Mon Oct 10 14:00:21 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+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 Mon Oct 10 2011 at 14:00:22 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: 273 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2576 !!! WARNING: SEP 139 has a net charge of -0.4750 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6525286 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): -25.17700 29.38000 ymin,ymax (A): 11.15900 63.54100 zmin,zma (A): -9.345000 36.24600 x,y,z range (A): 54.55700 52.38200 45.59100 scale (grids/A): 0.6525286 object centre (A): 2.101501 37.35000 13.45050 number of atom coordinates read : 2576 total number of charged atoms : 2430 net assigned charge : 4.525008 assigned positive charge : 390.0179 centred at (gu) : 89.89510 90.22047 91.02948 assigned negative charge : -385.4936 centred at (gu) : 89.83301 90.25387 90.98750 start vw surface at 0.1200000 fill in re-entrant regions at 0.1300000 boundary points on vw surface= 7194 nv = 96 ne = 84 npr = 52438 no. pairs analyzed = 52438 no. exposed pairs = 3010 no. arc points = 21541 no. surface atoms = 1028 nbur = 1548 mkacc time = 0.1400000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 380 mr = 3967 m= 3 mr = 59 m= 0 mr = 0 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 42 time to turn everything in is 0.3100000 number of dielectric boundary points 3551 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2149 ## 178 charges are in solution ## iepsmp to db, and charging done at 0.4400000 number of grid points assigned charge 8651 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.0961821E-09 1.9945547E-08 midg,1,midg; midg,igrid,midg 1.4052434E-08 4.0590766E-09 1,midg,midg; igrid,midg,midg -8.2471052E-10 1.8885174E-08 gauss-seidel spectral radius is 0.9878259 estimated iterations to convergence 74 setup time was (sec) 0.6100000 now iterating at: 14:00:23 rms-change max change #iterations 0.1544051 21.47198 at 10iterations 1.6129065E-02 2.604451 at 20iterations 1.6857344E-03 0.2267566 at 30iterations 1.7610413E-04 2.5582314E-02 at 40iterations 1.8078246E-05 2.6817322E-03 at 50iterations finished qdiffx linear iterations at : 14:00:27 total time elapsed so far: 4.860000 # loops : 50 mean,max change (kT/e) : 1.8078246E-05 2.6817322E-03 energy calculations done at 4.860000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 5.020000 DelPhi exited at 14:00:29 5.025u 0.396s 0:07.34 73.7% 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 Mon Oct 10 2011 at 14:00:29 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: 273 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2576 !!! WARNING: SEP 139 has a net charge of -0.4750 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.957586 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): -25.17700 29.38000 ymin,ymax (A): 11.15900 63.54100 zmin,zma (A): -9.345000 36.24600 x,y,z range (A): 54.55700 52.38200 45.59100 scale (grids/A): 1.957586 object centre (A): 2.101501 37.35000 13.45050 number of atom coordinates read : 2576 total number of charged atoms : 2430 net assigned charge : 4.525008 assigned positive charge : 390.0179 centred at (gu) : 89.68475 90.66071 93.08781 assigned negative charge : -385.4936 centred at (gu) : 89.49883 90.76173 92.96255 start vw surface at 0.1200000 fill in re-entrant regions at 0.2600000 boundary points on vw surface= 78092 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21541 grid for indexing accessible points = 1.400000 m= 27559 mr = 54415 m= 4399 mr = 20382 m= 346 mr = 2849 m= 8 mr = 161 m= 0 mr = 0 time to grow re-entrant surface = 0.3300000 no. cavity mid-points inaccessible to solvent = 1675 time to turn everything in is 0.6400000 number of dielectric boundary points 32597 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 145 iepsmp to db, and charging done at 0.7600000 number of grid points assigned charge 19154 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) : 0.6525286 object centre at (A) : 2.101501 37.35000 13.45050 