Tue Nov 22 14:12:07 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 Tue Nov 22 2011 at 14:12:12 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: 260 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1956 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6465791 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): -5.544000 34.69600 ymin,ymax (A): -3.383000 49.42200 zmin,zma (A): -8.212000 46.84700 x,y,z range (A): 40.24000 52.80500 55.05900 scale (grids/A): 0.6465791 object centre (A): 14.57600 23.01950 19.31750 number of atom coordinates read : 1956 total number of charged atoms : 1824 net assigned charge : 5.000011 assigned positive charge : 291.7599 centred at (gu) : 89.47234 92.07296 90.07111 assigned negative charge : -286.7603 centred at (gu) : 89.40219 92.16906 90.11438 start vw surface at 7.9999998E-02 fill in re-entrant regions at 7.9999998E-02 boundary points on vw surface= 5554 nv = 96 ne = 84 npr = 40473 no. pairs analyzed = 40473 no. exposed pairs = 2507 no. arc points = 17629 no. surface atoms = 849 nbur = 1107 mkacc time = 7.0000008E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 269 mr = 3012 m= 1 mr = 33 m= 0 mr = 0 time to grow re-entrant surface = 7.9999998E-02 no. cavity mid-points inaccessible to solvent = 7 time to turn everything in is 0.1600000 number of dielectric boundary points 2779 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1823 ## 179 charges are in solution ## iepsmp to db, and charging done at 0.2300000 number of grid points assigned charge 6577 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.3229607E-08 4.6326356E-09 midg,1,midg; midg,igrid,midg 1.2183651E-08 -1.7965887E-09 1,midg,midg; igrid,midg,midg 1.9386217E-09 1.4457880E-08 gauss-seidel spectral radius is 0.9875497 estimated iterations to convergence 73 setup time was (sec) 0.3700000 now iterating at: 14:12:15 rms-change max change #iterations 0.1370331 22.03763 at 10iterations 1.3614669E-02 2.478897 at 20iterations 1.3684223E-03 0.2445054 at 30iterations 1.3854372E-04 2.3853302E-02 at 40iterations 1.3631738E-05 1.9881725E-03 at 50iterations finished qdiffx linear iterations at : 14:12:25 total time elapsed so far: 3.670000 # loops : 50 mean,max change (kT/e) : 1.3631738E-05 1.9881725E-03 energy calculations done at 3.670000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.790000 DelPhi exited at 14:12:27 3.796u 0.242s 0:16.09 25.0% 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 Tue Nov 22 2011 at 14:12:29 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: 260 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1956 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.939737 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): -5.544000 34.69600 ymin,ymax (A): -3.383000 49.42200 zmin,zma (A): -8.212000 46.84700 x,y,z range (A): 40.24000 52.80500 55.05900 scale (grids/A): 1.939737 object centre (A): 14.57600 23.01950 19.31750 number of atom coordinates read : 1956 total number of charged atoms : 1824 net assigned charge : 5.000011 assigned positive charge : 291.7599 centred at (gu) : 88.41696 96.21877 90.21348 assigned negative charge : -286.7603 centred at (gu) : 88.20675 96.50736 90.34322 start vw surface at 7.0000000E-02 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 59841 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17629 grid for indexing accessible points = 1.400000 m= 21172 mr = 40829 m= 3001 mr = 15891 m= 120 mr = 1898 m= 2 mr = 34 m= 0 mr = 0 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 214 time to turn everything in is 0.3100000 number of dielectric boundary points 25484 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 115 iepsmp to db, and charging done at 0.4000000 number of grid points assigned charge 14391 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) : 0.6465791 object centre at (A) : 14.57600 23.01950 19.31750 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.1438060E-02 