609 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): 0.3140000 54.79700 ymin,ymax (A): 19.97300 63.45700 zmin,zma (A): -11.96600 43.38200 x,y,z range (A): 54.48300 43.48400 55.34800 scale (grids/A): 1.929609 object centre (A): 27.55550 41.71500 15.70800 number of atom coordinates read : 2453 total number of charged atoms : 2317 net assigned charge : 11.50002 assigned positive charge : 358.2842 centred at (gu) : 88.70364 88.64249 91.94003 assigned negative charge : -346.7850 centred at (gu) : 88.77673 88.88293 91.85048 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 73757 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23785 grid for indexing accessible points = 1.400000 m= 27267 mr = 48875 m= 4941 mr = 19321 m= 365 mr = 3001 m= 10 mr = 155 m= 0 mr = 0 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 335 time to turn everything in is 0.3700000 number of dielectric boundary points 34988 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 145 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.4500000 number of grid points assigned charge 18251 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) : 0.6432030 object centre at (A) : 27.55550 41.71500 15.70800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.6740651E-02 3.3279564E-02 midg,1,midg; midg,igrid,midg 3.0766858E-02 4.4128201E-03 1,midg,midg; igrid,midg,midg 5.4930776E-02 1.6147686E-02 gauss-seidel spectral radius is 0.9986692 estimated iterations to convergence 217 setup time was (sec) 0.6000000 now iterating at: 23:13:27 rms-change max change #iterations 4.094864 209.2738 at 10iterations 1.930743 74.52745 at 20iterations 0.9137619 29.97917 at 30iterations 0.4303787 14.61828 at 40iterations 0.2027592 6.281627 at 50iterations 9.5840774E-02 3.227209 at 60iterations 4.5214277E-02 1.428741 at 70iterations 2.1354593E-02 0.6696389 at 80iterations 1.0146250E-02 0.3399575 at 90iterations 4.7998787E-03 0.1575146 at 100iterations 2.2867301E-03 7.1975708E-02 at 110iterations 1.1017056E-03 3.7517548E-02 at 120iterations finished qdiffx linear iterations at : 23:13:34 total time elapsed so far: 8.150000 # loops : 120 mean,max change (kT/e) : 1.1017056E-03 3.7517548E-02 energy calculations done at 8.150000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.280000 DelPhi exited at 23:13:35 8.278u 0.242s 0:08.81 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 Sat Oct 8 2011 at 23:13:35 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2453 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.894413 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): 0.3140000 54.79700 ymin,ymax (A): 19.97300 63.45700 zmin,zma (A): -11.96600 43.38200 x,y,z range (A): 54.48300 43.48400 55.34800 scale (grids/A): 2.894413 object centre (A): 27.55550 41.71500 15.70800 number of atom coordinates read : 2453 total number of charged atoms : 2317 net assigned charge : 11.50002 assigned positive charge : 358.2842 centred at (gu) : 88.05520 87.96368 92.91000 assigned negative charge : -346.7850 centred at (gu) : 88.16505 88.32432 92.77571 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.3300000 boundary points on vw surface= 170614 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23785 grid for indexing accessible points = 1.400000 m= 85372 mr = 119249 m= 33017 mr = 67984 m= 9111 mr = 25966 m= 1567 mr = 6578 m= 119 mr = 1043 m= 4 mr = 55 m= 0 mr = 0 time to grow re-entrant surface = 0.5700000 no. cavity mid-points inaccessible to solvent = 1105 time to turn everything in is 0.9800000 number of dielectric boundary points 78929 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.080000 number of grid points assigned charge 18535 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) : 1.929609 object centre at (A) : 27.55550 41.71500 15.70800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.6652086 0.3651062 midg,1,midg; midg,igrid,midg 0.2968225 2.4392905E-02 1,midg,midg; igrid,midg,midg 0.5275220 0.1306784 gauss-seidel spectral radius is 0.9992779 estimated iterations to convergence 294 setup time was (sec) 1.230000 now iterating at: 23:13:36 rms-change max change #iterations 9.781355 340.0468 at 10iterations 5.824798 142.3414 at 20iterations 3.446791 71.63428 at 30iterations 2.024498 46.91143 at 40iterations 1.185644 25.54024 at 50iterations 0.6913723 13.34464 at 60iterations 0.4029463 7.704887 at 70iterations 0.2344276 4.673767 at 80iterations 0.1364489 2.570086 at 90iterations 7.9130523E-02 1.501474 at 100iterations 4.5891047E-02 0.8428612 at 110iterations 2.6661782E-02 0.5244501 at 120iterations 1.5447582E-02 0.2787476 at 130iterations 8.9653647E-03 0.1637650 at 140iterations 5.1834644E-03 0.1010246 at 150iterations 3.0133787E-03 5.9219360E-02 at 160iterations 1.7478393E-03 3.1417847E-02 at 170iterations 1.0175311E-03 1.7902374E-02 at 180iterations finished qdiffx linear iterations at : 23:13:48 total time elapsed so far: 13.40000 # loops : 180 mean,max change (kT/e) : 1.0175311E-03 1.7902374E-02 energy calculations done at 13.40000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.53000 DelPhi exited at 23:13:49 13.530u 0.238s 0:14.02 98.1% 0+0k 0+0io 0pf+0w