Sun Oct 9 15:15:24 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 Sun Oct 9 2011 at 15:15:24 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5441 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: 0.4977838 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): -18.52400 52.99300 ymin,ymax (A): 97.31100 163.6770 zmin,zma (A): -30.05300 31.88200 x,y,z range (A): 71.51700 66.36600 61.93500 scale (grids/A): 0.4977838 object centre (A): 17.23450 130.4940 0.9145002 number of atom coordinates read : 5441 total number of charged atoms : 5270 net assigned charge : -6.499958 assigned positive charge : 831.2363 centred at (gu) : 89.73395 89.18098 88.41039 assigned negative charge : -837.7433 centred at (gu) : 89.75666 89.25745 88.36407 start vw surface at 0.1300000 fill in re-entrant regions at 0.1300000 boundary points on vw surface= 8143 nv = 96 ne = 84 npr = 112117 no. pairs analyzed = 112117 no. exposed pairs = 6452 no. arc points = 44368 no. surface atoms = 2159 nbur = 3282 mkacc time = 0.1900000 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 = 1.708000 m= 279 mr = 4321 m= 1 mr = 8 m= 0 mr = 0 time to grow re-entrant surface = 0.2000000 no. cavity mid-points inaccessible to solvent = 46 time to turn everything in is 0.3400000 number of dielectric boundary points 4094 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4219 ## 660 charges are in solution ## iepsmp to db, and charging done at 0.4100000 number of grid points assigned charge 11236 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -2.0275116E-10 1.7929056E-11 midg,1,midg; midg,igrid,midg 1.0053598E-10 -1.4800239E-10 1,midg,midg; igrid,midg,midg -1.2609055E-11 -8.4185076E-11 gauss-seidel spectral radius is 0.9794013 estimated iterations to convergence 58 setup time was (sec) 0.5300000 now iterating at: 15:15:25 rms-change max change #iterations 6.2062703E-02 8.170101 at 10iterations 3.5785525E-03 0.5247391 at 20iterations 3.3676773E-04 5.3870201E-02 at 30iterations 6.3024279E-05 8.8462830E-03 at 40iterations 1.3804859E-05 1.9054413E-03 at 50iterations finished qdiffx linear iterations at : 15:15:27 total time elapsed so far: 3.390000 # loops : 50 mean,max change (kT/e) : 1.3804859E-05 1.9054413E-03 energy calculations done at 3.390000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.510000 DelPhi exited at 15:15:28 3.511u 0.193s 0:03.99 92.7% 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 15:15:28 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5441 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: 1.493351 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): -18.52400 52.99300 ymin,ymax (A): 97.31100 163.6770 zmin,zma (A): -30.05300 31.88200 x,y,z range (A): 71.51700 66.36600 61.93500 scale (grids/A): 1.493351 object centre (A): 17.23450 130.4940 0.9145002 number of atom coordinates read : 5441 total number of charged atoms : 5270 net assigned charge : -6.499958 assigned positive charge : 831.2363 centred at (gu) : 89.19993 87.54147 85.22974 assigned negative charge : -837.7433 centred at (gu) : 89.27001 87.77229 85.09245 start vw surface at 0.1500000 fill in re-entrant regions at 0.2300000 boundary points on vw surface= 93642 reading accessible surface arcs data from file ARCDAT no. of arc points read = 44368 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.596000 m= 25900 mr = 65318 m= 2088 mr = 17340 m= 31 mr = 834 m= 0 mr = 0 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 4249 time to turn everything in is 0.4600000 number of dielectric boundary points 38169 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 585 ## 8 charges are in solution ## iepsmp to db, and charging done at 0.5400000 number of grid points assigned charge 39273 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) : 0.4977838 object centre at (A) : 17.23450 130.4940 0.9145002 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -4.6155029E-03 -4.7671259E-03 