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.1722788E-02 9.8518748E-03 midg,1,midg; midg,igrid,midg 2.9602481E-02 -1.6437821E-02 1,midg,midg; igrid,midg,midg 4.3208797E-02 2.4929833E-02 gauss-seidel spectral radius is 0.9986931 estimated iterations to convergence 219 setup time was (sec) 0.9500000 now iterating at: 14:00:31 rms-change max change #iterations 4.453771 180.1393 at 10iterations 2.113615 71.86556 at 20iterations 1.005461 35.97871 at 30iterations 0.4771661 15.02966 at 40iterations 0.2277744 6.687172 at 50iterations 0.1081053 3.141043 at 60iterations 5.1559411E-02 1.694912 at 70iterations 2.4485625E-02 0.7168732 at 80iterations 1.1633998E-02 0.3546295 at 90iterations 5.5530695E-03 0.1733475 at 100iterations 2.6469904E-03 8.4312439E-02 at 110iterations 1.2579777E-03 4.1564941E-02 at 120iterations finished qdiffx linear iterations at : 14:00:42 total time elapsed so far: 11.86000 # loops : 120 mean,max change (kT/e) : 1.2579777E-03 4.1564941E-02 energy calculations done at 11.86000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.03000 DelPhi exited at 14:00:43 12.036u 0.463s 0:13.80 90.5% 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 Mon Oct 10 2011 at 14:00:43 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: 273 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2576 !!! WARNING: SEP 139 has a net charge of -0.4750 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.936378 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): -25.17700 29.38000 ymin,ymax (A): 11.15900 63.54100 zmin,zma (A): -9.345000 36.24600 x,y,z range (A): 54.55700 52.38200 45.59100 scale (grids/A): 2.936378 object centre (A): 2.101501 37.35000 13.45050 number of atom coordinates read : 2576 total number of charged atoms : 2430 net assigned charge : 4.525008 assigned positive charge : 390.0179 centred at (gu) : 89.52704 90.99097 94.63163 assigned negative charge : -385.4936 centred at (gu) : 89.24813 91.14256 94.44363 start vw surface at 0.1100000 fill in re-entrant regions at 0.5400000 boundary points on vw surface= 180718 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21541 grid for indexing accessible points = 1.400000 m= 89987 mr = 131540 m= 32047 mr = 74230 m= 8092 mr = 25765 m= 1371 mr = 6129 m= 104 mr = 1036 m= 1 mr = 62 m= 0 mr = 0 time to grow re-entrant surface = 1.000000 no. cavity mid-points inaccessible to solvent = 5778 time to turn everything in is 1.660000 number of dielectric boundary points 73558 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.810000 number of grid points assigned charge 19440 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) : 1.957586 object centre at (A) : 2.101501 37.35000 13.45050 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1673649 0.1598892 midg,1,midg; midg,igrid,midg 0.3748351 -0.3235106 1,midg,midg; igrid,midg,midg 5.4280996E-02 0.2270125 gauss-seidel spectral radius is 0.9992719 estimated iterations to convergence 292 setup time was (sec) 2.000000 now iterating at: 14:00:46 rms-change max change #iterations 10.24053 343.2628 at 10iterations 5.939368 121.8770 at 20iterations 3.452660 71.83877 at 30iterations 1.996547 38.77225 at 40iterations 1.155908 20.79346 at 50iterations 0.6678367 12.17051 at 60iterations 0.3851543 7.412039 at 70iterations 0.2227719 3.800655 at 80iterations 0.1285377 2.293121 at 90iterations 7.4103504E-02 1.307521 at 100iterations 4.2740267E-02 0.7279034 at 110iterations 2.4676530E-02 0.4297571 at 120iterations 1.4197228E-02 0.2542152 at 130iterations 8.2035102E-03 0.1421719 at 140iterations 4.7328467E-03 7.9719543E-02 at 150iterations 2.7317475E-03 4.8957825E-02 at 160iterations 1.5760672E-03 2.8806686E-02 at 170iterations 9.0771582E-04 1.5103817E-02 at 180iterations finished qdiffx linear iterations at : 14:01:04 total time elapsed so far: 20.00000 # loops : 180 mean,max change (kT/e) : 9.0771582E-04 1.5103817E-02 energy calculations done at 20.00000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 20.16000 DelPhi exited at 14:01:05 20.168u 0.492s 0:21.50 96.0% 0+0k 0+0io 0pf+0w