Mon Oct 10 19:33:39 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 19:33:39 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: 284 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2732 !!! 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= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 0.6215518 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): -9.428000 47.84800 ymin,ymax (A): -7.313000 39.17300 zmin,zma (A): 0.8449999 56.15300 x,y,z range (A): 57.27600 46.48600 55.30800 scale (grids/A): 0.6215518 object centre (A): 19.21000 15.93000 28.49900 number of atom coordinates read : 2732 total number of charged atoms : 2592 net assigned charge : -0.9859699 assigned positive charge : 412.3744 centred at (gu) : 89.51218 89.75954 88.78818 assigned negative charge : -413.3613 centred at (gu) : 89.44926 89.66621 88.72433 start vw surface at 0.1600000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 7092 nv = 96 ne = 84 npr = 53899 no. pairs analyzed = 53899 no. exposed pairs = 3693 no. arc points = 26024 no. surface atoms = 1247 nbur = 1485 mkacc time = 0.1800000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 363 mr = 3604 m= 3 mr = 32 m= 0 mr = 0 time to grow re-entrant surface = 0.2200000 no. cavity mid-points inaccessible to solvent = 16 time to turn everything in is 0.4000000 number of dielectric boundary points 3822 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2591 ## 265 charges are in solution ## iepsmp to db, and charging done at 0.5100000 number of grid points assigned charge 8644 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -7.1769031E-09 3.0234066E-09 midg,1,midg; midg,igrid,midg -8.1124405E-09 5.7891296E-09 1,midg,midg; igrid,midg,midg -6.0218492E-09 3.4956487E-09 gauss-seidel spectral radius is 0.9866141 estimated iterations to convergence 71 setup time was (sec) 0.7000000 now iterating at: 19:33:40 rms-change max change #iterations 0.1284163 19.34031 at 10iterations 1.2023445E-02 1.765924 at 20iterations 1.0993115E-03 0.1547623 at 30iterations 1.0154671E-04 1.5933990E-02 at 40iterations 9.6208478E-06 1.4724731E-03 at 50iterations finished qdiffx linear iterations at : 19:33:45 total time elapsed so far: 4.880000 # loops : 50 mean,max change (kT/e) : 9.6208478E-06 1.4724731E-03 energy calculations done at 4.880000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 5.110000 DelPhi exited at 19:33:46 5.113u 0.420s 0:06.34 87.2% 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 Mon Oct 10 2011 at 19:33:46 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: 284 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2732 !!! 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= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 1.864655 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): -9.428000 47.84800 ymin,ymax (A): -7.313000 39.17300 zmin,zma (A): 0.8449999 56.15300 x,y,z range (A): 57.27600 46.48600 55.30800 scale (grids/A): 1.864655 object centre (A): 19.21000 15.93000 28.49900 number of atom coordinates read : 2732 total number of charged atoms : 2592 net assigned charge : -0.9859699 assigned positive charge : 412.3744 centred at (gu) : 88.53558 89.27776 86.36353 assigned negative charge : -413.3613 centred at (gu) : 88.34755 88.99844 86.17273 start vw surface at 0.1700000 fill in re-entrant regions at 0.3300000 boundary points on vw surface= 76818 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26024 grid for indexing accessible points = 1.400000 m= 26101 mr = 51030 m= 3681 mr = 18325 m= 179 mr = 2063 m= 4 mr = 35 m= 0 mr = 0 time to grow re-entrant surface = 0.4000000 no. cavity mid-points inaccessible to solvent = 1329 time to turn everything in is 0.7900000 number of dielectric boundary points 35330 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 192 iepsmp to db, and charging done at 0.9200000 number of grid points assigned charge 20318 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) : 0.6215518 object centre at (A) : 19.21000 15.93000 28.49900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 