midg,1,midg; midg,igrid,midg 1.1119684E-02 -1.2963586E-02 1,midg,midg; igrid,midg,midg -1.9944008E-02 -4.5448714E-03 gauss-seidel spectral radius is 0.9980460 estimated iterations to convergence 180 setup time was (sec) 0.6700000 now iterating at: 15:15:29 rms-change max change #iterations 3.883335 164.3612 at 10iterations 1.567019 51.91356 at 20iterations 0.6303094 20.72961 at 30iterations 0.2554980 7.872199 at 40iterations 0.1031834 3.371848 at 50iterations 4.1868296E-02 1.305172 at 60iterations 1.6988441E-02 0.5686934 at 70iterations 6.8544941E-03 0.2212975 at 80iterations 2.7878755E-03 9.3490601E-02 at 90iterations 1.1274248E-03 3.8961411E-02 at 100iterations 4.5903132E-04 1.4448643E-02 at 110iterations 1.8853284E-04 6.3633919E-03 at 120iterations finished qdiffx linear iterations at : 15:15:36 total time elapsed so far: 7.700000 # loops : 120 mean,max change (kT/e) : 1.8853284E-04 6.3633919E-03 energy calculations done at 7.700000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.830000 DelPhi exited at 15:15:36 7.830u 0.194s 0:08.35 96.0% 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 15:15:36 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5441 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: 2.240027 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): -18.52400 52.99300 ymin,ymax (A): 97.31100 163.6770 zmin,zma (A): -30.05300 31.88200 x,y,z range (A): 71.51700 66.36600 61.93500 scale (grids/A): 2.240027 object centre (A): 17.23450 130.4940 0.9145002 number of atom coordinates read : 5441 total number of charged atoms : 5270 net assigned charge : -6.499958 assigned positive charge : 831.2363 centred at (gu) : 88.79916 86.31156 82.84399 assigned negative charge : -837.7433 centred at (gu) : 88.90485 86.65849 82.63866 start vw surface at 0.1300000 fill in re-entrant regions at 0.4000000 boundary points on vw surface= 219154 reading accessible surface arcs data from file ARCDAT no. of arc points read = 44368 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.596000 m= 94739 mr = 161146 m= 22838 mr = 74195 m= 2819 mr = 16407 m= 116 mr = 1673 m= 0 mr = 28 time to grow re-entrant surface = 0.6000000 no. cavity mid-points inaccessible to solvent = 14750 time to turn everything in is 1.100000 number of dielectric boundary points 86217 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 89 iepsmp to db, and charging done at 1.190000 number of grid points assigned charge 42009 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) : 1.493351 object centre at (A) : 17.23450 130.4940 0.9145002 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.7176036E-02 -0.1277814 midg,1,midg; midg,igrid,midg 0.2240848 -0.2802456 1,midg,midg; igrid,midg,midg -0.2941255 1.9932063E-02 gauss-seidel spectral radius is 0.9991453 estimated iterations to convergence 270 setup time was (sec) 1.340000 now iterating at: 15:15:38 rms-change max change #iterations 10.61330 258.9047 at 10iterations 5.994355 149.7171 at 20iterations 3.365661 80.99052 at 30iterations 1.881293 40.94747 at 40iterations 1.046183 21.65195 at 50iterations 0.5812845 12.79141 at 60iterations 0.3219666 6.754820 at 70iterations 0.1786691 3.311389 at 80iterations 9.8569281E-02 1.870180 at 90iterations 5.4458410E-02 1.001104 at 100iterations 3.0099912E-02 0.5542955 at 110iterations 1.6622011E-02 0.2695074 at 120iterations 9.1768941E-03 0.1592827 at 130iterations 5.0483621E-03 9.0957642E-02 at 140iterations 2.7837583E-03 5.0576210E-02 at 150iterations 1.5389374E-03 2.8736115E-02 at 160iterations 8.4956601E-04 1.4969826E-02 at 170iterations 4.6746901E-04 8.4629059E-03 at 180iterations finished qdiffx linear iterations at : 15:15:49 total time elapsed so far: 12.88000 # loops : 180 mean,max change (kT/e) : 4.6746901E-04 8.4629059E-03 energy calculations done at 12.88000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.00000 DelPhi exited at 15:15:50 13.006u 0.223s 0:13.50 97.9% 0+0k 0+0io 0pf+0w