Tue Oct 11 06:19:02 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 06:19:02 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: 319 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2072 !!! WARNING: HIR 57 has a net charge of 0.5140 !!! WARNING: GLM 175 has a net charge of -0.0940 !!! WARNING: SEP 190 has a net charge of -0.4750 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 0.7049226 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): -20.72000 29.78200 ymin,ymax (A): -11.82100 30.66700 zmin,zma (A): -8.559000 38.39100 x,y,z range (A): 50.50200 42.48800 46.95000 scale (grids/A): 0.7049226 object centre (A): 4.531000 9.423000 14.91600 number of atom coordinates read : 2072 total number of charged atoms : 1938 net assigned charge : 5.945010 assigned positive charge : 317.3581 centred at (gu) : 91.13844 89.77936 90.88841 assigned negative charge : -311.4131 centred at (gu) : 91.06666 89.71213 90.77857 start vw surface at 0.1000000 fill in re-entrant regions at 0.1100000 boundary points on vw surface= 7020 nv = 96 ne = 84 npr = 41471 no. pairs analyzed = 41471 no. exposed pairs = 2494 no. arc points = 17169 no. surface atoms = 839 nbur = 1233 mkacc time = 0.1100000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 484 mr = 4096 m= 2 mr = 107 m= 0 mr = 0 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2500000 number of dielectric boundary points 3303 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1584 ## 136 charges are in solution ## iepsmp to db, and charging done at 0.3500000 number of grid points assigned charge 7794 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -4.0830876E-09 1.1536974E-07 midg,1,midg; midg,igrid,midg 1.5369572E-08 7.4238201E-08 1,midg,midg; igrid,midg,midg 1.0616115E-08 9.9296201E-08 gauss-seidel spectral radius is 0.9895092 estimated iterations to convergence 79 setup time was (sec) 0.5100000 now iterating at: 06:19:03 rms-change max change #iterations 0.1969395 25.12680 at 10iterations 2.4744453E-02 3.594330 at 20iterations 3.3881948E-03 0.4418564 at 30iterations 5.9596932E-04 6.8145752E-02 at 40iterations 1.5772483E-04 1.8220901E-02 at 50iterations finished qdiffx linear iterations at : 06:19:06 total time elapsed so far: 4.220000 # loops : 50 mean,max change (kT/e) : 1.5772483E-04 1.8220901E-02 energy calculations done at 4.220000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.390000 DelPhi exited at 06:19:07 4.396u 0.406s 0:05.16 92.8% 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 Tue Oct 11 2011 at 06:19:07 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: 319 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2072 !!! WARNING: HIR 57 has a net charge of 0.5140 !!! WARNING: GLM 175 has a net charge of -0.0940 !!! WARNING: SEP 190 has a net charge of -0.4750 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: 2.114768 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): -20.72000 29.78200 ymin,ymax (A): -11.82100 30.66700 zmin,zma (A): -8.559000 38.39100 x,y,z range (A): 50.50200 42.48800 46.95000 scale (grids/A): 2.114768 object centre (A): 4.531000 9.423000 14.91600 number of atom coordinates read : 2072 total number of charged atoms : 1938 net assigned charge : 5.945010 assigned positive charge : 317.3581 centred at (gu) : 93.41557 89.33795 92.66543 assigned negative charge : -311.4131 centred at (gu) : 93.20011 89.13638 92.33587 start vw surface at 0.1100000 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 74572 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17169 grid for indexing accessible points = 1.400000 m= 30280 mr = 53356 m= 5772 mr = 23232 m= 454 mr = 3851 m= 4 mr = 250 m= 0 mr = 0 time to grow re-entrant surface = 0.3300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.6200000 number of dielectric boundary points 30393 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 69 iepsmp to db, and charging done at 0.7400000 number of grid points assigned charge 15390 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) : 0.7049226 object centre at (A) : 4.531000 9.423000 