Tue Oct 11 07:19:15 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 Tue Oct 11 2011 at 07:19:15 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: 305 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3274 !!! WARNING: UMP 527 has a net charge of -0.1000 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: 0.6484635 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): -14.16100 40.73800 ymin,ymax (A): 16.41700 69.24300 zmin,zma (A): -4.520000 43.71600 x,y,z range (A): 54.89900 52.82600 48.23600 scale (grids/A): 0.6484635 object centre (A): 13.28850 42.83000 19.59800 number of atom coordinates read : 3274 total number of charged atoms : 3121 net assigned charge : -0.5999917 assigned positive charge : 489.8787 centred at (gu) : 88.98078 90.04678 89.90150 assigned negative charge : -490.4798 centred at (gu) : 89.13861 90.03202 89.97706 start vw surface at 0.1600000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 9297 nv = 96 ne = 84 npr = 67949 no. pairs analyzed = 67949 no. exposed pairs = 3961 no. arc points = 26741 no. surface atoms = 1350 nbur = 1924 mkacc time = 0.1400000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 517 mr = 5459 m= 0 mr = 82 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 93 time to turn everything in is 0.3500000 number of dielectric boundary points 4273 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2528 ## 225 charges are in solution ## iepsmp to db, and charging done at 0.4600000 number of grid points assigned charge 11053 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.2707795E-08 -1.5204259E-08 midg,1,midg; midg,igrid,midg -4.1261545E-09 1.3102276E-09 1,midg,midg; igrid,midg,midg 3.4054572E-08 -2.5033923E-08 gauss-seidel spectral radius is 0.9877332 estimated iterations to convergence 74 setup time was (sec) 0.5900000 now iterating at: 07:19:16 rms-change max change #iterations 0.1712318 24.15637 at 10iterations 1.7912339E-02 2.137783 at 20iterations 2.1650421E-03 0.2798557 at 30iterations 4.9727206E-04 8.3199501E-02 at 40iterations 1.7568374E-04 3.0450821E-02 at 50iterations finished qdiffx linear iterations at : 07:19:18 total time elapsed so far: 3.290000 # loops : 50 mean,max change (kT/e) : 1.7568374E-04 3.0450821E-02 energy calculations done at 3.290000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.450000 DelPhi exited at 07:19:19 3.458u 0.225s 0:04.09 89.7% 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 Oct 11 2011 at 07:19:19 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: 305 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3274 !!! WARNING: UMP 527 has a net charge of -0.1000 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: 1.945391 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): -14.16100 40.73800 ymin,ymax (A): 16.41700 69.24300 zmin,zma (A): -4.520000 43.71600 x,y,z range (A): 54.89900 52.82600 48.23600 scale (grids/A): 1.945391 object centre (A): 13.28850 42.83000 19.59800 number of atom coordinates read : 3274 total number of charged atoms : 3121 net assigned charge : -0.5999917 assigned positive charge : 489.8787 centred at (gu) : 86.94155 90.13955 89.70369 assigned negative charge : -490.4798 centred at (gu) : 87.41541 90.09571 89.93047 start vw surface at 0.1800000 fill in re-entrant regions at 0.3100000 boundary points on vw surface= 100062 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26741 grid for indexing accessible points = 1.400000 m= 38661 mr = 72083 m= 6485 mr = 29443 m= 410 mr = 4315 m= 6 mr = 179 m= 0 mr = 0 time to grow re-entrant surface = 0.3400000 no. cavity mid-points inaccessible to solvent = 2632 time to turn everything in is 0.7000000 number of dielectric boundary points 39604 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 128 iepsmp to db, and charging done at 0.8200000 number of grid points assigned charge 24579 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) : 0.6484635 object centre at (A) : 13.28850 42.83000 19.59800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.9249342E-02 