Mon Oct 10 10:25:27 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+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 Mon Oct 10 2011 at 10:25:27 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: 310 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2567 !!! WARNING: HIT 232 has a net charge of 0.5140 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: 0.5825179 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): -18.41000 31.87500 ymin,ymax (A): -61.21500 -2.786000 zmin,zma (A): -0.4820000 60.63200 x,y,z range (A): 50.28500 58.42900 61.11400 scale (grids/A): 0.5825179 object centre (A): 6.732500 -32.00050 30.07500 number of atom coordinates read : 2567 total number of charged atoms : 2423 net assigned charge : 9.014019 assigned positive charge : 379.5393 centred at (gu) : 88.52978 88.69817 87.38866 assigned negative charge : -370.5257 centred at (gu) : 88.52803 88.57539 87.35471 start vw surface at 0.1400000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 6054 nv = 96 ne = 84 npr = 48812 no. pairs analyzed = 48812 no. exposed pairs = 4076 no. arc points = 29583 no. surface atoms = 1327 nbur = 1240 mkacc time = 0.1500000 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 = 1.484000 m= 307 mr = 2588 m= 4 mr = 15 m= 0 mr = 0 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3200000 number of dielectric boundary points 3762 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2869 ## 297 charges are in solution ## iepsmp to db, and charging done at 0.4300000 number of grid points assigned charge 7411 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.7089224E-09 1.5799528E-09 midg,1,midg; midg,igrid,midg -4.1520953E-10 3.3789969E-09 1,midg,midg; igrid,midg,midg 2.9976599E-09 1.5919626E-09 gauss-seidel spectral radius is 0.9847754 estimated iterations to convergence 67 setup time was (sec) 0.5800000 now iterating at: 10:25:28 rms-change max change #iterations 9.3231283E-02 14.76028 at 10iterations 7.2294157E-03 1.242727 at 20iterations 5.8204588E-04 9.4528198E-02 at 30iterations 4.8424998E-05 9.3641281E-03 at 40iterations 5.5989854E-06 8.0490112E-04 at 50iterations finished qdiffx linear iterations at : 10:25:30 total time elapsed so far: 3.270000 # loops : 50 mean,max change (kT/e) : 5.5989854E-06 8.0490112E-04 energy calculations done at 3.270000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.470000 DelPhi exited at 10:25:31 3.469u 0.209s 0:04.00 91.5% 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 Mon Oct 10 2011 at 10:25:31 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: 310 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2567 !!! WARNING: HIT 232 has a net charge of 0.5140 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: 1.747554 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): -18.41000 31.87500 ymin,ymax (A): -61.21500 -2.786000 zmin,zma (A): -0.4820000 60.63200 x,y,z range (A): 50.28500 58.42900 61.11400 scale (grids/A): 1.747554 object centre (A): 6.732500 -32.00050 30.07500 number of atom coordinates read : 2567 total number of charged atoms : 2423 net assigned charge : 9.014019 assigned positive charge : 379.5393 centred at (gu) : 85.58897 86.09433 82.16569 assigned negative charge : -370.5257 centred at (gu) : 85.58408 85.72614 82.06400 start vw surface at 0.1800000 fill in re-entrant regions at 0.2700000 boundary points on vw surface= 64118 reading accessible surface arcs data from file ARCDAT no. of arc points read = 29583 grid for indexing accessible points = 1.400000 m= 20569 mr = 38591 m= 2738 mr = 12735 m= 132 mr = 1148 m= 1 mr = 19 m= 0 mr = 0 time to grow re-entrant surface = 0.2400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5500000 number of dielectric boundary points 35065 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 204 iepsmp to db, and charging done at 0.6800000 number of grid points assigned charge 18812 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) : 0.5825179 object centre at (A) : 6.732500 -32.00050 