Sat Oct 8 19:05:57 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 Sat Oct 8 2011 at 19:05:57 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: 280 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2594 !!! WARNING: HIZ 94 has a net charge of 0.2000 !!! WARNING: HIZ 96 has a net charge of 0.2000 !!! WARNING: HIY 119 has a net charge of 0.2000 !!! WARNING: ZN6 667 has a net charge of 1.4000 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: 0.6211180 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): -32.54400 17.52800 ymin,ymax (A): -24.24500 22.80400 zmin,zma (A): -12.54600 44.77000 x,y,z range (A): 50.07200 47.04900 57.31600 scale (grids/A): 0.6211180 object centre (A): -7.507999 -0.7205000 16.11200 number of atom coordinates read : 2594 total number of charged atoms : 2462 net assigned charge : 4.500007 assigned positive charge : 394.5700 centred at (gu) : 88.68246 89.14394 89.92692 assigned negative charge : -390.0706 centred at (gu) : 88.58654 89.18646 89.81703 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1000000 boundary points on vw surface= 6786 nv = 96 ne = 84 npr = 52819 no. pairs analyzed = 52819 no. exposed pairs = 3102 no. arc points = 21977 no. surface atoms = 1053 nbur = 1541 mkacc time = 8.9999996E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 336 mr = 3809 m= 3 mr = 37 m= 0 mr = 0 time to grow re-entrant surface = 0.1000000 no. cavity mid-points inaccessible to solvent = 9 time to turn everything in is 0.2000000 number of dielectric boundary points 3279 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2276 ## 216 charges are in solution ## iepsmp to db, and charging done at 0.2700000 number of grid points assigned charge 8202 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -3.9004804E-09 1.1114679E-08 midg,1,midg; midg,igrid,midg 8.1247684E-09 7.6046791E-10 1,midg,midg; igrid,midg,midg -3.9196268E-09 7.7689837E-09 gauss-seidel spectral radius is 0.9865768 estimated iterations to convergence 71 setup time was (sec) 0.3900000 now iterating at: 19:05:58 rms-change max change #iterations 0.1275242 20.09706 at 10iterations 1.1973969E-02 1.745592 at 20iterations 1.1531377E-03 0.1675816 at 30iterations 1.1193770E-04 1.8096924E-02 at 40iterations 1.1588008E-05 1.6613007E-03 at 50iterations finished qdiffx linear iterations at : 19:06:01 total time elapsed so far: 3.210000 # loops : 50 mean,max change (kT/e) : 1.1588008E-05 1.6613007E-03 energy calculations done at 3.210000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.340000 DelPhi exited at 19:06:01 3.345u 0.166s 0:03.78 92.5% 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 19:06:01 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: 280 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2594 !!! WARNING: HIZ 94 has a net charge of 0.2000 !!! WARNING: HIZ 96 has a net charge of 0.2000 !!! WARNING: HIY 119 has a net charge of 0.2000 !!! WARNING: ZN6 667 has a net charge of 1.4000 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: 1.863354 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): -32.54400 17.52800 ymin,ymax (A): -24.24500 22.80400 zmin,zma (A): -12.54600 44.77000 x,y,z range (A): 50.07200 47.04900 57.31600 scale (grids/A): 1.863354 object centre (A): -7.507999 -0.7205000 16.11200 number of atom coordinates read : 2594 total number of charged atoms : 2462 net assigned charge : 4.500007 assigned positive charge : 394.5700 centred at (gu) : 86.04706 87.43168 89.78047 assigned negative charge : -390.0706 centred at (gu) : 85.75944 87.55924 89.45110 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 72703 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21977 grid for indexing accessible points = 1.400000 m= 27060 mr = 50902 m= 4095 mr = 20336 m= 189 mr = 2488 m= 0 mr = 43 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 869 time to turn everything in is 0.3600000 number of dielectric boundary points 30278 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 149 iepsmp to db, and charging done at 0.4400000 number of grid points assigned charge 19292 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) : 0.6211180 object centre at (A) : -7.507999 -0.7205000 