Sat Oct 8 11:38:03 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 11:38:03 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: 253 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4872 !!! WARNING: HIR 353 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= 0.1500000 grid size : 179 scale,in grids/A, set to be: 0.5473050 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): 7.577000 72.55000 ymin,ymax (A): 5.379000 66.63700 zmin,zma (A): 9.273999 74.32000 x,y,z range (A): 64.97299 61.25800 65.04600 scale (grids/A): 0.5473050 object centre (A): 40.06350 36.00800 41.79700 number of atom coordinates read : 4872 total number of charged atoms : 4707 net assigned charge : 1.4046252E-02 assigned positive charge : 732.4941 centred at (gu) : 90.62399 89.89032 90.57839 assigned negative charge : -732.4843 centred at (gu) : 90.56492 89.93211 90.62918 start vw surface at 0.2700000 fill in re-entrant regions at 0.2800000 boundary points on vw surface= 9063 nv = 96 ne = 84 npr = 102364 no. pairs analyzed = 102364 no. exposed pairs = 5730 no. arc points = 39527 no. surface atoms = 1925 nbur = 2947 mkacc time = 0.2900000 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 = 1.568000 m= 390 mr = 4987 m= 0 mr = 16 time to grow re-entrant surface = 0.3200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.6200000 number of dielectric boundary points 4450 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3999 ## 501 charges are in solution ## iepsmp to db, and charging done at 0.7600000 number of grid points assigned charge 12304 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 5.0200677E-10 -6.8093331E-10 midg,1,midg; midg,igrid,midg 4.9129190E-10 -4.7063115E-10 1,midg,midg; igrid,midg,midg -5.8591210E-10 7.8902396E-10 gauss-seidel spectral radius is 0.9829201 estimated iterations to convergence 63 setup time was (sec) 0.8900000 now iterating at: 11:38:04 rms-change max change #iterations 9.7158670E-02 18.22504 at 10iterations 8.2114581E-03 1.430466 at 20iterations 1.3794978E-03 0.3336945 at 30iterations 3.5817132E-04 8.4228516E-02 at 40iterations 1.0436327E-04 2.2422791E-02 at 50iterations finished qdiffx linear iterations at : 11:38:07 total time elapsed so far: 4.200000 # loops : 50 mean,max change (kT/e) : 1.0436327E-04 2.2422791E-02 energy calculations done at 4.200000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.430000 DelPhi exited at 11:38:08 4.434u 0.187s 0:05.31 86.8% 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 Sat Oct 8 2011 at 11:38:08 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: 253 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4872 !!! WARNING: HIR 353 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= 0.1500000 grid size : 179 scale,in grids/A, set to be: 1.641915 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): 7.577000 72.55000 ymin,ymax (A): 5.379000 66.63700 zmin,zma (A): 9.273999 74.32000 x,y,z range (A): 64.97299 61.25800 65.04600 scale (grids/A): 1.641915 object centre (A): 40.06350 36.00800 41.79700 number of atom coordinates read : 4872 total number of charged atoms : 4707 net assigned charge : 1.4046252E-02 assigned positive charge : 732.4941 centred at (gu) : 91.86991 89.66938 91.73373 assigned negative charge : -732.4843 centred at (gu) : 91.69418 89.79588 91.88714 start vw surface at 0.2500000 fill in re-entrant regions at 0.4200000 boundary points on vw surface= 102620 reading accessible surface arcs data from file ARCDAT no. of arc points read = 39527 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 32548 mr = 72769 m= 3403 mr = 22762 m= 78 mr = 1654 m= 1 mr = 7 m= 0 mr = 0 time to grow re-entrant surface = 0.4200000 no. cavity mid-points inaccessible to solvent = 1535 time to turn everything in is 0.9000000 number of dielectric boundary points 41458 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 451 ## 5 charges are in solution ## iepsmp to db, and charging done at 1.050000 number of grid points assigned charge 36059 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) : 0.5473050 object centre at (A) : 40.06350 36.00800 41.79700 