4.2037040E-02 midg,1,midg; midg,igrid,midg -3.9667521E-02 9.1564941E-04 1,midg,midg; igrid,midg,midg -4.3805325E-03 -5.9828088E-02 gauss-seidel spectral radius is 0.9987494 estimated iterations to convergence 224 setup time was (sec) 0.9900000 now iterating at: 07:19:20 rms-change max change #iterations 5.048896 208.6198 at 10iterations 2.444203 75.17439 at 20iterations 1.185154 34.31503 at 30iterations 0.5748527 17.05607 at 40iterations 0.2780953 8.867893 at 50iterations 0.1350669 3.688147 at 60iterations 6.5516852E-02 1.955173 at 70iterations 3.1840276E-02 0.9600983 at 80iterations 1.5399403E-02 0.4210052 at 90iterations 7.5221998E-03 0.2151031 at 100iterations 3.6814858E-03 0.1087170 at 110iterations 1.8114126E-03 5.3909302E-02 at 120iterations finished qdiffx linear iterations at : 07:19:27 total time elapsed so far: 7.780000 # loops : 120 mean,max change (kT/e) : 1.8114126E-03 5.3909302E-02 energy calculations done at 7.780000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.960000 DelPhi exited at 07:19:28 7.958u 0.247s 0:08.54 95.9% 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 Oct 11 2011 at 07:19:28 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: 305 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3274 !!! WARNING: UMP 527 has a net charge of -0.1000 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: 2.918086 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): -14.16100 40.73800 ymin,ymax (A): 16.41700 69.24300 zmin,zma (A): -4.520000 43.71600 x,y,z range (A): 54.89900 52.82600 48.23600 scale (grids/A): 2.918086 object centre (A): 13.28850 42.83000 19.59800 number of atom coordinates read : 3274 total number of charged atoms : 3121 net assigned charge : -0.5999917 assigned positive charge : 489.8787 centred at (gu) : 85.41201 90.20904 89.55534 assigned negative charge : -490.4798 centred at (gu) : 86.12318 90.14340 89.89555 start vw surface at 0.1600000 fill in re-entrant regions at 0.5700000 boundary points on vw surface= 231316 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26741 grid for indexing accessible points = 1.400000 m= 123211 mr = 173630 m= 47101 mr = 102926 m= 11875 mr = 38941 m= 1863 mr = 9266 m= 132 mr = 1304 m= 5 mr = 64 m= 0 mr = 0 time to grow re-entrant surface = 1.080000 no. cavity mid-points inaccessible to solvent = 9118 time to turn everything in is 1.770000 number of dielectric boundary points 89372 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.930000 number of grid points assigned charge 24967 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) : 1.945391 object centre at (A) : 13.28850 42.83000 19.59800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.4160957 0.4936730 midg,1,midg; midg,igrid,midg -0.4226787 -8.8717677E-02 1,midg,midg; igrid,midg,midg -0.1305145 -0.5259838 gauss-seidel spectral radius is 0.9992979 estimated iterations to convergence 298 setup time was (sec) 2.110000 now iterating at: 07:19:30 rms-change max change #iterations 11.73549 408.6976 at 10iterations 6.962812 140.6420 at 20iterations 4.110294 70.30677 at 30iterations 2.419612 46.51131 at 40iterations 1.421981 23.19163 at 50iterations 0.8357198 13.48160 at 60iterations 0.4877813 8.314095 at 70iterations 0.2856720 4.704292 at 80iterations 0.1672278 2.669671 at 90iterations 9.7611837E-02 1.490659 at 100iterations 5.7023961E-02 0.9319239 at 110iterations 3.3326145E-02 0.4868822 at 120iterations 1.9498996E-02 0.3368568 at 130iterations 1.1418369E-02 0.1750755 at 140iterations 6.7049870E-03 0.1119967 at 150iterations 3.9538518E-03 6.2015533E-02 at 160iterations 2.3720169E-03 3.8037300E-02 at 170iterations 1.4467946E-03 2.4953842E-02 at 180iterations finished qdiffx linear iterations at : 07:19:41 total time elapsed so far: 13.29000 # loops : 180 mean,max change (kT/e) : 1.4467946E-03 2.4953842E-02 energy calculations done at 13.29000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.47000 DelPhi exited at 07:19:42 13.471u 0.265s 0:14.25 96.3% 0+0k 0+0io 0pf+0w