Sun Oct 9 11:14:15 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 Sun Oct 9 2011 at 11:14:15 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2908 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: 0.6394942 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): -13.99400 41.67500 ymin,ymax (A): -25.35800 30.17000 zmin,zma (A): -18.79600 35.93900 x,y,z range (A): 55.66900 55.52800 54.73500 scale (grids/A): 0.6394942 object centre (A): 13.84050 2.406000 8.571500 number of atom coordinates read : 2908 total number of charged atoms : 2827 net assigned charge : 4.000020 assigned positive charge : 433.8559 centred at (gu) : 90.91570 89.51247 89.15679 assigned negative charge : -429.8577 centred at (gu) : 90.99151 89.39341 89.10007 start vw surface at 0.1400000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 8356 nv = 96 ne = 84 npr = 55675 no. pairs analyzed = 55675 no. exposed pairs = 4124 no. arc points = 29304 no. surface atoms = 1369 nbur = 1539 mkacc time = 0.1500000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 516 mr = 4279 m= 4 mr = 45 m= 0 mr = 0 time to grow re-entrant surface = 0.2000000 no. cavity mid-points inaccessible to solvent = 12 time to turn everything in is 0.3500000 number of dielectric boundary points 4552 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2815 ## 234 charges are in solution ## iepsmp to db, and charging done at 0.4600000 number of grid points assigned charge 10044 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.5909385E-09 1.1007428E-08 midg,1,midg; midg,igrid,midg -1.0439638E-08 1.8864021E-08 1,midg,midg; igrid,midg,midg 1.2802173E-08 -4.6352704E-09 gauss-seidel spectral radius is 0.9873783 estimated iterations to convergence 73 setup time was (sec) 0.6600000 now iterating at: 11:14:16 rms-change max change #iterations 0.1500795 28.43816 at 10iterations 1.4986767E-02 2.497471 at 20iterations 1.5913780E-03 0.2086239 at 30iterations 2.3210770E-04 3.1393051E-02 at 40iterations 5.3707237E-05 6.9828033E-03 at 50iterations finished qdiffx linear iterations at : 11:14:21 total time elapsed so far: 5.650000 # loops : 50 mean,max change (kT/e) : 5.3707237E-05 6.9828033E-03 energy calculations done at 5.650000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 5.820000 DelPhi exited at 11:14:22 5.820u 0.457s 0:06.64 94.4% 0+0k 0+0io 4pf+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 11:14:22 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2908 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: 1.918483 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): -13.99400 41.67500 ymin,ymax (A): -25.35800 30.17000 zmin,zma (A): -18.79600 35.93900 x,y,z range (A): 55.66900 55.52800 54.73500 scale (grids/A): 1.918483 object centre (A): 13.84050 2.406000 8.571500 number of atom coordinates read : 2908 total number of charged atoms : 2827 net assigned charge : 4.000020 assigned positive charge : 433.8559 centred at (gu) : 92.74608 88.53647 87.46955 assigned negative charge : -429.8577 centred at (gu) : 92.97452 88.18034 87.30015 start vw surface at 0.1300000 fill in re-entrant regions at 0.2800000 boundary points on vw surface= 90327 reading accessible surface arcs data from file ARCDAT no. of arc points read = 29304 grid for indexing accessible points = 1.400000 m= 32200 mr = 60442 m= 5458 mr = 22441 m= 331 mr = 3258 m= 4 mr = 92 m= 0 mr = 0 time to grow re-entrant surface = 0.4300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.7700000 number of dielectric boundary points 42087 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 133 iepsmp to db, and charging done at 0.9700000 number of grid points assigned charge 22270 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) : 0.6394942 object centre at (A) : 13.84050 2.406000 8.571500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.1416405E-02 