Tue Nov 22 14:11:33 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 14:11:37 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: 242 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1958 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: 0.6511083 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): -3.625000 48.25800 ymin,ymax (A): -4.806000 34.78300 zmin,zma (A): -23.32700 31.34900 x,y,z range (A): 51.88300 39.58900 54.67600 scale (grids/A): 0.6511083 object centre (A): 22.31650 14.98850 4.011001 number of atom coordinates read : 1958 total number of charged atoms : 1826 net assigned charge : 5.000011 assigned positive charge : 289.7620 centred at (gu) : 92.48092 89.36193 89.84768 assigned negative charge : -284.7623 centred at (gu) : 92.57440 89.24803 89.78345 start vw surface at 7.0000000E-02 fill in re-entrant regions at 7.0000000E-02 boundary points on vw surface= 5700 nv = 96 ne = 84 npr = 40289 no. pairs analyzed = 40289 no. exposed pairs = 2464 no. arc points = 17299 no. surface atoms = 839 nbur = 1119 mkacc time = 7.0000000E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 295 mr = 3134 m= 1 mr = 43 m= 0 mr = 0 time to grow re-entrant surface = 8.0000006E-02 no. cavity mid-points inaccessible to solvent = 10 time to turn everything in is 0.1500000 number of dielectric boundary points 2819 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1838 ## 189 charges are in solution ## iepsmp to db, and charging done at 0.2200000 number of grid points assigned charge 6673 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.9976424E-09 1.7054633E-08 midg,1,midg; midg,igrid,midg -3.3812897E-09 2.0282311E-08 1,midg,midg; igrid,midg,midg 1.2527863E-08 -1.3429726E-09 gauss-seidel spectral radius is 0.9877198 estimated iterations to convergence 74 setup time was (sec) 0.3600000 now iterating at: 14:11:40 rms-change max change #iterations 0.1360972 20.46967 at 10iterations 1.3741530E-02 2.239144 at 20iterations 1.4084993E-03 0.2109604 at 30iterations 1.4370671E-04 2.1311760E-02 at 40iterations 1.4786264E-05 2.3460388E-03 at 50iterations finished qdiffx linear iterations at : 14:11:50 total time elapsed so far: 3.430000 # loops : 50 mean,max change (kT/e) : 1.4786264E-05 2.3460388E-03 energy calculations done at 3.430000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.570000 DelPhi exited at 14:11:51 3.573u 0.192s 0:15.12 24.8% 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 14:11:54 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: 242 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1958 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: 1.953325 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): -3.625000 48.25800 ymin,ymax (A): -4.806000 34.78300 zmin,zma (A): -23.32700 31.34900 x,y,z range (A): 51.88300 39.58900 54.67600 scale (grids/A): 1.953325 object centre (A): 22.31650 14.98850 4.011001 number of atom coordinates read : 1958 total number of charged atoms : 1826 net assigned charge : 5.000011 assigned positive charge : 289.7620 centred at (gu) : 97.44298 88.08588 89.54327 assigned negative charge : -284.7623 centred at (gu) : 97.72340 87.74435 89.35070 start vw surface at 7.0000000E-02 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 61005 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17299 grid for indexing accessible points = 1.400000 m= 22034 mr = 41945 m= 3322 mr = 16583 m= 185 mr = 2145 m= 2 mr = 72 m= 0 mr = 0 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 537 time to turn everything in is 0.3100000 number of dielectric boundary points 25803 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 104 iepsmp to db, and charging done at 0.3900000 number of grid points assigned charge 14396 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) : 0.6511083 object centre at (A) : 22.31650 14.98850 4.011001 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.5722857E-02 