Mon Oct 10 19:33:27 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 Mon Oct 10 2011 at 19:33:27 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: 249 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2538 !!! WARNING: HIZ 93 has a net charge of 0.2000 !!! WARNING: ZN7 760 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= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.5785608 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): -30.99500 30.53700 ymin,ymax (A): 8.276000 56.68500 zmin,zma (A): 37.69100 97.14400 x,y,z range (A): 61.53200 48.40900 59.45300 scale (grids/A): 0.5785608 object centre (A): -0.2290010 32.48050 67.41750 number of atom coordinates read : 2538 total number of charged atoms : 2399 net assigned charge : 17.60001 assigned positive charge : 381.0927 centred at (gu) : 88.40175 90.44511 88.98519 assigned negative charge : -363.4936 centred at (gu) : 88.51958 90.45739 89.06290 start vw surface at 0.1100000 fill in re-entrant regions at 0.1200000 boundary points on vw surface= 5654 nv = 96 ne = 84 npr = 50198 no. pairs analyzed = 50198 no. exposed pairs = 3382 no. arc points = 24414 no. surface atoms = 1128 nbur = 1410 mkacc time = 0.1300000 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 = 1.512000 m= 246 mr = 2801 m= 1 mr = 15 m= 0 mr = 0 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 13 time to turn everything in is 0.2800000 number of dielectric boundary points 3085 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2514 ## 333 charges are in solution ## iepsmp to db, and charging done at 0.4200000 number of grid points assigned charge 7217 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 6.2121397E-09 1.8044304E-09 midg,1,midg; midg,igrid,midg 3.4381171E-09 3.7434771E-09 1,midg,midg; igrid,midg,midg 8.1062819E-09 1.1089325E-09 gauss-seidel spectral radius is 0.9845506 estimated iterations to convergence 66 setup time was (sec) 0.5900000 now iterating at: 19:33:28 rms-change max change #iterations 8.7868296E-02 13.00812 at 10iterations 6.8731769E-03 1.087933 at 20iterations 5.3961237E-04 9.0656281E-02 at 30iterations 4.8863923E-05 8.0776215E-03 at 40iterations 5.6643166E-06 1.1997223E-03 at 50iterations finished qdiffx linear iterations at : 19:33:32 total time elapsed so far: 4.010000 # loops : 50 mean,max change (kT/e) : 5.6643166E-06 1.1997223E-03 energy calculations done at 4.010000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.190000 DelPhi exited at 19:33:33 4.194u 0.439s 0:05.45 84.7% 0+0k 0+0io 6pf+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 Mon Oct 10 2011 at 19:33:33 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: 249 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2538 !!! WARNING: HIZ 93 has a net charge of 0.2000 !!! WARNING: ZN7 760 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= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.735682 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): -30.99500 30.53700 ymin,ymax (A): 8.276000 56.68500 zmin,zma (A): 37.69100 97.14400 x,y,z range (A): 61.53200 48.40900 59.45300 scale (grids/A): 1.735682 object centre (A): -0.2290010 32.48050 67.41750 number of atom coordinates read : 2538 total number of charged atoms : 2399 net assigned charge : 17.60001 assigned positive charge : 381.0927 centred at (gu) : 85.20480 91.33470 86.95490 assigned negative charge : -363.4936 centred at (gu) : 85.55851 91.37200 87.18869 start vw surface at 0.1200000 fill in re-entrant regions at 0.2200000 boundary points on vw surface= 62148 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24414 grid for indexing accessible points = 1.400000 m= 19314 mr = 40950 m= 2164 mr = 12978 m= 83 mr = 1117 m= 1 mr = 10 m= 0 mr = 0 time to grow re-entrant surface = 0.2400000 no. cavity mid-points inaccessible to solvent = 596 time to turn everything in is 0.5000000 number of dielectric boundary points 28655 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 272 ## 3 charges are in solution ## iepsmp to db, and charging done at 0.6200000 number of grid points assigned charge 18628 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) : 0.5785608 object centre at (A) : -0.2290010 32.48050 