Sat Oct 8 22:54:54 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 Sat Oct 8 2011 at 22:54:54 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: 247 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2585 !!! WARNING: TPO 1 has a net charge of -1.2740 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: 0.6026238 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): -15.68500 32.00000 ymin,ymax (A): 17.89900 76.97400 zmin,zma (A): 30.81000 81.36000 x,y,z range (A): 47.68500 59.07500 50.55000 scale (grids/A): 0.6026238 object centre (A): 8.157499 47.43650 56.08500 number of atom coordinates read : 2585 total number of charged atoms : 2445 net assigned charge : 5.226027 assigned positive charge : 374.6159 centred at (gu) : 90.78299 89.77225 91.92792 assigned negative charge : -369.3909 centred at (gu) : 90.68925 89.90247 92.04020 start vw surface at 0.1400000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 6405 nv = 96 ne = 84 npr = 52331 no. pairs analyzed = 52331 no. exposed pairs = 3235 no. arc points = 22957 no. surface atoms = 1099 nbur = 1486 mkacc time = 0.1100000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 320 mr = 3442 m= 2 mr = 23 m= 0 mr = 0 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2800000 number of dielectric boundary points 3262 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2393 ## 248 charges are in solution ## iepsmp to db, and charging done at 0.3900000 number of grid points assigned charge 7928 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 4.3135091E-09 -2.8800928E-09 midg,1,midg; midg,igrid,midg 7.6739539E-09 -2.3386868E-09 1,midg,midg; igrid,midg,midg -8.7427665E-10 7.1121553E-09 gauss-seidel spectral radius is 0.9857510 estimated iterations to convergence 69 setup time was (sec) 0.4900000 now iterating at: 22:54:55 rms-change max change #iterations 0.1096556 16.51338 at 10iterations 9.4653154E-03 1.489801 at 20iterations 8.0286025E-04 0.1092072 at 30iterations 6.8896239E-05 1.1844635E-02 at 40iterations 5.9168842E-06 9.6905231E-04 at 50iterations finished qdiffx linear iterations at : 22:54:57 total time elapsed so far: 2.950000 # loops : 50 mean,max change (kT/e) : 5.9168842E-06 9.6905231E-04 energy calculations done at 2.950000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.120000 DelPhi exited at 22:54:58 3.127u 0.171s 0:03.63 90.6% 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 Sat Oct 8 2011 at 22:54:58 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: 247 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2585 !!! WARNING: TPO 1 has a net charge of -1.2740 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: 1.807871 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): -15.68500 32.00000 ymin,ymax (A): 17.89900 76.97400 zmin,zma (A): 30.81000 81.36000 x,y,z range (A): 47.68500 59.07500 50.55000 scale (grids/A): 1.807871 object centre (A): 8.157499 47.43650 56.08500 number of atom coordinates read : 2585 total number of charged atoms : 2445 net assigned charge : 5.226027 assigned positive charge : 374.6159 centred at (gu) : 92.34859 89.31605 95.78317 assigned negative charge : -369.3909 centred at (gu) : 92.06762 89.70731 96.12040 start vw surface at 0.1600000 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 69621 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22957 grid for indexing accessible points = 1.400000 m= 23956 mr = 47827 m= 3378 mr = 17179 m= 142 mr = 1920 m= 0 mr = 33 time to grow re-entrant surface = 0.2200000 no. cavity mid-points inaccessible to solvent = 1103 time to turn everything in is 0.5000000 number of dielectric boundary points 30138 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 200 iepsmp to db, and charging done at 0.6200000 number of grid points assigned charge 19149 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) : 0.6026238 object centre at (A) : 8.157499 47.43650 56.08500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.7345616E-02 4.6405685E-03 midg,1,midg; midg,igrid,midg 