Tue Nov 22 14:22:10 PST 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 Tue Nov 22 2011 at 14:22:14 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: 259 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1968 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6006107 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): -24.74200 34.53100 ymin,ymax (A): -19.13000 20.75300 zmin,zma (A): -4.640000 38.73100 x,y,z range (A): 59.27300 39.88300 43.37100 scale (grids/A): 0.6006107 object centre (A): 4.894502 0.8115005 17.04550 number of atom coordinates read : 1968 total number of charged atoms : 1836 net assigned charge : 5.000010 assigned positive charge : 292.6519 centred at (gu) : 90.13279 90.30759 90.78194 assigned negative charge : -287.6523 centred at (gu) : 90.16825 90.41182 90.90977 start vw surface at 0.1200000 fill in re-entrant regions at 0.1300000 boundary points on vw surface= 4756 nv = 96 ne = 84 npr = 39757 no. pairs analyzed = 39757 no. exposed pairs = 2607 no. arc points = 18506 no. surface atoms = 884 nbur = 1084 mkacc time = 7.9999998E-02 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 = 1.456000 m= 252 mr = 2488 m= 3 mr = 28 m= 0 mr = 0 time to grow re-entrant surface = 9.0000004E-02 no. cavity mid-points inaccessible to solvent = 12 time to turn everything in is 0.2200000 number of dielectric boundary points 2495 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1891 ## 214 charges are in solution ## iepsmp to db, and charging done at 0.3400000 number of grid points assigned charge 5867 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 4.7799582E-09 -1.6355296E-09 midg,1,midg; midg,igrid,midg 4.7286837E-09 -7.3391299E-10 1,midg,midg; igrid,midg,midg 3.1105793E-09 1.2855594E-09 gauss-seidel spectral radius is 0.9856012 estimated iterations to convergence 68 setup time was (sec) 0.4500000 now iterating at: 14:22:18 rms-change max change #iterations 9.4684072E-02 20.89929 at 10iterations 7.7931914E-03 1.354946 at 20iterations 6.7263679E-04 0.1374457 at 30iterations 5.5256402E-05 1.0238647E-02 at 40iterations 4.8587594E-06 9.8419189E-04 at 50iterations finished qdiffx linear iterations at : 14:22:25 total time elapsed so far: 2.920000 # loops : 50 mean,max change (kT/e) : 4.8587594E-06 9.8419189E-04 energy calculations done at 2.920000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.100000 DelPhi exited at 14:22:27 3.106u 0.136s 0:13.30 24.2% 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 Tue Nov 22 2011 at 14:22:29 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: 259 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1968 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.801832 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): -24.74200 34.53100 ymin,ymax (A): -19.13000 20.75300 zmin,zma (A): -4.640000 38.73100 x,y,z range (A): 59.27300 39.88300 43.37100 scale (grids/A): 1.801832 object centre (A): 4.894502 0.8115005 17.04550 number of atom coordinates read : 1968 total number of charged atoms : 1836 net assigned charge : 5.000010 assigned positive charge : 292.6519 centred at (gu) : 90.39855 90.92259 92.34592 assigned negative charge : -287.6523 centred at (gu) : 90.50476 91.23555 92.72939 start vw surface at 0.1100000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 51298 reading accessible surface arcs data from file ARCDAT no. of arc points read = 18506 grid for indexing accessible points = 1.400000 m= 18003 mr = 34033 m= 2644 mr = 13301 m= 99 mr = 1611 m= 1 mr = 20 m= 0 mr = 0 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 661 time to turn everything in is 0.3800000 number of dielectric boundary points 23080 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 177 iepsmp to db, and charging done at 0.4900000 number of grid points assigned charge 14345 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) : 0.6006107 object centre at (A) : 4.894502 0.8115005 17.04550 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 7.3531806E-03 -3.5461213E-03 midg,1,midg; midg,igrid,midg 7.8280540E-03 -1.5590435E-03 1,midg,midg; igrid,midg,midg 3.8155194E-02 2.2903020E-02 gauss-seidel spectral radius is 0.9984046 estimated iterations to convergence 199 setup time was (sec) 0.6500000 now iterating at: 14:22:33 rms-change max change #iterations 3.230340 185.6378 at 10iterations 1.416430 58.79494 at 20iterations 0.6237862 25.45024 at 30iterations 0.2746864 10.18623 at 40iterations 0.1198439 5.862067 at 50iterations 5.2913036E-02 2.003903 at 60iterations 2.3368530E-02 0.9806318 at 70iterations 1.0247201E-02 0.3700837 at 80iterations 4.5173340E-03 0.1734120 at 90iterations 1.9826791E-03 8.6158752E-02 at 100iterations 8.6993905E-04 3.3337593E-02 at 110iterations 3.8432828E-04 1.5241623E-02 at 120iterations finished qdiffx linear iterations at : 14:22:54 total time elapsed so far: 6.910000 # loops : 120 mean,max change (kT/e) : 3.8432828E-04 1.5241623E-02 energy calculations done at 6.910000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.080000 DelPhi exited at 14:22:56 7.086u 0.177s 0:27.20 26.6% 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 Tue Nov 22 2011 at 14:22:57 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: 259 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1968 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.702748 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): -24.74200 34.53100 ymin,ymax (A): -19.13000 20.75300 zmin,zma (A): -4.640000 38.73100 x,y,z range (A): 59.27300 39.88300 43.37100 scale (grids/A): 2.702748 object centre (A): 4.894502 0.8115005 17.04550 number of atom coordinates read : 1968 total number of charged atoms : 1836 net assigned charge : 5.000010 assigned positive charge : 292.6519 centred at (gu) : 90.59779 91.38400 93.51880 assigned negative charge : -287.6523 centred at (gu) : 90.75729 91.85342 94.09415 start vw surface at 0.1100000 fill in re-entrant regions at 0.3100000 boundary points on vw surface= 118422 reading accessible surface arcs data from file ARCDAT no. of arc points read = 18506 grid for indexing accessible points = 1.400000 m= 58614 mr = 82681 m= 20713 mr = 47581 m= 4544 mr = 16734 m= 430 mr = 3450 m= 11 mr = 240 m= 0 mr = 2 time to grow re-entrant surface = 0.5300000 no. cavity mid-points inaccessible to solvent = 2249 time to turn everything in is 0.9100000 number of dielectric boundary points 52046 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.040000 number of grid points assigned charge 14682 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) : 1.801832 object centre at (A) : 4.894502 0.8115005 17.04550 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 6.7221932E-02 -1.3990469E-02 midg,1,midg; midg,igrid,midg 6.4505287E-02 -1.7905973E-02 1,midg,midg; igrid,midg,midg 0.3873380 0.1863265 gauss-seidel spectral radius is 0.9991792 estimated iterations to convergence 276 setup time was (sec) 1.200000 now iterating at: 14:23:04 rms-change max change #iterations 7.860864 255.7612 at 10iterations 4.474724 136.9794 at 20iterations 2.530617 59.28359 at 30iterations 1.421104 35.49226 at 40iterations 0.7971586 19.39303 at 50iterations 0.4458342 10.67091 at 60iterations 0.2495779 5.945496 at 70iterations 0.1389744 3.225983 at 80iterations 7.7848554E-02 1.744078 at 90iterations 4.3380655E-02 0.9928131 at 100iterations 2.4142016E-02 0.5405273 at 110iterations 1.3453204E-02 0.3394707 at 120iterations 7.4988501E-03 0.1706676 at 130iterations 4.1797822E-03 8.9266777E-02 at 140iterations 2.3284538E-03 4.9041748E-02 at 150iterations 1.2952697E-03 2.7503967E-02 at 160iterations 7.2086998E-04 1.5235901E-02 at 170iterations 4.0168950E-04 8.5916519E-03 at 180iterations finished qdiffx linear iterations at : 14:23:34 total time elapsed so far: 11.05000 # loops : 180 mean,max change (kT/e) : 4.0168950E-04 8.5916519E-03 energy calculations done at 11.05000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.23000 DelPhi exited at 14:23:35 11.230u 0.180s 0:38.00 30.0% 0+0k 0+0io 0pf+0w