Sat Oct 8 20:26:17 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 Sat Oct 8 2011 at 20:26:17 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2571 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 0.6236205 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): -17.58000 31.79000 ymin,ymax (A): -24.28100 21.96500 zmin,zma (A): -12.49000 44.59600 x,y,z range (A): 49.37000 46.24600 57.08600 scale (grids/A): 0.6236205 object centre (A): 7.105000 -1.158000 16.05300 number of atom coordinates read : 2571 total number of charged atoms : 2453 net assigned charge : 3.500004 assigned positive charge : 390.0040 centred at (gu) : 91.49612 90.63594 89.74561 assigned negative charge : -386.5045 centred at (gu) : 91.58160 90.58818 89.63301 start vw surface at 0.1600000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 6541 nv = 96 ne = 84 npr = 53681 no. pairs analyzed = 53681 no. exposed pairs = 2959 no. arc points = 21467 no. surface atoms = 998 nbur = 1573 mkacc time = 0.1100000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 309 mr = 3675 m= 2 mr = 36 m= 0 mr = 0 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 126 time to turn everything in is 0.3000000 number of dielectric boundary points 3141 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2109 ## 215 charges are in solution ## iepsmp to db, and charging done at 0.3900000 number of grid points assigned charge 8111 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -5.4149658E-09 1.0777382E-08 midg,1,midg; midg,igrid,midg -2.1289417E-10 7.7349718E-09 1,midg,midg; igrid,midg,midg 6.8280257E-09 -4.3871076E-09 gauss-seidel spectral radius is 0.9866753 estimated iterations to convergence 71 setup time was (sec) 0.5000000 now iterating at: 20:26:17 rms-change max change #iterations 0.1288065 22.71517 at 10iterations 1.1979633E-02 2.039268 at 20iterations 1.1318993E-03 0.2035294 at 30iterations 1.0640643E-04 1.4730215E-02 at 40iterations 9.7301454E-06 1.6021729E-03 at 50iterations finished qdiffx linear iterations at : 20:26:20 total time elapsed so far: 2.910000 # loops : 50 mean,max change (kT/e) : 9.7301454E-06 1.6021729E-03 energy calculations done at 2.910000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.090000 DelPhi exited at 20:26:20 3.096u 0.147s 0:03.53 91.5% 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 Sat Oct 8 2011 at 20:26:20 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 = 2571 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: 1.870861 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): -17.58000 31.79000 ymin,ymax (A): -24.28100 21.96500 zmin,zma (A): -12.49000 44.59600 x,y,z range (A): 49.37000 46.24600 57.08600 scale (grids/A): 1.870861 object centre (A): 7.105000 -1.158000 16.05300 number of atom coordinates read : 2571 total number of charged atoms : 2453 net assigned charge : 3.500004 assigned positive charge : 390.0040 centred at (gu) : 94.48807 91.90739 89.23634 assigned negative charge : -386.5045 centred at (gu) : 94.74442 91.76418 88.89883 start vw surface at 0.1400000 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 71153 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21467 grid for indexing accessible points = 1.400000 m= 24348 mr = 49899 m= 3410 mr = 18047 m= 150 mr = 2059 m= 1 mr = 35 m= 0 mr = 0 time to grow re-entrant surface = 0.2200000 no. cavity mid-points inaccessible to solvent = 3784 time to turn everything in is 0.5000000 number of dielectric boundary points 29022 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 162 iepsmp to db, and charging done at 0.6300000 number of grid points assigned charge 19259 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) : 0.6236205 object centre at (A) : 7.105000 -1.158000 16.05300 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.1039469E-02 2.0527752E-02 midg,1,midg; midg,igrid,midg 