Wed Dec 21 14:21:14 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 Wed Dec 21 2011 at 14:21:14 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 = 1969 !!! WARNING: ASH 124 has a net charge of -0.3190 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: 0.5659057 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): -35.12100 10.13600 ymin,ymax (A): 0.9650000 41.45800 zmin,zma (A): -3.703000 59.20500 x,y,z range (A): 45.25700 40.49300 62.90800 scale (grids/A): 0.5659057 object centre (A): -12.49250 21.21150 27.75100 number of atom coordinates read : 1969 total number of charged atoms : 1836 net assigned charge : 2.681006 assigned positive charge : 293.7119 centred at (gu) : 90.50456 89.37130 89.99751 assigned negative charge : -291.0313 centred at (gu) : 90.42547 89.51144 89.99560 start vw surface at 7.0000000E-02 fill in re-entrant regions at 7.9999998E-02 boundary points on vw surface= 4134 nv = 96 ne = 84 npr = 40406 no. pairs analyzed = 40406 no. exposed pairs = 2410 no. arc points = 17157 no. surface atoms = 832 nbur = 1137 mkacc time = 6.0000002E-02 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 = 1.540000 m= 161 mr = 2178 m= 2 mr = 6 m= 0 mr = 0 time to grow re-entrant surface = 6.0000002E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.1500000 number of dielectric boundary points 2113 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1802 ## 254 charges are in solution ## iepsmp to db, and charging done at 0.2200000 number of grid points assigned charge 5278 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 3.2603506E-10 3.5974998E-10 midg,1,midg; midg,igrid,midg 1.8321822E-09 -7.9640433E-10 1,midg,midg; igrid,midg,midg -3.2585054E-10 1.1772288E-09 gauss-seidel spectral radius is 0.9838064 estimated iterations to convergence 65 setup time was (sec) 0.3600000 now iterating at: 14:21:14 rms-change max change #iterations 6.9302998E-02 18.07838 at 10iterations 5.1604277E-03 1.033080 at 20iterations 3.7668564E-04 7.5675964E-02 at 30iterations 2.7460359E-05 5.7325363E-03 at 40iterations 1.9809229E-06 3.5476685E-04 at 50iterations finished qdiffx linear iterations at : 14:21:17 total time elapsed so far: 3.440000 # loops : 50 mean,max change (kT/e) : 1.9809229E-06 3.5476685E-04 energy calculations done at 3.440000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.570000 DelPhi exited at 14:21:21 3.572u 0.283s 0:07.84 49.1% 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 Wed Dec 21 2011 at 14:21:22 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: 285 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1969 !!! WARNING: ASH 124 has a net charge of -0.3190 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: 1.697717 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): -35.12100 10.13600 ymin,ymax (A): 0.9650000 41.45800 zmin,zma (A): -3.703000 59.20500 x,y,z range (A): 45.25700 40.49300 62.90800 scale (grids/A): 1.697717 object centre (A): -12.49250 21.21150 27.75100 number of atom coordinates read : 1969 total number of charged atoms : 1836 net assigned charge : 2.681006 assigned positive charge : 293.7119 centred at (gu) : 91.51380 88.11367 89.99255 assigned negative charge : -291.0313 centred at (gu) : 91.27652 88.53456 89.98704 start vw surface at 7.0000000E-02 fill in re-entrant regions at 0.1200000 boundary points on vw surface= 45507 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17157 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 14624 mr = 30863 m= 1657 mr = 10474 m= 48 mr = 886 m= 0 mr = 7 time to grow re-entrant surface = 0.1000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2400000 number of dielectric boundary points 19606 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 183 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.3100000 number of grid points assigned charge 14178 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) : 0.5659057 object centre at (A) : -12.49250 21.21150 27.75100 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.7898388E-02 