1.6042210E-02 midg,1,midg; midg,igrid,midg 4.3071131E-03 1.0904723E-02 1,midg,midg; igrid,midg,midg 3.1565741E-02 7.0046359E-03 gauss-seidel spectral radius is 0.9986226 estimated iterations to convergence 214 setup time was (sec) 0.5400000 now iterating at: 14:11:58 rms-change max change #iterations 3.752317 160.4375 at 10iterations 1.752151 68.72414 at 20iterations 0.8161864 29.72681 at 30iterations 0.3808092 14.77934 at 40iterations 0.1779156 6.120698 at 50iterations 8.2622811E-02 3.143553 at 60iterations 3.8508493E-02 1.351445 at 70iterations 1.8051889E-02 0.6817675 at 80iterations 8.4074885E-03 0.2901049 at 90iterations 3.9175414E-03 0.1257507 at 100iterations 1.8240559E-03 6.0964584E-02 at 110iterations 8.5238047E-04 2.9190063E-02 at 120iterations finished qdiffx linear iterations at : 14:12:21 total time elapsed so far: 8.240000 # loops : 120 mean,max change (kT/e) : 8.5238047E-04 2.9190063E-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 14:12:22 8.377u 0.226s 0:29.01 29.6% 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 14:12:26 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: 242 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1958 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: 2.929987 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): -3.625000 48.25800 ymin,ymax (A): -4.806000 34.78300 zmin,zma (A): -23.32700 31.34900 x,y,z range (A): 51.88300 39.58900 54.67600 scale (grids/A): 2.929987 object centre (A): 22.31650 14.98850 4.011001 number of atom coordinates read : 1958 total number of charged atoms : 1826 net assigned charge : 5.000011 assigned positive charge : 289.7620 centred at (gu) : 101.1643 87.12880 89.31487 assigned negative charge : -284.7623 centred at (gu) : 101.5851 86.61659 89.02612 start vw surface at 7.0000000E-02 fill in re-entrant regions at 0.2800000 boundary points on vw surface= 140922 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17299 grid for indexing accessible points = 1.400000 m= 71156 mr = 101444 m= 25823 mr = 58801 m= 5845 mr = 21129 m= 849 mr = 4490 m= 51 mr = 580 m= 2 mr = 32 m= 0 mr = 0 time to grow re-entrant surface = 0.4400000 no. cavity mid-points inaccessible to solvent = 1875 time to turn everything in is 0.8000000 number of dielectric boundary points 58172 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 0.8800000 number of grid points assigned charge 14608 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) : 1.953325 object centre at (A) : 22.31650 14.98850 4.011001 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.9127639 2.6040163E-02 midg,1,midg; midg,igrid,midg 8.6375780E-02 7.0061952E-02 1,midg,midg; igrid,midg,midg 0.2706620 -1.2276784E-02 gauss-seidel spectral radius is 0.9992421 estimated iterations to convergence 287 setup time was (sec) 1.030000 now iterating at: 14:12:32 rms-change max change #iterations 8.789912 413.3789 at 10iterations 5.079978 130.8921 at 20iterations 2.913243 66.40111 at 30iterations 1.669101 38.99880 at 40iterations 0.9557886 21.20878 at 50iterations 0.5465919 12.88899 at 60iterations 0.3120461 5.913424 at 70iterations 0.1780776 3.652300 at 80iterations 0.1013858 2.001667 at 90iterations 5.7917885E-02 1.064949 at 100iterations 3.3016186E-02 0.6790401 at 110iterations 1.8833404E-02 0.3513794 at 120iterations 1.0706370E-02 0.2021484 at 130iterations 6.1292760E-03 0.1219864 at 140iterations 3.4753489E-03 7.0537567E-02 at 150iterations 1.9753941E-03 4.0300846E-02 at 160iterations 1.1295178E-03 2.2853374E-02 at 170iterations 6.4219284E-04 1.2750626E-02 at 180iterations finished qdiffx linear iterations at : 14:13:07 total time elapsed so far: 12.58000 # loops : 180 mean,max change (kT/e) : 6.4219284E-04 1.2750626E-02 energy calculations done at 12.58000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.71000 DelPhi exited at 14:13:09 12.711u 0.251s 0:43.48 29.8% 0+0k 0+0io 0pf+0w