14.91600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -4.1486058E-02 3.7302952E-02 midg,1,midg; midg,igrid,midg 1.9805998E-02 2.1732546E-02 1,midg,midg; igrid,midg,midg 3.9649121E-02 3.0607192E-02 gauss-seidel spectral radius is 0.9988211 estimated iterations to convergence 231 setup time was (sec) 0.9200000 now iterating at: 06:19:08 rms-change max change #iterations 4.592154 194.5286 at 10iterations 2.264719 79.97862 at 20iterations 1.120078 33.90134 at 30iterations 0.5545680 17.87518 at 40iterations 0.2750038 8.504519 at 50iterations 0.1360159 3.884565 at 60iterations 6.7422427E-02 2.009995 at 70iterations 3.3502400E-02 1.048954 at 80iterations 1.6686773E-02 0.4992332 at 90iterations 8.4269792E-03 0.2860050 at 100iterations 4.2476319E-03 0.1229115 at 110iterations 2.2011285E-03 6.5071106E-02 at 120iterations finished qdiffx linear iterations at : 06:19:18 total time elapsed so far: 10.38000 # loops : 120 mean,max change (kT/e) : 2.2011285E-03 6.5071106E-02 energy calculations done at 10.38000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.55000 DelPhi exited at 06:19:18 10.557u 0.414s 0:11.43 95.8% 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 Tue Oct 11 2011 at 06:19:19 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: 319 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2072 !!! WARNING: HIR 57 has a net charge of 0.5140 !!! WARNING: GLM 175 has a net charge of -0.0940 !!! WARNING: SEP 190 has a net charge of -0.4750 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 3.172152 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): -20.72000 29.78200 ymin,ymax (A): -11.82100 30.66700 zmin,zma (A): -8.559000 38.39100 x,y,z range (A): 50.50200 42.48800 46.95000 scale (grids/A): 3.172152 object centre (A): 4.531000 9.423000 14.91600 number of atom coordinates read : 2072 total number of charged atoms : 1938 net assigned charge : 5.945010 assigned positive charge : 317.3581 centred at (gu) : 95.12318 89.00704 93.99818 assigned negative charge : -311.4131 centred at (gu) : 94.80029 88.70461 93.50381 start vw surface at 0.1000000 fill in re-entrant regions at 0.7600000 boundary points on vw surface= 171905 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17169 grid for indexing accessible points = 1.400000 m= 94143 mr = 128332 m= 38540 mr = 78763 m= 10770 mr = 31964 m= 2000 mr = 8446 m= 222 mr = 1421 m= 6 mr = 133 m= 0 mr = 0 time to grow re-entrant surface = 1.050000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.920000 number of dielectric boundary points 68527 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.050000 number of grid points assigned charge 15504 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) : 2.114768 object centre at (A) : 4.531000 9.423000 14.91600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.4952532 0.2693045 midg,1,midg; midg,igrid,midg 0.1468674 0.1311570 1,midg,midg; igrid,midg,midg 0.3247133 0.1478204 gauss-seidel spectral radius is 0.9992934 estimated iterations to convergence 297 setup time was (sec) 2.250000 now iterating at: 06:19:21 rms-change max change #iterations 10.29297 342.1166 at 10iterations 6.066576 118.8620 at 20iterations 3.591863 73.01465 at 30iterations 2.110464 40.51207 at 40iterations 1.241613 22.92392 at 50iterations 0.7301617 14.26278 at 60iterations 0.4283865 8.514750 at 70iterations 0.2508175 4.711090 at 80iterations 0.1470224 2.675817 at 90iterations 8.6396016E-02 1.595655 at 100iterations 5.0847873E-02 0.9418011 at 110iterations 3.0019747E-02 0.5601461 at 120iterations 1.7951250E-02 0.3461571 at 130iterations 1.0958244E-02 0.2181625 at 140iterations 6.9006034E-03 0.1313362 at 150iterations 4.5456518E-03 8.9775085E-02 at 160iterations 3.1766489E-03 5.8887482E-02 at 170iterations 2.3515325E-03 4.4742584E-02 at 180iterations finished qdiffx linear iterations at : 06:19:37 total time elapsed so far: 18.01000 # loops : 180 mean,max change (kT/e) : 2.3515325E-03 4.4742584E-02 energy calculations done at 18.01000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 18.19000 DelPhi exited at 06:19:37 18.194u 0.466s 0:18.95 98.4% 0+0k 0+0io 0pf+0w