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.5886275E-02 -3.0484637E-03 midg,1,midg; midg,igrid,midg -8.3973818E-03 -6.5774973E-03 1,midg,midg; igrid,midg,midg -1.3451844E-02 -3.0847760E-03 gauss-seidel spectral radius is 0.9983906 estimated iterations to convergence 198 setup time was (sec) 1.250000 now iterating at: 11:38:10 rms-change max change #iterations 4.507326 148.3067 at 10iterations 1.963321 64.86723 at 20iterations 0.8636860 24.16027 at 30iterations 0.3804430 12.03769 at 40iterations 0.1673743 5.301382 at 50iterations 7.3726669E-02 2.047591 at 60iterations 3.2565564E-02 0.9072361 at 70iterations 1.4434275E-02 0.5198851 at 80iterations 6.4512873E-03 0.1914635 at 90iterations 2.9131141E-03 9.1499329E-02 at 100iterations 1.3472969E-03 4.2701721E-02 at 110iterations 6.4868369E-04 2.4002075E-02 at 120iterations finished qdiffx linear iterations at : 11:38:18 total time elapsed so far: 9.010000 # loops : 120 mean,max change (kT/e) : 6.4868369E-04 2.4002075E-02 energy calculations done at 9.010000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.280000 DelPhi exited at 11:38:18 9.278u 0.231s 0:09.82 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 Sat Oct 8 2011 at 11:38:18 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: 253 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4872 !!! WARNING: HIR 353 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= 0.1500000 grid size : 179 scale,in grids/A, set to be: 2.462873 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): 7.577000 72.55000 ymin,ymax (A): 5.379000 66.63700 zmin,zma (A): 9.273999 74.32000 x,y,z range (A): 64.97299 61.25800 65.04600 scale (grids/A): 2.462873 object centre (A): 40.06350 36.00800 41.79700 number of atom coordinates read : 4872 total number of charged atoms : 4707 net assigned charge : 1.4046252E-02 assigned positive charge : 732.4941 centred at (gu) : 92.80447 89.50359 92.60036 assigned negative charge : -732.4843 centred at (gu) : 92.54121 89.69378 92.83054 start vw surface at 0.2500000 fill in re-entrant regions at 0.7500000 boundary points on vw surface= 239101 reading accessible surface arcs data from file ARCDAT no. of arc points read = 39527 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 112035 mr = 177731 m= 32487 mr = 89557 m= 5354 mr = 24759 m= 359 mr = 3534 m= 2 mr = 145 m= 0 mr = 0 time to grow re-entrant surface = 1.300000 no. cavity mid-points inaccessible to solvent = 4827 time to turn everything in is 2.210000 number of dielectric boundary points 93612 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 30 iepsmp to db, and charging done at 2.380000 number of grid points assigned charge 37605 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) : 1.641915 object centre at (A) : 40.06350 36.00800 41.79700 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.3709688 -0.2020984 midg,1,midg; midg,igrid,midg -0.1451110 -0.1372374 1,midg,midg; igrid,midg,midg -0.4346812 -0.1944047 gauss-seidel spectral radius is 0.9992421 estimated iterations to convergence 287 setup time was (sec) 2.580000 now iterating at: 11:38:21 rms-change max change #iterations 11.58625 379.4108 at 10iterations 6.862037 163.2115 at 20iterations 4.035159 80.53170 at 30iterations 2.361516 45.87912 at 40iterations 1.378015 25.43799 at 50iterations 0.7985823 15.53409 at 60iterations 0.4636957 8.982840 at 70iterations 0.2683860 5.626842 at 80iterations 0.1549506 3.011370 at 90iterations 8.9497745E-02 1.503225 at 100iterations 5.1547732E-02 0.9450846 at 110iterations 2.9701434E-02 0.5818024 at 120iterations 1.7159298E-02 0.3118057 at 130iterations 9.8694190E-03 0.1956043 at 140iterations 5.7075103E-03 0.1069107 at 150iterations 3.2982933E-03 5.7685256E-02 at 160iterations 1.9110566E-03 3.3582687E-02 at 170iterations 1.1135857E-03 1.9920349E-02 at 180iterations finished qdiffx linear iterations at : 11:38:34 total time elapsed so far: 15.37000 # loops : 180 mean,max change (kT/e) : 1.1135857E-03 1.9920349E-02 energy calculations done at 15.37000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.60000 DelPhi exited at 11:38:34 15.606u 0.218s 0:16.28 97.1% 0+0k 0+0io 0pf+0w