Sat Oct 8 14:02:57 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 14:02:58 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 = 3043 !!! WARNING: NAP 500 has a net charge of -2.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 0.6404721 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): -12.43700 43.14700 ymin,ymax (A): -22.34500 22.54200 zmin,zma (A): -7.244000 47.32200 x,y,z range (A): 55.58400 44.88700 54.56600 scale (grids/A): 0.6404721 object centre (A): 15.35500 9.8499298E-02 20.03900 number of atom coordinates read : 3043 total number of charged atoms : 2896 net assigned charge : 7.1674585E-06 assigned positive charge : 455.8235 centred at (gu) : 88.74001 89.57024 91.63966 assigned negative charge : -455.8243 centred at (gu) : 88.73254 89.47810 91.55501 start vw surface at 0.1100000 fill in re-entrant regions at 0.1200000 boundary points on vw surface= 8238 nv = 96 ne = 84 npr = 64188 no. pairs analyzed = 64188 no. exposed pairs = 3449 no. arc points = 23913 no. surface atoms = 1179 nbur = 1864 mkacc time = 0.1600000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 400 mr = 4826 m= 2 mr = 34 m= 0 mr = 0 time to grow re-entrant surface = 0.2000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3400000 number of dielectric boundary points 3780 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2375 ## 216 charges are in solution ## iepsmp to db, and charging done at 0.4700000 number of grid points assigned charge 10100 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -8.3719014E-09 1.6443897E-08 midg,1,midg; midg,igrid,midg -1.4265546E-08 1.1360223E-08 1,midg,midg; igrid,midg,midg -1.5319740E-09 6.8728828E-10 gauss-seidel spectral radius is 0.9874004 estimated iterations to convergence 73 setup time was (sec) 0.6300000 now iterating at: 14:02:59 rms-change max change #iterations 0.1606061 25.63315 at 10iterations 1.6656376E-02 2.217834 at 20iterations 1.7000617E-03 0.2659683 at 30iterations 2.0729518E-04 2.5623322E-02 at 40iterations 3.1613406E-05 4.0435791E-03 at 50iterations finished qdiffx linear iterations at : 14:03:02 total time elapsed so far: 4.470000 # loops : 50 mean,max change (kT/e) : 3.1613406E-05 4.0435791E-03 energy calculations done at 4.470000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.630000 DelPhi exited at 14:03:03 4.639u 0.405s 0:05.31 94.7% 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 14:03:03 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 = 3043 !!! WARNING: NAP 500 has a net charge of -2.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 1.921416 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): -12.43700 43.14700 ymin,ymax (A): -22.34500 22.54200 zmin,zma (A): -7.244000 47.32200 x,y,z range (A): 55.58400 44.88700 54.56600 scale (grids/A): 1.921416 object centre (A): 15.35500 9.8499298E-02 20.03900 number of atom coordinates read : 3043 total number of charged atoms : 2896 net assigned charge : 7.1674585E-06 assigned positive charge : 455.8235 centred at (gu) : 86.21951 88.71037 94.91824 assigned negative charge : -455.8243 centred at (gu) : 86.19730 88.43410 94.66477 start vw surface at 0.1400000 fill in re-entrant regions at 0.2900000 boundary points on vw surface= 89816 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23913 grid for indexing accessible points = 1.400000 m= 32384 mr = 65117 m= 4703 mr = 24333 m= 277 mr = 2849 m= 5 mr = 101 m= 0 mr = 0 time to grow re-entrant surface = 0.3800000 no. cavity mid-points inaccessible to solvent = 170 time to turn everything in is 0.7300000 number of dielectric boundary points 34785 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 153 iepsmp to db, and charging done at 0.8500000 number of grid points assigned charge 22824 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) : 0.6404721 object centre at (A) : 15.35500 9.8499298E-02 20.03900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.4264203E-02 