1.8823324E-02 midg,1,midg; midg,igrid,midg 2.4368218E-03 -4.5336783E-03 1,midg,midg; igrid,midg,midg -2.5303185E-03 -7.6330715E-04 gauss-seidel spectral radius is 0.9982014 estimated iterations to convergence 187 setup time was (sec) 0.4700000 now iterating at: 14:21:22 rms-change max change #iterations 2.870604 166.3245 at 10iterations 1.193451 51.77332 at 20iterations 0.4981154 20.76952 at 30iterations 0.2092383 10.26112 at 40iterations 8.7063000E-02 3.687378 at 50iterations 3.6493588E-02 1.533344 at 60iterations 1.5277648E-02 0.5979071 at 70iterations 6.3980431E-03 0.2763889 at 80iterations 2.6752329E-03 0.1229939 at 90iterations 1.1240592E-03 4.7255039E-02 at 100iterations 4.6930488E-04 2.1394253E-02 at 110iterations 1.9622323E-04 8.3603859E-03 at 120iterations finished qdiffx linear iterations at : 14:21:30 total time elapsed so far: 7.630000 # loops : 120 mean,max change (kT/e) : 1.9622323E-04 8.3603859E-03 energy calculations done at 7.630000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.770000 DelPhi exited at 14:21:37 7.777u 0.322s 0:15.29 52.9% 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 Wed Dec 21 2011 at 14:21:38 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 = 1969 !!! WARNING: ASH 124 has a net charge of -0.3190 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: 2.546576 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): -35.12100 10.13600 ymin,ymax (A): 0.9650000 41.45800 zmin,zma (A): -3.703000 59.20500 x,y,z range (A): 45.25700 40.49300 62.90800 scale (grids/A): 2.546576 object centre (A): -12.49250 21.21150 27.75100 number of atom coordinates read : 1969 total number of charged atoms : 1836 net assigned charge : 2.681006 assigned positive charge : 293.7119 centred at (gu) : 92.27058 87.17058 89.98875 assigned negative charge : -291.0313 centred at (gu) : 91.91479 87.80183 89.98063 start vw surface at 7.0000000E-02 fill in re-entrant regions at 0.2100000 boundary points on vw surface= 105478 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17157 grid for indexing accessible points = 1.400000 m= 50127 mr = 75207 m= 15163 mr = 40462 m= 2689 mr = 11819 m= 194 mr = 1838 m= 5 mr = 104 m= 1 mr = 0 m= 0 mr = 0 time to grow re-entrant surface = 0.3100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5800000 number of dielectric boundary points 44227 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 8 iepsmp to db, and charging done at 0.6800000 number of grid points assigned charge 14687 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) : 1.697717 object centre at (A) : -12.49250 21.21150 27.75100 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1708920 0.1695673 midg,1,midg; midg,igrid,midg 9.7493047E-04 -6.6337109E-02 1,midg,midg; igrid,midg,midg -4.9616475E-02 -3.5527363E-02 gauss-seidel spectral radius is 0.9991087 estimated iterations to convergence 265 setup time was (sec) 0.8500000 now iterating at: 14:21:39 rms-change max change #iterations 7.194393 302.1614 at 10iterations 3.950092 128.6410 at 20iterations 2.162044 55.26563 at 30iterations 1.182032 28.36037 at 40iterations 0.6427264 16.24879 at 50iterations 0.3491102 9.359512 at 60iterations 0.1897897 5.026713 at 70iterations 0.1032154 2.281735 at 80iterations 5.5947762E-02 1.441923 at 90iterations 3.0448286E-02 0.7900658 at 100iterations 1.6562590E-02 0.4177198 at 110iterations 8.9826183E-03 0.2066813 at 120iterations 4.8743328E-03 0.1078663 at 130iterations 2.6396655E-03 5.8319092E-02 at 140iterations 1.4357880E-03 3.6066055E-02 at 150iterations 7.7874062E-04 1.9084990E-02 at 160iterations 4.2238482E-04 9.4518661E-03 at 170iterations 2.2935131E-04 5.1720142E-03 at 180iterations finished qdiffx linear iterations at : 14:21:51 total time elapsed so far: 12.72000 # loops : 180 mean,max change (kT/e) : 2.2935131E-04 5.1720142E-03 energy calculations done at 12.72000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.86000 DelPhi exited at 14:22:03 12.864u 0.258s 0:25.56 51.2% 0+0k 0+0io 0pf+0w