Sat Oct 15 13:26:53 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 15 2011 at 13:26:54 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: 237 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5510 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1300000 grid size : 179 scale,in grids/A, set to be: 0.4861927 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): -8.608000 49.90900 ymin,ymax (A): -6.503000 66.71900 zmin,zma (A): -11.09100 52.68600 x,y,z range (A): 58.51700 73.22200 63.77700 scale (grids/A): 0.4861927 object centre (A): 20.65050 30.10800 20.79750 number of atom coordinates read : 5510 total number of charged atoms : 5356 net assigned charge : -13.99998 assigned positive charge : 820.4758 centred at (gu) : 89.78487 89.83697 89.97646 assigned negative charge : -834.4830 centred at (gu) : 89.82029 89.98870 90.01649 start vw surface at 0.1900000 fill in re-entrant regions at 0.2100000 boundary points on vw surface= 7905 nv = 96 ne = 84 npr = 114025 no. pairs analyzed = 114025 no. exposed pairs = 6953 no. arc points = 46598 no. surface atoms = 2358 nbur = 3152 mkacc time = 0.3000000 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 = 1.736000 m= 227 mr = 3991 m= 1 mr = 4 m= 0 mr = 0 time to grow re-entrant surface = 0.3600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5800000 number of dielectric boundary points 4138 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4388 ## 677 charges are in solution ## iepsmp to db, and charging done at 0.6900000 number of grid points assigned charge 10903 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -2.3454995E-11 -1.0387981E-10 midg,1,midg; midg,igrid,midg 9.1199312E-11 -2.1122570E-10 1,midg,midg; igrid,midg,midg -2.9512337E-11 -9.4145726E-11 gauss-seidel spectral radius is 0.9784222 estimated iterations to convergence 56 setup time was (sec) 0.8900000 now iterating at: 13:26:57 rms-change max change #iterations 5.7782762E-02 8.891090 at 10iterations 3.4593840E-03 0.5502777 at 20iterations 4.6054774E-04 7.8149796E-02 at 30iterations 1.2290943E-04 1.7494202E-02 at 40iterations 4.1840736E-05 5.6667328E-03 at 50iterations finished qdiffx linear iterations at : 13:27:11 total time elapsed so far: 5.410000 # loops : 50 mean,max change (kT/e) : 4.1840736E-05 5.6667328E-03 energy calculations done at 5.410000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 5.600000 DelPhi exited at 13:27:12 5.607u 0.418s 0:19.33 31.0% 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 Sat Oct 15 2011 at 13:27:14 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: 237 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5510 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1200000 grid size : 179 scale,in grids/A, set to be: 1.458578 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): -8.608000 49.90900 ymin,ymax (A): -6.503000 66.71900 zmin,zma (A): -11.09100 52.68600 x,y,z range (A): 58.51700 73.22200 63.77700 scale (grids/A): 1.458578 object centre (A): 20.65050 30.10800 20.79750 number of atom coordinates read : 5510 total number of charged atoms : 5356 net assigned charge : -13.99998 assigned positive charge : 820.4758 centred at (gu) : 89.35288 89.50867 89.92764 assigned negative charge : -834.4830 centred at (gu) : 89.46078 89.96567 90.04932 start vw surface at 0.1900000 fill in re-entrant regions at 0.3300000 boundary points on vw surface= 90975 reading accessible surface arcs data from file ARCDAT no. of arc points read = 46598 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.624000 m= 24580 mr = 62171 m= 1812 mr = 15549 m= 37 mr = 692 m= 1 mr = 0 m= 0 mr = 0 time to grow re-entrant surface = 0.4100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.8100000 number of dielectric boundary points 38993 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 591 ## 16 charges are in solution ## iepsmp to db, and charging done at 0.9500000 number of grid points assigned charge 39538 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) : 0.4861927 object centre at (A) : 20.65050 30.10800 20.79750 