2.6028926E-02 midg,1,midg; midg,igrid,midg -1.4279519E-03 1.6534539E-02 1,midg,midg; igrid,midg,midg -3.6575366E-02 1.1341867E-02 gauss-seidel spectral radius is 0.9986913 estimated iterations to convergence 219 setup time was (sec) 1.030000 now iterating at: 14:03:04 rms-change max change #iterations 4.728106 172.5605 at 10iterations 2.258428 62.76699 at 20iterations 1.075825 31.54764 at 30iterations 0.5133933 15.23367 at 40iterations 0.2443471 7.060481 at 50iterations 0.1168440 3.505714 at 60iterations 5.5559967E-02 1.579538 at 70iterations 2.6496582E-02 0.7698956 at 80iterations 1.2637090E-02 0.3669162 at 90iterations 6.0402779E-03 0.1800432 at 100iterations 2.8837761E-03 8.4308863E-02 at 110iterations 1.3795733E-03 4.2801380E-02 at 120iterations finished qdiffx linear iterations at : 14:03:14 total time elapsed so far: 10.94000 # loops : 120 mean,max change (kT/e) : 1.3795733E-03 4.2801380E-02 energy calculations done at 10.94000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.10000 DelPhi exited at 14:03:15 11.104u 0.436s 0:11.79 97.7% 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 14:03:15 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 = 3043 !!! WARNING: NAP 500 has a net charge of -2.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 2.882124 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): -12.43700 43.14700 ymin,ymax (A): -22.34500 22.54200 zmin,zma (A): -7.244000 47.32200 x,y,z range (A): 55.58400 44.88700 54.56600 scale (grids/A): 2.882124 object centre (A): 15.35500 9.8499298E-02 20.03900 number of atom coordinates read : 3043 total number of charged atoms : 2896 net assigned charge : 7.1674585E-06 assigned positive charge : 455.8235 centred at (gu) : 84.32927 88.06541 97.37727 assigned negative charge : -455.8243 centred at (gu) : 84.29591 87.65096 96.99711 start vw surface at 0.1200000 fill in re-entrant regions at 0.6000000 boundary points on vw surface= 208138 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23913 grid for indexing accessible points = 1.400000 m= 106535 mr = 157204 m= 36996 mr = 88863 m= 8318 mr = 29876 m= 1188 mr = 6066 m= 86 mr = 781 m= 1 mr = 28 m= 0 mr = 0 time to grow re-entrant surface = 1.150000 no. cavity mid-points inaccessible to solvent = 595 time to turn everything in is 1.870000 number of dielectric boundary points 78444 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 2.000000 number of grid points assigned charge 23167 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) : 1.921416 object centre at (A) : 15.35500 9.8499298E-02 20.03900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1139827 0.5570387 midg,1,midg; midg,igrid,midg -1.0864046E-02 0.2004616 1,midg,midg; igrid,midg,midg -0.6203291 0.1644193 gauss-seidel spectral radius is 0.9992769 estimated iterations to convergence 293 setup time was (sec) 2.210000 now iterating at: 14:03:17 rms-change max change #iterations 11.00452 376.0115 at 10iterations 6.478725 131.0138 at 20iterations 3.795179 67.61545 at 30iterations 2.219754 43.66132 at 40iterations 1.290585 21.98911 at 50iterations 0.7544410 12.42220 at 60iterations 0.4382984 7.820137 at 70iterations 0.2545152 4.387176 at 80iterations 0.1476015 2.383114 at 90iterations 8.5653134E-02 1.579865 at 100iterations 4.9558211E-02 0.8198185 at 110iterations 2.8763259E-02 0.4960499 at 120iterations 1.6732203E-02 0.2867050 at 130iterations 9.6900268E-03 0.1604986 at 140iterations 5.6299781E-03 0.1007690 at 150iterations 3.2688244E-03 5.1425934E-02 at 160iterations 1.9040209E-03 3.2320023E-02 at 170iterations 1.1153119E-03 1.8774033E-02 at 180iterations finished qdiffx linear iterations at : 14:03:34 total time elapsed so far: 18.74000 # loops : 180 mean,max change (kT/e) : 1.1153119E-03 1.8774033E-02 energy calculations done at 18.74000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 18.90000 DelPhi exited at 14:03:34 18.910u 0.487s 0:19.68 98.5% 0+0k 0+0io 0pf+0w