Mon Oct 10 17:02:17 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 Mon Oct 10 2011 at 17:02:17 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: 246 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3172 !!! WARNING: WAT 4 has a net charge of -0.8340 !!! WARNING: WAT 5 has a net charge of -0.8340 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 0.5831477 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): 13.77500 72.12400 ymin,ymax (A): -0.8700000 51.35300 zmin,zma (A): 6.504000 67.55200 x,y,z range (A): 58.34900 52.22300 61.04800 scale (grids/A): 0.5831477 object centre (A): 42.94950 25.24150 37.02800 number of atom coordinates read : 3172 total number of charged atoms : 3021 net assigned charge : -4.667961 assigned positive charge : 475.6376 centred at (gu) : 89.66836 91.41058 91.20074 assigned negative charge : -480.3070 centred at (gu) : 89.62740 91.53089 91.30556 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1000000 boundary points on vw surface= 7282 nv = 96 ne = 84 npr = 62222 no. pairs analyzed = 62222 no. exposed pairs = 4211 no. arc points = 29683 no. surface atoms = 1433 nbur = 1739 mkacc time = 0.1100000 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 = 1.512000 m= 393 mr = 3797 m= 0 mr = 36 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2200000 number of dielectric boundary points 3842 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3069 ## 349 charges are in solution ## iepsmp to db, and charging done at 0.2900000 number of grid points assigned charge 9195 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.2554993E-09 -5.0774105E-09 midg,1,midg; midg,igrid,midg 1.4779389E-09 -5.9231899E-09 1,midg,midg; igrid,midg,midg -2.2883551E-09 2.5877007E-11 gauss-seidel spectral radius is 0.9848460 estimated iterations to convergence 67 setup time was (sec) 0.4200000 now iterating at: 17:02:17 rms-change max change #iterations 0.1021460 17.44879 at 10iterations 8.0310656E-03 1.111800 at 20iterations 6.4073579E-04 9.8808289E-02 at 30iterations 5.3069245E-05 7.2402954E-03 at 40iterations 5.8146034E-06 1.1310279E-03 at 50iterations finished qdiffx linear iterations at : 17:02:20 total time elapsed so far: 3.350000 # loops : 50 mean,max change (kT/e) : 5.8146034E-06 1.1310279E-03 energy calculations done at 3.350000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.480000 DelPhi exited at 17:02:21 3.486u 0.206s 0:04.27 86.1% 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 17:02:21 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: 246 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3172 !!! WARNING: WAT 4 has a net charge of -0.8340 !!! WARNING: WAT 5 has a net charge of -0.8340 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 1.749443 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): 13.77500 72.12400 ymin,ymax (A): -0.8700000 51.35300 zmin,zma (A): 6.504000 67.55200 x,y,z range (A): 58.34900 52.22300 61.04800 scale (grids/A): 1.749443 object centre (A): 42.94950 25.24150 37.02800 number of atom coordinates read : 3172 total number of charged atoms : 3021 net assigned charge : -4.667961 assigned positive charge : 475.6376 centred at (gu) : 89.00424 94.23104 93.60133 assigned negative charge : -480.3070 centred at (gu) : 88.88165 94.59234 93.91613 start vw surface at 0.1000000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 79798 reading accessible surface arcs data from file ARCDAT no. of arc points read = 29683 grid for indexing accessible points = 1.400000 m= 26399 mr = 53827 m= 3310 mr = 18503 m= 109 mr = 1785 m= 0 mr = 26 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 1329 time to turn everything in is 0.3800000 number of dielectric boundary points 35475 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 308 iepsmp to db, and charging done at 0.4600000 number of grid points assigned charge 23484 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) : 0.5831477 object centre at (A) : 42.94950 25.24150 37.02800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.9632295E-02 6.7370599E-03 