1.0684843E-03 1.1354492E-02 1,midg,midg; igrid,midg,midg 3.0273208E-02 -1.2750896E-03 gauss-seidel spectral radius is 0.9985796 estimated iterations to convergence 210 setup time was (sec) 0.7800000 now iterating at: 20:26:21 rms-change max change #iterations 4.053072 175.5089 at 10iterations 1.871724 65.10265 at 20iterations 0.8632669 29.14305 at 30iterations 0.3975394 14.26821 at 40iterations 0.1843223 6.281219 at 50iterations 8.4974431E-02 2.723093 at 60iterations 3.9289497E-02 1.189756 at 70iterations 1.8130360E-02 0.5653844 at 80iterations 8.3587980E-03 0.2585678 at 90iterations 3.8604692E-03 0.1211662 at 100iterations 1.7833459E-03 6.1935425E-02 at 110iterations 8.2243147E-04 2.5337219E-02 at 120iterations finished qdiffx linear iterations at : 20:26:28 total time elapsed so far: 7.220000 # loops : 120 mean,max change (kT/e) : 8.2243147E-04 2.5337219E-02 energy calculations done at 7.220000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.410000 DelPhi exited at 20:26:28 7.409u 0.210s 0:07.94 95.8% 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 Sat Oct 8 2011 at 20:26:28 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 = 2571 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 2.806292 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): -17.58000 31.79000 ymin,ymax (A): -24.28100 21.96500 zmin,zma (A): -12.49000 44.59600 x,y,z range (A): 49.37000 46.24600 57.08600 scale (grids/A): 2.806292 object centre (A): 7.105000 -1.158000 16.05300 number of atom coordinates read : 2571 total number of charged atoms : 2453 net assigned charge : 3.500004 assigned positive charge : 390.0040 centred at (gu) : 96.73206 92.86101 88.85443 assigned negative charge : -386.5045 centred at (gu) : 97.11654 92.64629 88.34824 start vw surface at 0.1600000 fill in re-entrant regions at 0.4500000 boundary points on vw surface= 164699 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21467 grid for indexing accessible points = 1.400000 m= 81192 mr = 120788 m= 26964 mr = 66820 m= 6055 mr = 21491 m= 764 mr = 4508 m= 30 mr = 480 m= 0 mr = 6 time to grow re-entrant surface = 0.6900001 no. cavity mid-points inaccessible to solvent = 13027 time to turn everything in is 1.240000 number of dielectric boundary points 65611 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.380000 number of grid points assigned charge 19618 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) : 1.870861 object centre at (A) : 7.105000 -1.158000 16.05300 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1433966 0.2457880 midg,1,midg; midg,igrid,midg 7.4165491E-03 0.1441607 1,midg,midg; igrid,midg,midg 0.4121431 -1.3014616E-02 gauss-seidel spectral radius is 0.9992375 estimated iterations to convergence 286 setup time was (sec) 1.550000 now iterating at: 20:26:30 rms-change max change #iterations 9.499898 359.9519 at 10iterations 5.457019 109.5467 at 20iterations 3.112725 64.96005 at 30iterations 1.778826 38.25642 at 40iterations 1.012775 21.51878 at 50iterations 0.5769070 10.82225 at 60iterations 0.3295055 7.347763 at 70iterations 0.1875209 3.535148 at 80iterations 0.1068153 1.974637 at 90iterations 6.0801383E-02 1.119625 at 100iterations 3.4586575E-02 0.6153278 at 110iterations 1.9698232E-02 0.3697186 at 120iterations 1.1224931E-02 0.2257462 at 130iterations 6.3952012E-03 0.1260662 at 140iterations 3.6442059E-03 7.6162338E-02 at 150iterations 2.0702719E-03 3.9307594E-02 at 160iterations 1.1782905E-03 2.1905899E-02 at 170iterations 6.7296060E-04 1.2999535E-02 at 180iterations finished qdiffx linear iterations at : 20:26:40 total time elapsed so far: 11.82000 # loops : 180 mean,max change (kT/e) : 6.7296060E-04 1.2999535E-02 energy calculations done at 11.82000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.00000 DelPhi exited at 20:26:41 12.002u 0.207s 0:12.48 97.7% 0+0k 0+0io 0pf+0w