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -3.3176965E-03 -1.1345806E-02 midg,1,midg; midg,igrid,midg 5.5239815E-03 -2.2263169E-02 1,midg,midg; igrid,midg,midg -1.3512566E-03 -5.9975521E-03 gauss-seidel spectral radius is 0.9979469 estimated iterations to convergence 176 setup time was (sec) 1.160000 now iterating at: 13:27:16 rms-change max change #iterations 3.671691 140.1654 at 10iterations 1.450786 52.90449 at 20iterations 0.5728523 20.90541 at 30iterations 0.2261453 7.153951 at 40iterations 8.9585729E-02 3.246262 at 50iterations 3.5367567E-02 1.080050 at 60iterations 1.4058447E-02 0.4350815 at 70iterations 5.5987909E-03 0.1936951 at 80iterations 2.2577918E-03 7.6383591E-02 at 90iterations 9.2679908E-04 3.1505585E-02 at 100iterations 3.9710759E-04 1.4991760E-02 at 110iterations 1.8645819E-04 5.8135986E-03 at 120iterations finished qdiffx linear iterations at : 13:27:38 total time elapsed so far: 13.37000 # loops : 120 mean,max change (kT/e) : 1.8645819E-04 5.8135986E-03 energy calculations done at 13.37000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.54000 DelPhi exited at 13:27:40 13.540u 0.520s 0:26.42 53.2% 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 15 2011 at 13:27:42 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: 237 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5510 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1300000 grid size : 179 scale,in grids/A, set to be: 2.187867 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): -8.608000 49.90900 ymin,ymax (A): -6.503000 66.71900 zmin,zma (A): -11.09100 52.68600 x,y,z range (A): 58.51700 73.22200 63.77700 scale (grids/A): 2.187867 object centre (A): 20.65050 30.10800 20.79750 number of atom coordinates read : 5510 total number of charged atoms : 5356 net assigned charge : -13.99998 assigned positive charge : 820.4758 centred at (gu) : 89.02867 89.26260 89.89113 assigned negative charge : -834.4830 centred at (gu) : 89.19112 89.94846 90.07410 start vw surface at 0.2000000 fill in re-entrant regions at 0.6100000 boundary points on vw surface= 212696 reading accessible surface arcs data from file ARCDAT no. of arc points read = 46598 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.596000 m= 90566 mr = 154148 m= 20820 mr = 68846 m= 2432 mr = 14272 m= 100 mr = 1381 m= 0 mr = 15 time to grow re-entrant surface = 1.200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.960000 number of dielectric boundary points 87952 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 79 iepsmp to db, and charging done at 2.130000 number of grid points assigned charge 42665 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) : 1.458578 object centre at (A) : 20.65050 30.10800 20.79750 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -8.8543437E-02 -0.2256326 midg,1,midg; midg,igrid,midg -3.4780595E-02 -0.4750953 1,midg,midg; igrid,midg,midg -4.2743124E-02 -0.1231054 gauss-seidel spectral radius is 0.9991270 estimated iterations to convergence 267 setup time was (sec) 2.370000 now iterating at: 13:27:49 rms-change max change #iterations 10.38703 303.2361 at 10iterations 5.955986 145.0548 at 20iterations 3.372623 72.51430 at 30iterations 1.893706 40.72995 at 40iterations 1.062197 25.65645 at 50iterations 0.5906392 12.43619 at 60iterations 0.3278637 6.677809 at 70iterations 0.1812915 3.815904 at 80iterations 0.1002147 2.100094 at 90iterations 5.5302054E-02 1.263655 at 100iterations 3.0493556E-02 0.5824432 at 110iterations 1.6741052E-02 0.3394527 at 120iterations 9.2179421E-03 0.1688538 at 130iterations 5.0735306E-03 9.1215134E-02 at 140iterations 2.7901034E-03 5.1701546E-02 at 150iterations 1.5350339E-03 2.9953003E-02 at 160iterations 8.4407179E-04 1.6186714E-02 at 170iterations 4.6615937E-04 8.4190369E-03 at 180iterations finished qdiffx linear iterations at : 13:28:44 total time elapsed so far: 23.65000 # loops : 180 mean,max change (kT/e) : 4.6615937E-04 8.4190369E-03 energy calculations done at 23.65000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 23.84000 DelPhi exited at 13:28:45 23.840u 0.561s 1:03.82 38.2% 0+0k 0+0io 0pf+0w