midg,1,midg; midg,igrid,midg 2.3248792E-03 -2.3800561E-02 1,midg,midg; igrid,midg,midg -3.5778288E-02 7.5890222E-03 gauss-seidel spectral radius is 0.9984509 estimated iterations to convergence 202 setup time was (sec) 0.6000000 now iterating at: 17:02:22 rms-change max change #iterations 4.022698 179.0292 at 10iterations 1.777097 62.01112 at 20iterations 0.7907596 25.38469 at 30iterations 0.3527368 12.11243 at 40iterations 0.1566591 5.550552 at 50iterations 6.9745317E-02 2.385005 at 60iterations 3.0982098E-02 0.9476204 at 70iterations 1.3795018E-02 0.4067154 at 80iterations 6.1469544E-03 0.2153368 at 90iterations 2.7373638E-03 8.6645126E-02 at 100iterations 1.2215461E-03 4.3235779E-02 at 110iterations 5.4407259E-04 1.7485619E-02 at 120iterations finished qdiffx linear iterations at : 17:02:29 total time elapsed so far: 8.040000 # loops : 120 mean,max change (kT/e) : 5.4407259E-04 1.7485619E-02 energy calculations done at 8.040000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.170000 DelPhi exited at 17:02:30 8.170u 0.201s 0:09.07 92.2% 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 Mon Oct 10 2011 at 17:02:30 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: 246 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3172 !!! WARNING: WAT 4 has a net charge of -0.8340 !!! WARNING: WAT 5 has a net charge of -0.8340 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 2.624165 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): 13.77500 72.12400 ymin,ymax (A): -0.8700000 51.35300 zmin,zma (A): 6.504000 67.55200 x,y,z range (A): 58.34900 52.22300 61.04800 scale (grids/A): 2.624165 object centre (A): 42.94950 25.24150 37.02800 number of atom coordinates read : 3172 total number of charged atoms : 3021 net assigned charge : -4.667961 assigned positive charge : 475.6376 centred at (gu) : 88.50598 96.34634 95.40184 assigned negative charge : -480.3070 centred at (gu) : 88.32238 96.88851 95.87422 start vw surface at 0.1000000 fill in re-entrant regions at 0.3400000 boundary points on vw surface= 184960 reading accessible surface arcs data from file ARCDAT no. of arc points read = 29683 grid for indexing accessible points = 1.400000 m= 88406 mr = 131323 m= 28347 mr = 70364 m= 5314 mr = 21797 m= 524 mr = 3699 m= 23 mr = 307 m= 0 mr = 6 time to grow re-entrant surface = 0.5400000 no. cavity mid-points inaccessible to solvent = 4830 time to turn everything in is 0.9800000 number of dielectric boundary points 80078 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 7 iepsmp to db, and charging done at 1.070000 number of grid points assigned charge 24162 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) : 1.749443 object centre at (A) : 42.94950 25.24150 37.02800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.4142717 0.1812042 midg,1,midg; midg,igrid,midg 2.7023284E-02 -0.2246800 1,midg,midg; igrid,midg,midg -0.4423160 0.1918819 gauss-seidel spectral radius is 0.9992294 estimated iterations to convergence 284 setup time was (sec) 1.230000 now iterating at: 17:02:32 rms-change max change #iterations 10.09394 292.9999 at 10iterations 5.882934 153.4277 at 20iterations 3.394655 74.62659 at 30iterations 1.953597 40.86220 at 40iterations 1.121809 24.10991 at 50iterations 0.6409414 13.86470 at 60iterations 0.3667832 7.836243 at 70iterations 0.2089254 3.994913 at 80iterations 0.1188651 2.420952 at 90iterations 6.7665718E-02 1.221600 at 100iterations 3.8492128E-02 0.7434540 at 110iterations 2.1910273E-02 0.4100723 at 120iterations 1.2434602E-02 0.2665024 at 130iterations 7.0749521E-03 0.1220407 at 140iterations 4.0231375E-03 7.5893924E-02 at 150iterations 2.2894931E-03 3.9445400E-02 at 160iterations 1.3004738E-03 2.5121689E-02 at 170iterations 7.4252166E-04 1.3052464E-02 at 180iterations finished qdiffx linear iterations at : 17:02:44 total time elapsed so far: 13.52000 # loops : 180 mean,max change (kT/e) : 7.4252166E-04 1.3052464E-02 energy calculations done at 13.52000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.66000 DelPhi exited at 17:02:45 13.657u 0.203s 0:14.59 94.9% 0+0k 0+0io 0pf+0w