Sun Oct 9 19:12:26 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 Sun Oct 9 2011 at 19:12:26 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: 345 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5129 !!! WARNING: HIQ 377 has a net charge of 0.5140 !!! WARNING: HIR 571 has a net charge of 0.5140 !!! WARNING: LLP 1 has a net charge of 1.7400 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: 0.5241230 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): 3.341000 68.16000 ymin,ymax (A): -8.724000 59.19900 zmin,zma (A): -2.280000 62.00600 x,y,z range (A): 64.81900 67.92300 64.28600 scale (grids/A): 0.5241230 object centre (A): 35.75050 25.23750 29.86300 number of atom coordinates read : 5129 total number of charged atoms : 4954 net assigned charge : 3.268036 assigned positive charge : 786.6781 centred at (gu) : 87.74669 88.15080 89.28674 assigned negative charge : -783.4158 centred at (gu) : 87.61639 88.16283 89.28938 start vw surface at 0.1300000 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 9063 nv = 96 ne = 84 npr = 103693 no. pairs analyzed = 103693 no. exposed pairs = 6038 no. arc points = 40740 no. surface atoms = 2061 nbur = 3068 mkacc time = 0.1800000 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 = 1.652000 m= 354 mr = 5093 m= 0 mr = 13 time to grow re-entrant surface = 0.2000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3400000 number of dielectric boundary points 4311 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4091 ## 549 charges are in solution ## iepsmp to db, and charging done at 0.4100000 number of grid points assigned charge 12106 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.3281598E-10 7.1007880E-11 midg,1,midg; midg,igrid,midg 2.5316391E-10 2.4884131E-11 1,midg,midg; igrid,midg,midg -1.0148297E-09 4.0970416E-10 gauss-seidel spectral radius is 0.9814017 estimated iterations to convergence 61 setup time was (sec) 0.5400000 now iterating at: 19:12:27 rms-change max change #iterations 8.6340949E-02 10.91474 at 10iterations 1.2084822E-02 1.868492 at 20iterations 4.8985104E-03 0.7830200 at 30iterations 2.1567186E-03 0.3368530 at 40iterations 9.5616397E-04 0.1455994 at 50iterations finished qdiffx linear iterations at : 19:12:30 total time elapsed so far: 3.440000 # loops : 50 mean,max change (kT/e) : 9.5616397E-04 0.1455994 energy calculations done at 3.440000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.570000 DelPhi exited at 19:12:30 3.571u 0.171s 0:04.01 93.2% 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 Sun Oct 9 2011 at 19:12:30 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: 345 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5129 !!! WARNING: HIQ 377 has a net charge of 0.5140 !!! WARNING: HIR 571 has a net charge of 0.5140 !!! WARNING: LLP 1 has a net charge of 1.7400 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: 1.572369 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): 3.341000 68.16000 ymin,ymax (A): -8.724000 59.19900 zmin,zma (A): -2.280000 62.00600 x,y,z range (A): 64.81900 67.92300 64.28600 scale (grids/A): 1.572369 object centre (A): 35.75050 25.23750 29.86300 number of atom coordinates read : 5129 total number of charged atoms : 4954 net assigned charge : 3.268036 assigned positive charge : 786.6781 centred at (gu) : 83.23895 84.45120 87.85891 assigned negative charge : -783.4158 centred at (gu) : 82.84936 84.48853 87.86832 start vw surface at 0.1400000 fill in re-entrant regions at 0.2300000 boundary points on vw surface= 103490 reading accessible surface arcs data from file ARCDAT no. of arc points read = 40740 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.540000 m= 33285 mr = 74754 m= 3405 mr = 23386 m= 75 mr = 1667 m= 0 mr = 3 time to grow re-entrant surface = 0.2400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5100000 number of dielectric boundary points 40445 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 477 ## 6 charges are in solution ## iepsmp to db, and charging done at 0.5900000 number of grid points assigned charge 37487 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) : 0.5241230 object centre at (A) : 35.75050 25.23750 29.86300 