Sun Oct 9 00:04:39 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 Sun Oct 9 2011 at 00:04:39 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 = 3328 !!! WARNING: TPO 1 has a net charge of -1.2740 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 0.5665722 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): -52.51200 4.010000 ymin,ymax (A): -49.59300 13.24100 zmin,zma (A): 25.69000 87.51600 x,y,z range (A): 56.52200 62.83400 61.82600 scale (grids/A): 0.5665722 object centre (A): -24.25100 -18.17600 56.60300 number of atom coordinates read : 3328 total number of charged atoms : 3184 net assigned charge : 12.72602 assigned positive charge : 494.3325 centred at (gu) : 89.61797 89.80397 90.91936 assigned negative charge : -481.6082 centred at (gu) : 89.47320 89.83727 91.10268 start vw surface at 0.1000000 fill in re-entrant regions at 0.1100000 boundary points on vw surface= 7325 nv = 96 ne = 84 npr = 64351 no. pairs analyzed = 64351 no. exposed pairs = 4444 no. arc points = 32234 no. surface atoms = 1468 nbur = 1860 mkacc time = 0.1100000 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 = 1.512000 m= 354 mr = 3729 m= 3 mr = 8 m= 0 mr = 0 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2300000 number of dielectric boundary points 3945 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3229 ## 391 charges are in solution ## iepsmp to db, and charging done at 0.3100000 number of grid points assigned charge 9276 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 3.5955150E-09 -1.3613721E-09 midg,1,midg; midg,igrid,midg 2.3723812E-09 1.2047804E-09 1,midg,midg; igrid,midg,midg -5.1517829E-10 3.5738246E-09 gauss-seidel spectral radius is 0.9839707 estimated iterations to convergence 65 setup time was (sec) 0.4300000 now iterating at: 00:04:40 rms-change max change #iterations 9.8264113E-02 22.60387 at 10iterations 7.1093594E-03 1.082256 at 20iterations 5.3151639E-04 7.8025818E-02 at 30iterations 4.4685396E-05 7.7695847E-03 at 40iterations 4.7633994E-06 4.6539307E-04 at 50iterations finished qdiffx linear iterations at : 00:04:43 total time elapsed so far: 3.490000 # loops : 50 mean,max change (kT/e) : 4.7633994E-06 4.6539307E-04 energy calculations done at 3.490000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.620000 DelPhi exited at 00:04:43 3.627u 0.190s 0:04.09 93.1% 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 Sun Oct 9 2011 at 00:04:43 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: 284 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3328 !!! WARNING: TPO 1 has a net charge of -1.2740 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: 1.699717 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): -52.51200 4.010000 ymin,ymax (A): -49.59300 13.24100 zmin,zma (A): 25.69000 87.51600 x,y,z range (A): 56.52200 62.83400 61.82600 scale (grids/A): 1.699717 object centre (A): -24.25100 -18.17600 56.60300 number of atom coordinates read : 3328 total number of charged atoms : 3184 net assigned charge : 12.72602 assigned positive charge : 494.3325 centred at (gu) : 88.85286 89.41087 92.75715 assigned negative charge : -481.6082 centred at (gu) : 88.41953 89.51141 93.30778 start vw surface at 0.1100000 fill in re-entrant regions at 0.1900000 boundary points on vw surface= 80405 reading accessible surface arcs data from file ARCDAT no. of arc points read = 32234 grid for indexing accessible points = 1.400000 m= 25805 mr = 53397 m= 2960 mr = 17671 m= 105 mr = 1536 m= 2 mr = 25 m= 0 mr = 0 time to grow re-entrant surface = 0.2000000 no. cavity mid-points inaccessible to solvent = 1100 time to turn everything in is 0.4300000 number of dielectric boundary points 36648 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 341 ## 2 charges are in solution ## iepsmp to db, and charging done at 0.5200000 number of grid points assigned charge 24638 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) : 0.5665722 object centre at (A) : -24.25100 -18.17600 56.60300 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.7383279E-02 