Sat Oct 8 17:06:11 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 17:06:11 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: 315 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3589 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 0.5099337 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): -27.24200 42.57100 ymin,ymax (A): -35.12800 33.56600 zmin,zma (A): 16.34800 64.27500 x,y,z range (A): 69.81300 68.69400 47.92700 scale (grids/A): 0.5099337 object centre (A): 7.664500 -0.7810001 40.31150 number of atom coordinates read : 3589 total number of charged atoms : 3443 net assigned charge : -4.999990 assigned positive charge : 546.5797 centred at (gu) : 91.17699 89.67837 90.01452 assigned negative charge : -551.5817 centred at (gu) : 91.19164 89.66506 89.99774 start vw surface at 0.1400000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 6072 nv = 96 ne = 84 npr = 72046 no. pairs analyzed = 72046 no. exposed pairs = 4489 no. arc points = 31790 no. surface atoms = 1512 nbur = 2077 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 = 1.652000 m= 206 mr = 3159 m= 0 mr = 1 time to grow re-entrant surface = 0.2200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3900000 number of dielectric boundary points 3118 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3175 ## 480 charges are in solution ## iepsmp to db, and charging done at 0.5200000 number of grid points assigned charge 8090 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.0067934E-10 -3.5928999E-11 midg,1,midg; midg,igrid,midg -1.0250729E-10 -3.9257122E-11 1,midg,midg; igrid,midg,midg -2.9883370E-11 -1.3181635E-10 gauss-seidel spectral radius is 0.9802521 estimated iterations to convergence 59 setup time was (sec) 0.6800000 now iterating at: 17:06:12 rms-change max change #iterations 5.9973456E-02 10.60543 at 10iterations 3.2935995E-03 0.5342865 at 20iterations 2.1751141E-04 3.7039161E-02 at 30iterations 2.9196673E-05 5.6138039E-03 at 40iterations 6.0289949E-06 1.2412071E-03 at 50iterations finished qdiffx linear iterations at : 17:06:16 total time elapsed so far: 4.470000 # loops : 50 mean,max change (kT/e) : 6.0289949E-06 1.2412071E-03 energy calculations done at 4.470000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.630000 DelPhi exited at 17:06:16 4.637u 0.386s 0:05.37 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 Sat Oct 8 2011 at 17:06:16 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: 315 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3589 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 1.529801 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): -27.24200 42.57100 ymin,ymax (A): -35.12800 33.56600 zmin,zma (A): 16.34800 64.27500 x,y,z range (A): 69.81300 68.69400 47.92700 scale (grids/A): 1.529801 object centre (A): 7.664500 -0.7810001 40.31150 number of atom coordinates read : 3589 total number of charged atoms : 3443 net assigned charge : -4.999990 assigned positive charge : 546.5797 centred at (gu) : 93.52982 89.03404 90.04196 assigned negative charge : -551.5817 centred at (gu) : 93.57442 88.99474 89.99281 start vw surface at 0.1400000 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 68021 reading accessible surface arcs data from file ARCDAT no. of arc points read = 31790 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.568000 m= 19929 mr = 46579 m= 1779 mr = 13319 m= 49 mr = 699 m= 0 mr = 0 time to grow re-entrant surface = 0.2800000 no. cavity mid-points inaccessible to solvent = 120 time to turn everything in is 0.5700000 number of dielectric boundary points 29181 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 397 ## 2 charges are in solution ## iepsmp to db, and charging done at 0.6700000 number of grid points assigned charge 25843 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) : 0.5099337 object centre at (A) : 7.664500 -0.7810001 40.31150 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.5818285E-04 -8.4253104E-04 midg,1,midg; midg,igrid,midg 