16.11200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.8133538E-02 2.6372371E-02 midg,1,midg; midg,igrid,midg 1.6210921E-02 2.5409237E-03 1,midg,midg; igrid,midg,midg -2.6288701E-03 3.4478437E-02 gauss-seidel spectral radius is 0.9985763 estimated iterations to convergence 210 setup time was (sec) 0.5700000 now iterating at: 19:06:02 rms-change max change #iterations 4.082321 187.3190 at 10iterations 1.879975 63.86061 at 20iterations 0.8677145 29.22068 at 30iterations 0.3983026 12.59590 at 40iterations 0.1837777 5.686560 at 50iterations 8.4805936E-02 2.532547 at 60iterations 3.9162964E-02 1.263367 at 70iterations 1.8059408E-02 0.5693207 at 80iterations 8.3084116E-03 0.3000603 at 90iterations 3.8369671E-03 0.1259232 at 100iterations 1.7709119E-03 5.3665161E-02 at 110iterations 8.2120870E-04 2.7072906E-02 at 120iterations finished qdiffx linear iterations at : 19:06:09 total time elapsed so far: 7.540000 # loops : 120 mean,max change (kT/e) : 8.2120870E-04 2.7072906E-02 energy calculations done at 7.540000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.680000 DelPhi exited at 19:06:09 7.680u 0.186s 0:08.15 96.4% 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 19:06:09 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: 280 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2594 !!! WARNING: HIZ 94 has a net charge of 0.2000 !!! WARNING: HIZ 96 has a net charge of 0.2000 !!! WARNING: HIY 119 has a net charge of 0.2000 !!! WARNING: ZN6 667 has a net charge of 1.4000 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: 2.795031 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): -32.54400 17.52800 ymin,ymax (A): -24.24500 22.80400 zmin,zma (A): -12.54600 44.77000 x,y,z range (A): 50.07200 47.04900 57.31600 scale (grids/A): 2.795031 object centre (A): -7.507999 -0.7205000 16.11200 number of atom coordinates read : 2594 total number of charged atoms : 2462 net assigned charge : 4.500007 assigned positive charge : 394.5700 centred at (gu) : 84.07059 86.14734 89.67066 assigned negative charge : -390.0706 centred at (gu) : 83.63908 86.33887 89.17650 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.3600000 boundary points on vw surface= 168116 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21977 grid for indexing accessible points = 1.400000 m= 86948 mr = 122914 m= 31882 mr = 72143 m= 7293 mr = 25852 m= 915 mr = 5332 m= 28 mr = 529 m= 0 mr = 5 time to grow re-entrant surface = 0.5300000 no. cavity mid-points inaccessible to solvent = 2812 time to turn everything in is 0.9600000 number of dielectric boundary points 68407 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2 iepsmp to db, and charging done at 1.050000 number of grid points assigned charge 19691 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) : 1.863354 object centre at (A) : -7.507999 -0.7205000 16.11200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -6.5270178E-02 0.3142290 midg,1,midg; midg,igrid,midg 0.1844016 2.4654219E-02 1,midg,midg; igrid,midg,midg -1.4429692E-02 0.4331472 gauss-seidel spectral radius is 0.9992375 estimated iterations to convergence 286 setup time was (sec) 1.190000 now iterating at: 19:06:11 rms-change max change #iterations 9.566335 353.1762 at 10iterations 5.501411 126.5993 at 20iterations 3.155931 59.88894 at 30iterations 1.807583 34.24899 at 40iterations 1.035450 18.80471 at 50iterations 0.5893048 11.95205 at 60iterations 0.3364544 6.860035 at 70iterations 0.1916607 3.624624 at 80iterations 0.1092233 2.070750 at 90iterations 6.2177949E-02 1.185402 at 100iterations 3.5477474E-02 0.7094040 at 110iterations 2.0220447E-02 0.3885193 at 120iterations 1.1526130E-02 0.2495804 at 130iterations 6.5717790E-03 0.1198196 at 140iterations 3.7485610E-03 6.9122314E-02 at 150iterations 2.1430498E-03 3.7772179E-02 at 160iterations 1.2255320E-03 2.2293091E-02 at 170iterations 7.0441904E-04 1.4085770E-02 at 180iterations finished qdiffx linear iterations at : 19:06:22 total time elapsed so far: 12.29000 # loops : 180 mean,max change (kT/e) : 7.0441904E-04 1.4085770E-02 energy calculations done at 12.29000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.41000 DelPhi exited at 19:06:22 12.415u 0.208s 0:12.89 97.8% 0+0k 0+0io 0pf+0w