5.7282019E-02 3.3095031E-04 1,midg,midg; igrid,midg,midg -5.6808810E-03 5.3768922E-03 gauss-seidel spectral radius is 0.9984872 estimated iterations to convergence 204 setup time was (sec) 0.7800000 now iterating at: 22:54:59 rms-change max change #iterations 3.729523 168.2062 at 10iterations 1.674114 65.88050 at 20iterations 0.7539560 25.91689 at 30iterations 0.3381230 11.49784 at 40iterations 0.1523213 5.234783 at 50iterations 6.8214312E-02 2.250005 at 60iterations 3.0747937E-02 1.166073 at 70iterations 1.3817308E-02 0.5560484 at 80iterations 6.2199705E-03 0.2054329 at 90iterations 2.7842587E-03 9.0577602E-02 at 100iterations 1.2583337E-03 4.4494629E-02 at 110iterations 5.6569639E-04 1.8710017E-02 at 120iterations finished qdiffx linear iterations at : 22:55:05 total time elapsed so far: 7.190000 # loops : 120 mean,max change (kT/e) : 5.6569639E-04 1.8710017E-02 energy calculations done at 7.190000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.360000 DelPhi exited at 22:55:06 7.363u 0.210s 0:07.94 95.3% 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 Sat Oct 8 2011 at 22:55:06 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: 247 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2585 !!! WARNING: TPO 1 has a net charge of -1.2740 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: 2.711807 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): -15.68500 32.00000 ymin,ymax (A): 17.89900 76.97400 zmin,zma (A): 30.81000 81.36000 x,y,z range (A): 47.68500 59.07500 50.55000 scale (grids/A): 2.711807 object centre (A): 8.157499 47.43650 56.08500 number of atom coordinates read : 2585 total number of charged atoms : 2445 net assigned charge : 5.226027 assigned positive charge : 374.6159 centred at (gu) : 93.52260 88.97400 98.67448 assigned negative charge : -369.3909 centred at (gu) : 93.10155 89.56090 99.18058 start vw surface at 0.1500000 fill in re-entrant regions at 0.4200000 boundary points on vw surface= 161079 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22957 grid for indexing accessible points = 1.400000 m= 79088 mr = 116357 m= 27091 mr = 63776 m= 5818 mr = 21140 m= 698 mr = 4158 m= 25 mr = 428 m= 0 mr = 5 time to grow re-entrant surface = 0.7000000 no. cavity mid-points inaccessible to solvent = 3618 time to turn everything in is 1.220000 number of dielectric boundary points 67935 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2 iepsmp to db, and charging done at 1.360000 number of grid points assigned charge 19537 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) : 1.807871 object centre at (A) : 8.157499 47.43650 56.08500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.3941276 5.5287756E-02 midg,1,midg; midg,igrid,midg 0.8267794 8.1565715E-02 1,midg,midg; igrid,midg,midg -3.6191102E-02 6.4666085E-02 gauss-seidel spectral radius is 0.9992210 estimated iterations to convergence 283 setup time was (sec) 1.540000 now iterating at: 22:55:08 rms-change max change #iterations 9.087630 282.6653 at 10iterations 5.224213 136.7105 at 20iterations 2.993483 71.84441 at 30iterations 1.708350 33.17284 at 40iterations 0.9702666 17.49745 at 50iterations 0.5496098 10.56313 at 60iterations 0.3120446 6.187857 at 70iterations 0.1765988 3.500778 at 80iterations 9.9971078E-02 2.226013 at 90iterations 5.6558643E-02 1.167809 at 100iterations 3.1995222E-02 0.6062880 at 110iterations 1.8074788E-02 0.3624878 at 120iterations 1.0221888E-02 0.1919365 at 130iterations 5.7795132E-03 0.1127170 at 140iterations 3.2670151E-03 6.4599991E-02 at 150iterations 1.8464003E-03 3.3638000E-02 at 160iterations 1.0442601E-03 1.9594193E-02 at 170iterations 5.9043884E-04 1.1276245E-02 at 180iterations finished qdiffx linear iterations at : 22:55:19 total time elapsed so far: 12.94000 # loops : 180 mean,max change (kT/e) : 5.9043884E-04 1.1276245E-02 energy calculations done at 12.94000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.11000 DelPhi exited at 22:55:20 13.113u 0.209s 0:13.59 97.9% 0+0k 0+0io 0pf+0w