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -7.3530311E-03 -1.3089428E-02 midg,1,midg; midg,igrid,midg 1.8814296E-02 -1.2702466E-03 1,midg,midg; igrid,midg,midg -1.2889877E-02 1.3125452E-02 gauss-seidel spectral radius is 0.9982369 estimated iterations to convergence 189 setup time was (sec) 0.7200000 now iterating at: 19:12:31 rms-change max change #iterations 4.289686 141.8018 at 10iterations 1.809438 58.13071 at 20iterations 0.7676042 22.36873 at 30iterations 0.3266568 10.74122 at 40iterations 0.1397347 4.497599 at 50iterations 6.0822103E-02 1.805852 at 60iterations 2.8322274E-02 0.9628754 at 70iterations 1.4786386E-02 0.5222778 at 80iterations 8.9007551E-03 0.2973785 at 90iterations 6.1182580E-03 0.2036715 at 100iterations 4.4829031E-03 0.1435165 at 110iterations 3.3372955E-03 0.1066055 at 120iterations finished qdiffx linear iterations at : 19:12:38 total time elapsed so far: 7.910000 # loops : 120 mean,max change (kT/e) : 3.3372955E-03 0.1066055 energy calculations done at 7.910000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.040000 DelPhi exited at 19:12:39 8.045u 0.204s 0:08.52 96.7% 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 Sun Oct 9 2011 at 19:12:39 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: 345 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5129 !!! WARNING: HIQ 377 has a net charge of 0.5140 !!! WARNING: HIR 571 has a net charge of 0.5140 !!! WARNING: LLP 1 has a net charge of 1.7400 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: 2.358553 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): 3.341000 68.16000 ymin,ymax (A): -8.724000 59.19900 zmin,zma (A): -2.280000 62.00600 x,y,z range (A): 64.81900 67.92300 64.28600 scale (grids/A): 2.358553 object centre (A): 35.75050 25.23750 29.86300 number of atom coordinates read : 5129 total number of charged atoms : 4954 net assigned charge : 3.268036 assigned positive charge : 786.6781 centred at (gu) : 79.85817 81.67625 86.78798 assigned negative charge : -783.4158 centred at (gu) : 79.27412 81.73268 86.80244 start vw surface at 0.1300000 fill in re-entrant regions at 0.4200000 boundary points on vw surface= 241051 reading accessible surface arcs data from file ARCDAT no. of arc points read = 40740 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.512000 m= 116958 mr = 182163 m= 33053 mr = 94547 m= 5321 mr = 24995 m= 319 mr = 3463 m= 6 mr = 141 m= 0 mr = 0 time to grow re-entrant surface = 0.7200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.250000 number of dielectric boundary points 91399 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 39 iepsmp to db, and charging done at 1.340000 number of grid points assigned charge 39530 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) : 1.572369 object centre at (A) : 35.75050 25.23750 29.86300 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1658324 -0.2994888 midg,1,midg; midg,igrid,midg 9.9940576E-02 -0.1047630 1,midg,midg; igrid,midg,midg -0.2519854 0.2158345 gauss-seidel spectral radius is 0.9991959 estimated iterations to convergence 278 setup time was (sec) 1.490000 now iterating at: 19:12:40 rms-change max change #iterations 11.34214 325.0289 at 10iterations 6.566556 148.6522 at 20iterations 3.772835 73.42889 at 30iterations 2.149870 41.77611 at 40iterations 1.224521 22.80224 at 50iterations 0.6957583 11.35068 at 60iterations 0.3936710 7.307129 at 70iterations 0.2231207 3.951439 at 80iterations 0.1262726 2.059551 at 90iterations 7.1645610E-02 1.338989 at 100iterations 4.1101608E-02 0.6897678 at 110iterations 2.3987895E-02 0.4394836 at 120iterations 1.4492242E-02 0.2720566 at 130iterations 9.2477342E-03 0.1893616 at 140iterations 6.3362368E-03 0.1260529 at 150iterations 4.6816343E-03 9.2391968E-02 at 160iterations 3.6487835E-03 7.4256897E-02 at 170iterations 2.9327222E-03 5.5564880E-02 at 180iterations finished qdiffx linear iterations at : 19:12:52 total time elapsed so far: 13.19000 # loops : 180 mean,max change (kT/e) : 2.9327222E-03 5.5564880E-02 energy calculations done at 13.19000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.32000 DelPhi exited at 19:12:52 13.322u 0.220s 0:13.81 98.0% 0+0k 0+0io 0pf+0w