1.7176397E-02 midg,1,midg; midg,igrid,midg 4.1997705E-02 3.2564003E-02 1,midg,midg; igrid,midg,midg -9.3114795E-03 1.5303670E-02 gauss-seidel spectral radius is 0.9983847 estimated iterations to convergence 197 setup time was (sec) 0.6700000 now iterating at: 00:04:44 rms-change max change #iterations 3.855114 169.9985 at 10iterations 1.673010 59.91787 at 20iterations 0.7310317 23.96544 at 30iterations 0.3180774 10.23474 at 40iterations 0.1393500 4.488624 at 50iterations 6.1097670E-02 2.125476 at 60iterations 2.6687687E-02 0.8528156 at 70iterations 1.1665433E-02 0.3718929 at 80iterations 5.0913333E-03 0.1728570 at 90iterations 2.2375034E-03 7.4613571E-02 at 100iterations 9.8163297E-04 3.3338547E-02 at 110iterations 4.2910455E-04 1.3914108E-02 at 120iterations finished qdiffx linear iterations at : 00:04:52 total time elapsed so far: 8.240000 # loops : 120 mean,max change (kT/e) : 4.2910455E-04 1.3914108E-02 energy calculations done at 8.240000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.370000 DelPhi exited at 00:04:52 8.376u 0.223s 0:08.92 96.3% 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 Sun Oct 9 2011 at 00:04:52 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 = 3328 !!! WARNING: TPO 1 has a net charge of -1.2740 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 2.549575 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): -52.51200 4.010000 ymin,ymax (A): -49.59300 13.24100 zmin,zma (A): 25.69000 87.51600 x,y,z range (A): 56.52200 62.83400 61.82600 scale (grids/A): 2.549575 object centre (A): -24.25100 -18.17600 56.60300 number of atom coordinates read : 3328 total number of charged atoms : 3184 net assigned charge : 12.72602 assigned positive charge : 494.3325 centred at (gu) : 88.27915 89.11610 94.13545 assigned negative charge : -481.6082 centred at (gu) : 87.62923 89.26704 94.96169 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.3200000 boundary points on vw surface= 186126 reading accessible surface arcs data from file ARCDAT no. of arc points read = 32234 grid for indexing accessible points = 1.400000 m= 86964 mr = 130509 m= 26969 mr = 68381 m= 4917 mr = 20394 m= 451 mr = 3288 m= 14 mr = 231 m= 0 mr = 0 time to grow re-entrant surface = 0.5400000 no. cavity mid-points inaccessible to solvent = 3861 time to turn everything in is 0.9600000 number of dielectric boundary points 82638 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 15 iepsmp to db, and charging done at 1.060000 number of grid points assigned charge 25424 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) : 1.699717 object centre at (A) : -24.25100 -18.17600 56.60300 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.7536901 0.2832989 midg,1,midg; midg,igrid,midg 0.7533609 0.6313238 1,midg,midg; igrid,midg,midg -8.7107681E-02 0.2023038 gauss-seidel spectral radius is 0.9992196 estimated iterations to convergence 283 setup time was (sec) 1.210000 now iterating at: 00:04:54 rms-change max change #iterations 9.816118 302.4734 at 10iterations 5.714530 135.3865 at 20iterations 3.301877 78.11584 at 30iterations 1.900036 44.81793 at 40iterations 1.088842 21.93170 at 50iterations 0.6205294 13.51240 at 60iterations 0.3538933 7.325758 at 70iterations 0.2015526 4.561291 at 80iterations 0.1143430 2.435844 at 90iterations 6.4876333E-02 1.283882 at 100iterations 3.6942553E-02 0.7353859 at 110iterations 2.0829810E-02 0.4007511 at 120iterations 1.1785924E-02 0.2227888 at 130iterations 6.6883825E-03 0.1434364 at 140iterations 3.7742886E-03 6.7775726E-02 at 150iterations 2.1377106E-03 3.9093018E-02 at 160iterations 1.2100642E-03 2.3281097E-02 at 170iterations 6.8490510E-04 1.3790131E-02 at 180iterations finished qdiffx linear iterations at : 00:05:06 total time elapsed so far: 13.28000 # loops : 180 mean,max change (kT/e) : 6.8490510E-04 1.3790131E-02 energy calculations done at 13.28000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.42000 DelPhi exited at 00:05:06 13.418u 0.251s 0:13.96 97.8% 0+0k 0+0io 0pf+0w