8.3026951E-03 midg,1,midg; midg,igrid,midg 1.1001945E-02 5.1674433E-02 1,midg,midg; igrid,midg,midg 6.3065393E-03 -7.9775732E-03 gauss-seidel spectral radius is 0.9987150 estimated iterations to convergence 221 setup time was (sec) 1.210000 now iterating at: 11:14:24 rms-change max change #iterations 4.608204 219.4436 at 10iterations 2.190334 65.87795 at 20iterations 1.049327 33.40759 at 30iterations 0.5009832 14.63164 at 40iterations 0.2390979 7.230536 at 50iterations 0.1140178 3.326828 at 60iterations 5.4718658E-02 1.586201 at 70iterations 2.6200622E-02 0.8052044 at 80iterations 1.2572041E-02 0.3448229 at 90iterations 6.0342881E-03 0.1767545 at 100iterations 2.9080326E-03 8.4480286E-02 at 110iterations 1.4016574E-03 4.2969704E-02 at 120iterations finished qdiffx linear iterations at : 11:14:36 total time elapsed so far: 13.71000 # loops : 120 mean,max change (kT/e) : 1.4016574E-03 4.2969704E-02 energy calculations done at 13.71000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.88000 DelPhi exited at 11:14:37 13.884u 0.534s 0:14.92 96.5% 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 11:14:37 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2908 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: 2.877724 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): -13.99400 41.67500 ymin,ymax (A): -25.35800 30.17000 zmin,zma (A): -18.79600 35.93900 x,y,z range (A): 55.66900 55.52800 54.73500 scale (grids/A): 2.877724 object centre (A): 13.84050 2.406000 8.571500 number of atom coordinates read : 2908 total number of charged atoms : 2827 net assigned charge : 4.000020 assigned positive charge : 433.8559 centred at (gu) : 94.11900 87.80450 86.20421 assigned negative charge : -429.8577 centred at (gu) : 94.46184 87.27049 85.95023 start vw surface at 0.1300000 fill in re-entrant regions at 0.6100000 boundary points on vw surface= 208821 reading accessible surface arcs data from file ARCDAT no. of arc points read = 29304 grid for indexing accessible points = 1.400000 m= 102665 mr = 147406 m= 38071 mr = 81062 m= 9822 mr = 29498 m= 1357 mr = 7035 m= 58 mr = 839 m= 0 mr = 12 time to grow re-entrant surface = 1.290000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 2.070000 number of dielectric boundary points 94942 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.250000 number of grid points assigned charge 22616 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) : 1.918483 object centre at (A) : 13.84050 2.406000 8.571500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2301745 0.1560842 midg,1,midg; midg,igrid,midg 0.1436277 0.6143805 1,midg,midg; igrid,midg,midg 3.5563063E-02 7.6809116E-02 gauss-seidel spectral radius is 0.9993026 estimated iterations to convergence 299 setup time was (sec) 2.490000 now iterating at: 11:14:40 rms-change max change #iterations 10.95835 508.7936 at 10iterations 6.630943 151.3614 at 20iterations 3.974220 87.29045 at 30iterations 2.373882 44.45658 at 40iterations 1.410365 27.67562 at 50iterations 0.8348793 16.51888 at 60iterations 0.4928758 9.077612 at 70iterations 0.2902113 5.452703 at 80iterations 0.1707810 3.137373 at 90iterations 0.1001809 1.641205 at 100iterations 5.8860809E-02 0.9409943 at 110iterations 3.4495462E-02 0.6034393 at 120iterations 2.0207055E-02 0.3416929 at 130iterations 1.1833963E-02 0.2079220 at 140iterations 6.9448096E-03 0.1147385 at 150iterations 4.0684799E-03 6.8950176E-02 at 160iterations 2.3882189E-03 3.9859772E-02 at 170iterations 1.4043231E-03 2.2155762E-02 at 180iterations finished qdiffx linear iterations at : 11:15:01 total time elapsed so far: 23.96000 # loops : 180 mean,max change (kT/e) : 1.4043231E-03 2.2155762E-02 energy calculations done at 23.96000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 24.13000 DelPhi exited at 11:15:02 24.135u 0.550s 0:24.99 98.7% 0+0k 0+0io 0pf+0w