Mon Oct 10 17:02:54 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 17:02:54 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2884 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: 0.5514080 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): -30.23100 34.33100 ymin,ymax (A): -25.36500 22.87900 zmin,zma (A): -37.69000 8.358000 x,y,z range (A): 64.56200 48.24400 46.04800 scale (grids/A): 0.5514080 object centre (A): 2.050001 -1.243000 -14.66600 number of atom coordinates read : 2884 total number of charged atoms : 2744 net assigned charge : 1.000017 assigned positive charge : 428.7991 centred at (gu) : 90.02222 89.78567 89.69749 assigned negative charge : -427.8003 centred at (gu) : 89.98244 89.96771 89.78965 start vw surface at 0.1100000 fill in re-entrant regions at 0.1200000 boundary points on vw surface= 5802 nv = 96 ne = 84 npr = 57298 no. pairs analyzed = 57298 no. exposed pairs = 3775 no. arc points = 26724 no. surface atoms = 1276 nbur = 1608 mkacc time = 0.1500000 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 = 1.568000 m= 245 mr = 2914 m= 1 mr = 14 m= 0 mr = 0 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3100000 number of dielectric boundary points 3120 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2744 ## 362 charges are in solution ## iepsmp to db, and charging done at 0.4600000 number of grid points assigned charge 7484 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 8.4727014E-10 -6.0896288E-10 midg,1,midg; midg,igrid,midg 1.5460382E-09 -1.3126042E-09 1,midg,midg; igrid,midg,midg -2.3885835E-10 3.8470871E-10 gauss-seidel spectral radius is 0.9830384 estimated iterations to convergence 63 setup time was (sec) 0.6300000 now iterating at: 17:02:56 rms-change max change #iterations 7.3739521E-02 13.97013 at 10iterations 5.0527076E-03 0.9740658 at 20iterations 3.3905962E-04 6.3530922E-02 at 30iterations 2.3624038E-05 4.3792725E-03 at 40iterations 1.7093570E-06 2.7465820E-04 at 50iterations finished qdiffx linear iterations at : 17:03:00 total time elapsed so far: 4.910000 # loops : 50 mean,max change (kT/e) : 1.7093570E-06 2.7465820E-04 energy calculations done at 4.910000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 5.100000 DelPhi exited at 17:03:01 5.103u 0.498s 0:06.62 84.4% 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 Mon Oct 10 2011 at 17:03:01 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 = 2884 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: 1.654224 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): -30.23100 34.33100 ymin,ymax (A): -25.36500 22.87900 zmin,zma (A): -37.69000 8.358000 x,y,z range (A): 64.56200 48.24400 46.04800 scale (grids/A): 1.654224 object centre (A): 2.050001 -1.243000 -14.66600 number of atom coordinates read : 2884 total number of charged atoms : 2744 net assigned charge : 1.000017 assigned positive charge : 428.7991 centred at (gu) : 90.06598 89.35607 89.09177 assigned negative charge : -427.8003 centred at (gu) : 89.94692 89.90284 89.36864 start vw surface at 0.1300000 fill in re-entrant regions at 0.2300000 boundary points on vw surface= 63724 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26724 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 19114 mr = 42261 m= 1952 mr = 12871 m= 46 mr = 900 m= 0 mr = 6 time to grow re-entrant surface = 0.2600000 no. cavity mid-points inaccessible to solvent = 1043 time to turn everything in is 0.5300000 number of dielectric boundary points 28798 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 336 ## 6 charges are in solution ## iepsmp to db, and charging done at 0.6700000 number of grid points assigned charge 21077 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) : 0.5514080 object centre at (A) : 2.050001 -1.243000 -14.66600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.9131902E-03 -1.6392990E-03 midg,1,midg; midg,igrid,midg 1.1412933E-02 -1.9500488E-02 1,midg,midg; igrid,midg,midg -4.9574752E-03 1.2701625E-02 gauss-seidel spectral radius is 0.9982289 estimated iterations to convergence 189 setup time was (sec) 0.8800000 now iterating at: 17:03:02 rms-change max change #iterations 3.330999 152.5582 at 10iterations 1.399954 59.34324 at 20iterations 0.5857974 26.33139 at 30iterations 0.2471806 8.865997 at 40iterations 0.1038781 3.900757 at 50iterations 4.3757871E-02 1.809814 at 60iterations 1.8371042E-02 0.7503843 at 70iterations 7.7846111E-03 0.3093863 at 80iterations 3.2563622E-03 0.1173716 at 90iterations 1.3716337E-03 5.0683975E-02 at 100iterations 5.8184896E-04 2.0684838E-02 at 110iterations 2.4386671E-04 8.4989369E-03 at 120iterations finished qdiffx linear iterations at : 17:03:13 total time elapsed so far: 11.46000 # loops : 120 mean,max change (kT/e) : 2.4386671E-04 8.4989369E-03 energy calculations done at 11.46000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.63000 DelPhi exited at 17:03:14 11.633u 0.520s 0:12.70 95.6% 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 Mon Oct 10 2011 at 17:03:14 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2884 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: 2.481336 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): -30.23100 34.33100 ymin,ymax (A): -25.36500 22.87900 zmin,zma (A): -37.69000 8.358000 x,y,z range (A): 64.56200 48.24400 46.04800 scale (grids/A): 2.481336 object centre (A): 2.050001 -1.243000 -14.66600 number of atom coordinates read : 2884 total number of charged atoms : 2744 net assigned charge : 1.000017 assigned positive charge : 428.7991 centred at (gu) : 90.09872 89.03384 88.63740 assigned negative charge : -427.8003 centred at (gu) : 89.92045 89.85417 89.05271 start vw surface at 0.1400000 fill in re-entrant regions at 0.4400000 boundary points on vw surface= 148360 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26724 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 66174 mr = 104088 m= 18650 mr = 51582 m= 2782 mr = 13667 m= 178 mr = 1739 m= 3 mr = 82 m= 0 mr = 0 time to grow re-entrant surface = 0.7800000 no. cavity mid-points inaccessible to solvent = 3397 time to turn everything in is 1.310000 number of dielectric boundary points 64989 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 18 iepsmp to db, and charging done at 1.450000 number of grid points assigned charge 21934 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) : 1.654224 object centre at (A) : 2.050001 -1.243000 -14.66600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.9832655E-02 -1.3091539E-02 midg,1,midg; midg,igrid,midg 0.1763975 -0.2645327 1,midg,midg; igrid,midg,midg 0.3098305 0.2591486 gauss-seidel spectral radius is 0.9991550 estimated iterations to convergence 272 setup time was (sec) 1.660000 now iterating at: 17:03:16 rms-change max change #iterations 8.652297 305.0618 at 10iterations 4.879464 172.6198 at 20iterations 2.749497 74.62624 at 30iterations 1.536517 43.73557 at 40iterations 0.8578761 21.70610 at 50iterations 0.4772393 11.44575 at 60iterations 0.2654277 6.292339 at 70iterations 0.1467087 3.155441 at 80iterations 8.1334613E-02 1.867617 at 90iterations 4.5032542E-02 0.9073372 at 100iterations 2.4893105E-02 0.6808662 at 110iterations 1.3744568E-02 0.3392277 at 120iterations 7.5900061E-03 0.1532841 at 130iterations 4.1941977E-03 9.8123550E-02 at 140iterations 2.3200214E-03 5.4540634E-02 at 150iterations 1.2779355E-03 2.8713226E-02 at 160iterations 7.0765492E-04 1.4842987E-02 at 170iterations 3.9109366E-04 8.4457397E-03 at 180iterations finished qdiffx linear iterations at : 17:03:33 total time elapsed so far: 19.11000 # loops : 180 mean,max change (kT/e) : 3.9109366E-04 8.4457397E-03 energy calculations done at 19.11000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 19.28000 DelPhi exited at 17:03:34 19.286u 0.528s 0:20.50 96.5% 0+0k 0+0io 0pf+0w