67.41750 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.5614976E-02 2.2443106E-02 midg,1,midg; midg,igrid,midg 1.2091503E-02 1.9426964E-02 1,midg,midg; igrid,midg,midg 3.0456815E-02 1.1242237E-02 gauss-seidel spectral radius is 0.9983557 estimated iterations to convergence 196 setup time was (sec) 0.7900000 now iterating at: 19:33:34 rms-change max change #iterations 3.422144 177.2609 at 10iterations 1.475186 62.52897 at 20iterations 0.6389063 22.96692 at 30iterations 0.2772350 10.69483 at 40iterations 0.1210031 4.806378 at 50iterations 5.2305032E-02 1.875336 at 60iterations 2.2588629E-02 0.7368474 at 70iterations 9.8862667E-03 0.3948638 at 80iterations 4.2839907E-03 0.1555367 at 90iterations 1.8646680E-03 7.1653366E-02 at 100iterations 8.0873794E-04 3.5981178E-02 at 110iterations 3.5462473E-04 1.3990402E-02 at 120iterations finished qdiffx linear iterations at : 19:33:42 total time elapsed so far: 9.080000 # loops : 120 mean,max change (kT/e) : 3.5462473E-04 1.3990402E-02 energy calculations done at 9.080000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.270000 DelPhi exited at 19:33:43 9.274u 0.461s 0:10.05 96.8% 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 Mon Oct 10 2011 at 19:33:43 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: 249 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2538 !!! WARNING: HIZ 93 has a net charge of 0.2000 !!! WARNING: ZN7 760 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= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.603523 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): -30.99500 30.53700 ymin,ymax (A): 8.276000 56.68500 zmin,zma (A): 37.69100 97.14400 x,y,z range (A): 61.53200 48.40900 59.45300 scale (grids/A): 2.603523 object centre (A): -0.2290010 32.48050 67.41750 number of atom coordinates read : 2538 total number of charged atoms : 2399 net assigned charge : 17.60001 assigned positive charge : 381.0927 centred at (gu) : 82.80702 92.00183 85.43230 assigned negative charge : -363.4936 centred at (gu) : 83.33773 92.05795 85.78304 start vw surface at 0.1100000 fill in re-entrant regions at 0.4100000 boundary points on vw surface= 143967 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24414 grid for indexing accessible points = 1.400000 m= 66109 mr = 100332 m= 19558 mr = 51470 m= 3570 mr = 14474 m= 380 mr = 2386 m= 10 mr = 192 m= 0 mr = 0 time to grow re-entrant surface = 0.7200000 no. cavity mid-points inaccessible to solvent = 1948 time to turn everything in is 1.230000 number of dielectric boundary points 64740 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 10 iepsmp to db, and charging done at 1.420000 number of grid points assigned charge 19187 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) : 1.735682 object centre at (A) : -0.2290010 32.48050 67.41750 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.5919163 0.3136267 midg,1,midg; midg,igrid,midg 0.1595815 0.3136199 1,midg,midg; igrid,midg,midg 0.1743463 5.2282423E-02 gauss-seidel spectral radius is 0.9991805 estimated iterations to convergence 276 setup time was (sec) 1.590000 now iterating at: 19:33:45 rms-change max change #iterations 8.607232 270.1371 at 10iterations 4.934649 157.3071 at 20iterations 2.802601 70.09331 at 30iterations 1.583292 36.32834 at 40iterations 0.8915471 19.01101 at 50iterations 0.5010092 10.59768 at 60iterations 0.2804806 6.057625 at 70iterations 0.1569750 4.077843 at 80iterations 8.7732017E-02 1.850094 at 90iterations 4.8939310E-02 0.9734898 at 100iterations 2.7345011E-02 0.5530071 at 110iterations 1.5271445E-02 0.3296428 at 120iterations 8.4976349E-03 0.1691780 at 130iterations 4.7530183E-03 9.2407227E-02 at 140iterations 2.6488798E-03 5.1563263E-02 at 150iterations 1.4780007E-03 3.1071663E-02 at 160iterations 8.2523038E-04 1.5425682E-02 at 170iterations 4.6031116E-04 9.3107224E-03 at 180iterations finished qdiffx linear iterations at : 19:33:59 total time elapsed so far: 15.61000 # loops : 180 mean,max change (kT/e) : 4.6031116E-04 9.3107224E-03 energy calculations done at 15.61000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.79000 DelPhi exited at 19:34:00 15.792u 0.510s 0:16.79 97.0% 0+0k 0+0io 0pf+0w