4.5676798E-02 midg,1,midg; midg,igrid,midg 3.4053914E-02 4.9067340E-03 1,midg,midg; igrid,midg,midg 8.2725631E-03 8.7244930E-03 gauss-seidel spectral radius is 0.9986075 estimated iterations to convergence 212 setup time was (sec) 0.5700000 now iterating at: 14:12:34 rms-change max change #iterations 3.751157 182.5285 at 10iterations 1.747298 78.33174 at 20iterations 0.8127348 30.61520 at 30iterations 0.3772310 13.33354 at 40iterations 0.1748898 6.006381 at 50iterations 8.1217885E-02 2.870422 at 60iterations 3.7654344E-02 1.303711 at 70iterations 1.7476387E-02 0.6003754 at 80iterations 8.1140138E-03 0.2789268 at 90iterations 3.7625523E-03 0.1386700 at 100iterations 1.7479067E-03 6.0424805E-02 at 110iterations 8.1557408E-04 2.7745247E-02 at 120iterations finished qdiffx linear iterations at : 14:12:58 total time elapsed so far: 8.490000 # loops : 120 mean,max change (kT/e) : 8.1557408E-04 2.7745247E-02 energy calculations done at 8.490000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.620000 DelPhi exited at 14:13:00 8.619u 0.259s 0:31.70 27.9% 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 Tue Nov 22 2011 at 14:13:02 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: 260 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1956 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.909606 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): -5.544000 34.69600 ymin,ymax (A): -3.383000 49.42200 zmin,zma (A): -8.212000 46.84700 x,y,z range (A): 40.24000 52.80500 55.05900 scale (grids/A): 2.909606 object centre (A): 14.57600 23.01950 19.31750 number of atom coordinates read : 1956 total number of charged atoms : 1824 net assigned charge : 5.000011 assigned positive charge : 291.7599 centred at (gu) : 87.62540 99.32819 90.32007 assigned negative charge : -286.7603 centred at (gu) : 87.31010 99.76116 90.51494 start vw surface at 7.0000000E-02 fill in re-entrant regions at 0.2900000 boundary points on vw surface= 138354 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17629 grid for indexing accessible points = 1.400000 m= 68960 mr = 98791 m= 24308 mr = 56867 m= 5397 mr = 19925 m= 674 mr = 4139 m= 16 mr = 482 m= 0 mr = 1 time to grow re-entrant surface = 0.4400000 no. cavity mid-points inaccessible to solvent = 720 time to turn everything in is 0.8300000 number of dielectric boundary points 57504 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 0.9300000 number of grid points assigned charge 14592 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) : 1.939737 object centre at (A) : 14.57600 23.01950 19.31750 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -5.4288916E-03 0.8425635 midg,1,midg; midg,igrid,midg 0.3531055 -5.1452145E-03 1,midg,midg; igrid,midg,midg 0.1514575 6.0056340E-02 gauss-seidel spectral radius is 0.9992406 estimated iterations to convergence 286 setup time was (sec) 1.100000 now iterating at: 14:13:09 rms-change max change #iterations 8.749713 408.2666 at 10iterations 5.041454 142.1833 at 20iterations 2.884790 60.72546 at 30iterations 1.648724 36.23745 at 40iterations 0.9424570 19.64244 at 50iterations 0.5378276 11.38560 at 60iterations 0.3055506 6.338778 at 70iterations 0.1743002 3.376904 at 80iterations 9.9476367E-02 1.910194 at 90iterations 5.6535788E-02 1.219385 at 100iterations 3.2142665E-02 0.6138654 at 110iterations 1.8324608E-02 0.3781424 at 120iterations 1.0426121E-02 0.2165251 at 130iterations 5.9302570E-03 0.1173782 at 140iterations 3.3783277E-03 7.0810318E-02 at 150iterations 1.9229733E-03 3.8403511E-02 at 160iterations 1.0941339E-03 2.0935059E-02 at 170iterations 6.2336976E-04 1.3062239E-02 at 180iterations finished qdiffx linear iterations at : 14:13:48 total time elapsed so far: 14.13000 # loops : 180 mean,max change (kT/e) : 6.2336976E-04 1.3062239E-02 energy calculations done at 14.13000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 14.25000 DelPhi exited at 14:13:55 14.256u 0.299s 0:53.10 27.3% 0+0k 0+0io 0pf+0w