1.4421855E-02 8.0766156E-03 1,midg,midg; igrid,midg,midg -3.8336178E-03 -3.2147538E-02 gauss-seidel spectral radius is 0.9979895 estimated iterations to convergence 177 setup time was (sec) 0.8600000 now iterating at: 17:06:17 rms-change max change #iterations 3.240745 150.9291 at 10iterations 1.287139 53.62096 at 20iterations 0.5146758 17.28028 at 30iterations 0.2037558 7.409466 at 40iterations 8.1925489E-02 2.898517 at 50iterations 3.2446083E-02 1.177853 at 60iterations 1.3020989E-02 0.4802933 at 70iterations 5.1870798E-03 0.1928492 at 80iterations 2.0785704E-03 7.1540833E-02 at 90iterations 8.3290652E-04 3.0924320E-02 at 100iterations 3.3681295E-04 1.1890471E-02 at 110iterations 1.3757283E-04 5.4597855E-03 at 120iterations finished qdiffx linear iterations at : 17:06:27 total time elapsed so far: 10.48000 # loops : 120 mean,max change (kT/e) : 1.3757283E-04 5.4597855E-03 energy calculations done at 10.48000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.66000 DelPhi exited at 17:06:28 10.664u 0.431s 0:11.39 97.3% 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 Sat Oct 8 2011 at 17:06:28 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: 315 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3589 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 2.294702 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): -27.24200 42.57100 ymin,ymax (A): -35.12800 33.56600 zmin,zma (A): 16.34800 64.27500 x,y,z range (A): 69.81300 68.69400 47.92700 scale (grids/A): 2.294702 object centre (A): 7.664500 -0.7810001 40.31150 number of atom coordinates read : 3589 total number of charged atoms : 3443 net assigned charge : -4.999990 assigned positive charge : 546.5797 centred at (gu) : 95.29438 88.55084 90.06284 assigned negative charge : -551.5817 centred at (gu) : 95.36153 88.49204 89.98912 start vw surface at 0.1400000 fill in re-entrant regions at 0.4300000 boundary points on vw surface= 158811 reading accessible surface arcs data from file ARCDAT no. of arc points read = 31790 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.540000 m= 71316 mr = 114623 m= 18298 mr = 55940 m= 2454 mr = 13077 m= 136 mr = 1395 m= 1 mr = 39 m= 0 mr = 0 time to grow re-entrant surface = 0.8500000 no. cavity mid-points inaccessible to solvent = 391 time to turn everything in is 1.390000 number of dielectric boundary points 65942 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 52 iepsmp to db, and charging done at 1.520000 number of grid points assigned charge 27470 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) : 1.529801 object centre at (A) : 7.664500 -0.7810001 40.31150 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.7056966E-02 1.4406238E-02 midg,1,midg; midg,igrid,midg 0.4901451 0.1411071 1,midg,midg; igrid,midg,midg -6.5287992E-02 -0.8506295 gauss-seidel spectral radius is 0.9990907 estimated iterations to convergence 262 setup time was (sec) 1.710000 now iterating at: 17:06:30 rms-change max change #iterations 8.772287 326.8083 at 10iterations 4.837841 141.2172 at 20iterations 2.648309 60.29011 at 30iterations 1.450592 34.28357 at 40iterations 0.7895238 16.82117 at 50iterations 0.4298992 9.566885 at 60iterations 0.2335908 4.693045 at 70iterations 0.1264916 2.812757 at 80iterations 6.8490781E-02 1.461040 at 90iterations 3.7083037E-02 0.8087196 at 100iterations 2.0099789E-02 0.4897614 at 110iterations 1.0878701E-02 0.2348328 at 120iterations 5.8811172E-03 0.1152970 at 130iterations 3.1885514E-03 6.7824125E-02 at 140iterations 1.7252708E-03 3.5465240E-02 at 150iterations 9.3449699E-04 2.0812988E-02 at 160iterations 5.0903496E-04 1.0845661E-02 at 170iterations 2.7758925E-04 5.7992935E-03 at 180iterations finished qdiffx linear iterations at : 17:06:45 total time elapsed so far: 17.28000 # loops : 180 mean,max change (kT/e) : 2.7758925E-04 5.7992935E-03 energy calculations done at 17.28000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 17.45000 DelPhi exited at 17:06:46 17.450u 0.461s 0:18.19 98.4% 0+0k 0+0io 0pf+0w