Sun Oct 9 14:46:53 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 Sun Oct 9 2011 at 14:46:53 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: 261 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3116 !!! WARNING: ASP 287 has a net charge of -2.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 0.5309708 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): 12.85000 67.52900 ymin,ymax (A): -25.98300 21.88600 zmin,zma (A): -33.50400 33.54300 x,y,z range (A): 54.67900 47.86900 67.04700 scale (grids/A): 0.5309708 object centre (A): 40.18950 -2.048500 1.9500732E-02 number of atom coordinates read : 3116 total number of charged atoms : 2968 net assigned charge : -4.499983 assigned positive charge : 468.2767 centred at (gu) : 90.21950 90.35385 90.08678 assigned negative charge : -472.7780 centred at (gu) : 90.11972 90.23537 90.08929 start vw surface at 0.1800000 fill in re-entrant regions at 0.1900000 boundary points on vw surface= 5846 nv = 96 ne = 84 npr = 60041 no. pairs analyzed = 60041 no. exposed pairs = 4655 no. arc points = 33683 no. surface atoms = 1511 nbur = 1605 mkacc time = 0.1400000 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 = 1.596000 m= 261 mr = 2622 m= 1 mr = 14 m= 0 mr = 0 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3600000 number of dielectric boundary points 3472 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3246 ## 416 charges are in solution ## iepsmp to db, and charging done at 0.4700000 number of grid points assigned charge 7695 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.4259763E-10 -1.6920913E-10 midg,1,midg; midg,igrid,midg -5.7884086E-10 3.3803529E-10 1,midg,midg; igrid,midg,midg -5.2680044E-10 2.4979280E-10 gauss-seidel spectral radius is 0.9817476 estimated iterations to convergence 61 setup time was (sec) 0.5900000 now iterating at: 14:46:54 rms-change max change #iterations 6.4825624E-02 11.12070 at 10iterations 3.9577167E-03 0.7754459 at 20iterations 2.8790298E-04 4.6661377E-02 at 30iterations 4.9381608E-05 6.2110424E-03 at 40iterations 1.4667207E-05 1.6851425E-03 at 50iterations finished qdiffx linear iterations at : 14:46:57 total time elapsed so far: 3.180000 # loops : 50 mean,max change (kT/e) : 1.4667207E-05 1.6851425E-03 energy calculations done at 3.180000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.360000 DelPhi exited at 14:46:57 3.364u 0.160s 0:03.80 92.6% 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 Sun Oct 9 2011 at 14:46:57 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: 261 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3116 !!! WARNING: ASP 287 has a net charge of -2.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 1.592913 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): 12.85000 67.52900 ymin,ymax (A): -25.98300 21.88600 zmin,zma (A): -33.50400 33.54300 x,y,z range (A): 54.67900 47.86900 67.04700 scale (grids/A): 1.592913 object centre (A): 40.18950 -2.048500 1.9500732E-02 number of atom coordinates read : 3116 total number of charged atoms : 2968 net assigned charge : -4.499983 assigned positive charge : 468.2767 centred at (gu) : 90.65785 91.06062 90.25940 assigned negative charge : -472.7780 centred at (gu) : 90.35886 90.70586 90.26744 start vw surface at 0.1800000 fill in re-entrant regions at 0.2600000 boundary points on vw surface= 63664 reading accessible surface arcs data from file ARCDAT no. of arc points read = 33683 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 19042 mr = 39882 m= 2072 mr = 11636 m= 64 mr = 798 m= 2 mr = 7 m= 0 mr = 0 time to grow re-entrant surface = 0.2400000 no. cavity mid-points inaccessible to solvent = 268 time to turn everything in is 0.5400000 number of dielectric boundary points 32521 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 401 ## 8 charges are in solution ## iepsmp to db, and charging done at 0.6600000 number of grid points assigned charge 22568 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) : 0.5309708 object centre at (A) : 40.18950 -2.048500 1.9500732E-02 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -3.1993970E-02 -1.0333196E-03 midg,1,midg; midg,igrid,midg -6.0826023E-03 2.7175571E-03 1,midg,midg; igrid,midg,midg -9.6588582E-03 3.9924501E-04 gauss-seidel spectral radius is 0.9981279 estimated iterations to convergence 184 setup time was (sec) 0.8300000 now iterating at: 14:46:58 rms-change max change #iterations 3.267354 154.4147 at 10iterations 1.332937 48.38480 at 20iterations 0.5455735 20.02781 at 30iterations 0.2236183 7.953683 at 40iterations 9.1757171E-02 3.625075 at 50iterations 3.7659381E-02 1.524204 at 60iterations 1.5457400E-02 0.7315369 at 70iterations 6.3337968E-03 0.2352676 at 80iterations 2.6100669E-03 9.9423885E-02 at 90iterations 1.0786329E-03 3.8846016E-02 at 100iterations 4.4992627E-04 1.6742706E-02 at 110iterations 1.8960319E-04 6.7956448E-03 at 120iterations finished qdiffx linear iterations at : 14:47:05 total time elapsed so far: 7.340000 # loops : 120 mean,max change (kT/e) : 1.8960319E-04 6.7956448E-03 energy calculations done at 7.340000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.540000 DelPhi exited at 14:47:05 7.544u 0.186s 0:08.01 96.3% 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 Sun Oct 9 2011 at 14:47:05 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: 261 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3116 !!! WARNING: ASP 287 has a net charge of -2.0000 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: 2.389369 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): 12.85000 67.52900 ymin,ymax (A): -25.98300 21.88600 zmin,zma (A): -33.50400 33.54300 x,y,z range (A): 54.67900 47.86900 67.04700 scale (grids/A): 2.389369 object centre (A): 40.18950 -2.048500 1.9500732E-02 number of atom coordinates read : 3116 total number of charged atoms : 2968 net assigned charge : -4.499983 assigned positive charge : 468.2767 centred at (gu) : 90.98638 91.59060 90.38901 assigned negative charge : -472.7780 centred at (gu) : 90.53817 91.05869 90.40098 start vw surface at 0.1600000 fill in re-entrant regions at 0.4000000 boundary points on vw surface= 147789 reading accessible surface arcs data from file ARCDAT no. of arc points read = 33683 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 65494 mr = 99009 m= 17999 mr = 48323 m= 3064 mr = 11972 m= 231 mr = 1657 m= 5 mr = 70 m= 0 mr = 0 time to grow re-entrant surface = 0.6899999 no. cavity mid-points inaccessible to solvent = 935 time to turn everything in is 1.170000 number of dielectric boundary points 73551 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 36 iepsmp to db, and charging done at 1.300000 number of grid points assigned charge 23710 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) : 1.592913 object centre at (A) : 40.18950 -2.048500 1.9500732E-02 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.053355 6.5368541E-02 midg,1,midg; midg,igrid,midg -9.9208929E-02 5.1676478E-02 1,midg,midg; igrid,midg,midg -0.1081244 -1.9941203E-02 gauss-seidel spectral radius is 0.9991397 estimated iterations to convergence 269 setup time was (sec) 1.470000 now iterating at: 14:47:07 rms-change max change #iterations 8.852353 301.2344 at 10iterations 5.084567 154.5525 at 20iterations 2.901365 85.92031 at 30iterations 1.635744 45.05895 at 40iterations 0.9196501 32.10787 at 50iterations 0.5126421 13.55291 at 60iterations 0.2858588 7.156484 at 70iterations 0.1587841 4.086880 at 80iterations 8.8226743E-02 2.504022 at 90iterations 4.8788134E-02 1.225220 at 100iterations 2.7082408E-02 0.7149663 at 110iterations 1.4938329E-02 0.3622894 at 120iterations 8.2553932E-03 0.1901580 at 130iterations 4.5543956E-03 0.1159344 at 140iterations 2.5162119E-03 5.6951642E-02 at 150iterations 1.3832859E-03 3.3276558E-02 at 160iterations 7.6468510E-04 1.8203735E-02 at 170iterations 4.2137579E-04 9.2918873E-03 at 180iterations finished qdiffx linear iterations at : 14:47:17 total time elapsed so far: 11.70000 # loops : 180 mean,max change (kT/e) : 4.2137579E-04 9.2918873E-03 energy calculations done at 11.70000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.89000 DelPhi exited at 14:47:18 11.888u 0.195s 0:12.43 97.1% 0+0k 0+0io 0pf+0w