9.4739981E-03 1.4685884E-02 midg,1,midg; midg,igrid,midg -1.8226916E-02 3.2717672E-03 1,midg,midg; igrid,midg,midg -4.3254007E-02 2.9850958E-02 gauss-seidel spectral radius is 0.9986011 estimated iterations to convergence 212 setup time was (sec) 1.110000 now iterating at: 19:33:47 rms-change max change #iterations 4.231149 158.9035 at 10iterations 1.957944 94.43121 at 20iterations 0.9052320 30.08380 at 30iterations 0.4187986 13.79920 at 40iterations 0.1938272 5.966087 at 50iterations 8.9670442E-02 2.903587 at 60iterations 4.1670527E-02 1.389489 at 70iterations 1.9311413E-02 0.6536846 at 80iterations 8.9180367E-03 0.2740669 at 90iterations 4.1349865E-03 0.1414781 at 100iterations 1.9141377E-03 6.2802315E-02 at 110iterations 8.8602549E-04 2.7877808E-02 at 120iterations finished qdiffx linear iterations at : 19:33:58 total time elapsed so far: 11.42000 # loops : 120 mean,max change (kT/e) : 8.8602549E-04 2.7877808E-02 energy calculations done at 11.42000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.65000 DelPhi exited at 19:33:58 11.650u 0.468s 0:12.71 95.2% 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 Mon Oct 10 2011 at 19:33:58 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: 284 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2732 !!! 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= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 2.796983 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): -9.428000 47.84800 ymin,ymax (A): -7.313000 39.17300 zmin,zma (A): 0.8449999 56.15300 x,y,z range (A): 57.27600 46.48600 55.30800 scale (grids/A): 2.796983 object centre (A): 19.21000 15.93000 28.49900 number of atom coordinates read : 2732 total number of charged atoms : 2592 net assigned charge : -0.9859699 assigned positive charge : 412.3744 centred at (gu) : 87.80326 88.91653 84.54532 assigned negative charge : -413.3613 centred at (gu) : 87.52121 88.49763 84.25909 start vw surface at 0.1600000 fill in re-entrant regions at 0.6600000 boundary points on vw surface= 177584 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26024 grid for indexing accessible points = 1.400000 m= 85522 mr = 124698 m= 29354 mr = 67775 m= 6359 mr = 22588 m= 690 mr = 4452 m= 36 mr = 363 m= 0 mr = 15 time to grow re-entrant surface = 1.230000 no. cavity mid-points inaccessible to solvent = 4609 time to turn everything in is 2.040000 number of dielectric boundary points 79654 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.210000 number of grid points assigned charge 20735 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) : 1.864655 object centre at (A) : 19.21000 15.93000 28.49900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.3050040 -1.3090504E-02 midg,1,midg; midg,igrid,midg -0.1822204 1.3542647E-02 1,midg,midg; igrid,midg,midg -0.5771298 0.3996513 gauss-seidel spectral radius is 0.9992719 estimated iterations to convergence 292 setup time was (sec) 2.440000 now iterating at: 19:34:01 rms-change max change #iterations 10.32097 320.3113 at 10iterations 6.150465 143.7596 at 20iterations 3.639228 80.93023 at 30iterations 2.136564 52.34508 at 40iterations 1.248064 25.85121 at 50iterations 0.7282143 16.19641 at 60iterations 0.4238989 9.401917 at 70iterations 0.2456449 4.971416 at 80iterations 0.1427092 3.122742 at 90iterations 8.2541630E-02 1.465092 at 100iterations 4.7806695E-02 0.9324460 at 110iterations 2.7614849E-02 0.5247192 at 120iterations 1.5964078E-02 0.3164070 at 130iterations 9.2282277E-03 0.1957846 at 140iterations 5.3336406E-03 0.1003159 at 150iterations 3.0784111E-03 5.7353973E-02 at 160iterations 1.7772275E-03 3.2600403E-02 at 170iterations 1.0242601E-03 1.9612312E-02 at 180iterations finished qdiffx linear iterations at : 19:34:19 total time elapsed so far: 19.94000 # loops : 180 mean,max change (kT/e) : 1.0242601E-03 1.9612312E-02 energy calculations done at 19.94000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 20.15000 DelPhi exited at 19:34:20 20.154u 0.514s 0:21.34 96.8% 0+0k 0+0io 0pf+0w