30.07500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.0158315E-02 6.4897258E-03 midg,1,midg; midg,igrid,midg 2.5888735E-02 3.0423753E-02 1,midg,midg; igrid,midg,midg 5.6933984E-03 9.2683015E-03 gauss-seidel spectral radius is 0.9984052 estimated iterations to convergence 199 setup time was (sec) 0.8600000 now iterating at: 10:25:32 rms-change max change #iterations 3.543134 175.3617 at 10iterations 1.554038 57.82251 at 20iterations 0.6801049 27.21280 at 30iterations 0.2985971 11.44673 at 40iterations 0.1314927 4.727270 at 50iterations 5.7630725E-02 2.027996 at 60iterations 2.5264122E-02 0.8684340 at 70iterations 1.1112417E-02 0.4431410 at 80iterations 4.8743426E-03 0.1639411 at 90iterations 2.1427530E-03 8.1087112E-02 at 100iterations 9.4452710E-04 3.5133362E-02 at 110iterations 4.1522924E-04 1.5578270E-02 at 120iterations finished qdiffx linear iterations at : 10:25:39 total time elapsed so far: 8.140000 # loops : 120 mean,max change (kT/e) : 4.1522924E-04 1.5578270E-02 energy calculations done at 8.140000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.330000 DelPhi exited at 10:25:40 8.333u 0.247s 0:09.08 94.3% 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 10:25:40 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: 310 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2567 !!! WARNING: HIT 232 has a net charge of 0.5140 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: 2.621331 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): -18.41000 31.87500 ymin,ymax (A): -61.21500 -2.786000 zmin,zma (A): -0.4820000 60.63200 x,y,z range (A): 50.28500 58.42900 61.11400 scale (grids/A): 2.621331 object centre (A): 6.732500 -32.00050 30.07500 number of atom coordinates read : 2567 total number of charged atoms : 2423 net assigned charge : 9.014019 assigned positive charge : 379.5393 centred at (gu) : 83.38338 84.14136 78.24853 assigned negative charge : -370.5257 centred at (gu) : 83.37608 83.58923 78.09589 start vw surface at 0.1600000 fill in re-entrant regions at 0.4300000 boundary points on vw surface= 147922 reading accessible surface arcs data from file ARCDAT no. of arc points read = 29583 grid for indexing accessible points = 1.400000 m= 67063 mr = 95322 m= 22164 mr = 49157 m= 4463 mr = 15505 m= 387 mr = 2560 m= 21 mr = 167 m= 0 mr = 4 time to grow re-entrant surface = 0.7200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.280000 number of dielectric boundary points 79305 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.430000 number of grid points assigned charge 19382 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) : 1.747554 object centre at (A) : 6.732500 -32.00050 30.07500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1672562 5.6919638E-02 midg,1,midg; midg,igrid,midg 0.4278325 0.4082523 1,midg,midg; igrid,midg,midg -1.8577820E-02 8.9598127E-02 gauss-seidel spectral radius is 0.9992190 estimated iterations to convergence 282 setup time was (sec) 1.620000 now iterating at: 10:25:42 rms-change max change #iterations 9.047768 299.8528 at 10iterations 5.333847 161.7871 at 20iterations 3.116684 75.33801 at 30iterations 1.805994 47.06608 at 40iterations 1.040057 24.83403 at 50iterations 0.5942683 16.54306 at 60iterations 0.3407875 7.877625 at 70iterations 0.1939954 5.163963 at 80iterations 0.1106348 2.577612 at 90iterations 6.2744260E-02 1.386105 at 100iterations 3.5652041E-02 0.8232727 at 110iterations 2.0171825E-02 0.4129467 at 120iterations 1.1453330E-02 0.2466946 at 130iterations 6.4630806E-03 0.1373091 at 140iterations 3.6690065E-03 7.9277039E-02 at 150iterations 2.0783341E-03 4.4082642E-02 at 160iterations 1.1728528E-03 2.4978638E-02 at 170iterations 6.6285953E-04 1.4236450E-02 at 180iterations finished qdiffx linear iterations at : 10:25:53 total time elapsed so far: 13.00000 # loops : 180 mean,max change (kT/e) : 6.6285953E-04 1.4236450E-02 energy calculations done at 13.00000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.20000 DelPhi exited at 10:25:54 13.199u 0.258s 0:13.73 97.8% 0+0k 0+0io 0pf+0w