Sat Oct 15 14:24:52 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 15 2011 at 14:24:52 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: 252 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3358 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: 0.6483455 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): 12.20700 62.62900 ymin,ymax (A): -41.36800 10.98500 zmin,zma (A): 30.78900 85.69800 x,y,z range (A): 50.42200 52.35300 54.90900 scale (grids/A): 0.6483455 object centre (A): 37.41800 -15.19150 58.24350 number of atom coordinates read : 3358 total number of charged atoms : 3210 net assigned charge : 1.000035 assigned positive charge : 513.5885 centred at (gu) : 89.27285 90.89564 89.41357 assigned negative charge : -512.5895 centred at (gu) : 89.30196 90.82116 89.43117 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 9347 nv = 96 ne = 84 npr = 69347 no. pairs analyzed = 69347 no. exposed pairs = 3740 no. arc points = 25773 no. surface atoms = 1272 nbur = 2086 mkacc time = 0.1700000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 548 mr = 5612 m= 1 mr = 64 m= 0 mr = 0 time to grow re-entrant surface = 0.2300000 no. cavity mid-points inaccessible to solvent = 82 time to turn everything in is 0.4100000 number of dielectric boundary points 4220 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2489 ## 203 charges are in solution ## iepsmp to db, and charging done at 0.5200000 number of grid points assigned charge 11270 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 5.6824296E-09 -1.5404972E-09 midg,1,midg; midg,igrid,midg -1.0566755E-08 1.9245189E-08 1,midg,midg; igrid,midg,midg 8.4401544E-09 -3.3998953E-09 gauss-seidel spectral radius is 0.9877301 estimated iterations to convergence 74 setup time was (sec) 0.7100000 now iterating at: 14:24:54 rms-change max change #iterations 0.1835013 22.67196 at 10iterations 1.9071199E-02 2.155361 at 20iterations 2.2514085E-03 0.3104496 at 30iterations 5.0990656E-04 7.6452255E-02 at 40iterations 2.1395530E-04 3.2264709E-02 at 50iterations finished qdiffx linear iterations at : 14:24:58 total time elapsed so far: 5.480000 # loops : 50 mean,max change (kT/e) : 2.1395530E-04 3.2264709E-02 energy calculations done at 5.480000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 5.640000 DelPhi exited at 14:24:59 5.643u 0.445s 0:06.42 94.7% 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 15 2011 at 14:24:59 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: 252 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3358 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: 1.945036 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): 12.20700 62.62900 ymin,ymax (A): -41.36800 10.98500 zmin,zma (A): 30.78900 85.69800 x,y,z range (A): 50.42200 52.35300 54.90900 scale (grids/A): 1.945036 object centre (A): 37.41800 -15.19150 58.24350 number of atom coordinates read : 3358 total number of charged atoms : 3210 net assigned charge : 1.000035 assigned positive charge : 513.5885 centred at (gu) : 87.81788 92.68593 88.23967 assigned negative charge : -512.5895 centred at (gu) : 87.90530 92.46319 88.29295 start vw surface at 0.1200000 fill in re-entrant regions at 0.3000000 boundary points on vw surface= 101239 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25773 grid for indexing accessible points = 1.400000 m= 39701 mr = 74069 m= 6647 mr = 30560 m= 433 mr = 4328 m= 11 mr = 177 m= 0 mr = 0 time to grow re-entrant surface = 0.4600000 no. cavity mid-points inaccessible to solvent = 1621 time to turn everything in is 0.8500000 number of dielectric boundary points 38897 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 129 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.9900000 number of grid points assigned charge 25273 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) : 0.6483455 object centre at (A) : 37.41800 -15.19150 58.24350 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -3.9216396E-03 -2.0506302E-02 midg,1,midg; midg,igrid,midg -9.0199625E-03 3.6087364E-02 1,midg,midg; igrid,midg,midg 1.3870711E-02 4.2588789E-02 gauss-seidel spectral radius is 0.9987485 estimated iterations to convergence 224 setup time was (sec) 1.200000 now iterating at: 14:25:01 rms-change max change #iterations 5.169385 173.1207 at 10iterations 2.508430 69.63661 at 20iterations 1.223321 35.02909 at 30iterations 0.5934963 17.91955 at 40iterations 0.2880623 7.693161 at 50iterations 0.1402423 3.582088 at 60iterations 6.8177640E-02 1.783778 at 70iterations 3.3084422E-02 0.9182281 at 80iterations 1.6062025E-02 0.4398842 at 90iterations 7.8449445E-03 0.2202682 at 100iterations 3.8750113E-03 0.1119211 at 110iterations 1.9357449E-03 5.8279037E-02 at 120iterations finished qdiffx linear iterations at : 14:25:13 total time elapsed so far: 13.28000 # loops : 120 mean,max change (kT/e) : 1.9357449E-03 5.8279037E-02 energy calculations done at 13.28000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.44000 DelPhi exited at 14:25:13 13.443u 0.542s 0:14.33 97.5% 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 Sat Oct 15 2011 at 14:25:13 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: 252 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3358 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: 2.917555 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): 12.20700 62.62900 ymin,ymax (A): -41.36800 10.98500 zmin,zma (A): 30.78900 85.69800 x,y,z range (A): 50.42200 52.35300 54.90900 scale (grids/A): 2.917555 object centre (A): 37.41800 -15.19150 58.24350 number of atom coordinates read : 3358 total number of charged atoms : 3210 net assigned charge : 1.000035 assigned positive charge : 513.5885 centred at (gu) : 86.72657 94.02905 87.35938 assigned negative charge : -512.5895 centred at (gu) : 86.85779 93.69466 87.43927 start vw surface at 0.1400000 fill in re-entrant regions at 0.7100000 boundary points on vw surface= 233748 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25773 grid for indexing accessible points = 1.400000 m= 126996 mr = 177898 m= 48730 mr = 107027 m= 12327 mr = 40316 m= 1948 mr = 9471 m= 140 mr = 1274 m= 2 mr = 70 m= 0 mr = 0 time to grow re-entrant surface = 1.440000 no. cavity mid-points inaccessible to solvent = 5447 time to turn everything in is 2.320000 number of dielectric boundary points 87835 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 2.500000 number of grid points assigned charge 25679 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) : 1.945036 object centre at (A) : 37.41800 -15.19150 58.24350 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.1078952E-02 -7.8572579E-02 midg,1,midg; midg,igrid,midg -9.3307599E-02 0.4274705 1,midg,midg; igrid,midg,midg 0.1683143 0.5187058 gauss-seidel spectral radius is 0.9992959 estimated iterations to convergence 297 setup time was (sec) 2.730000 now iterating at: 14:25:17 rms-change max change #iterations 11.93577 447.5997 at 10iterations 7.100869 147.7679 at 20iterations 4.212652 89.26634 at 30iterations 2.490122 50.96773 at 40iterations 1.468061 26.32175 at 50iterations 0.8627477 15.51202 at 60iterations 0.5080559 8.533924 at 70iterations 0.2976884 5.376167 at 80iterations 0.1744996 3.002930 at 90iterations 0.1020596 1.502377 at 100iterations 5.9805501E-02 0.9085541 at 110iterations 3.4917019E-02 0.5632057 at 120iterations 2.0431696E-02 0.3434815 at 130iterations 1.1947313E-02 0.1885276 at 140iterations 6.9896812E-03 0.1018791 at 150iterations 4.0873652E-03 6.3591003E-02 at 160iterations 2.3893565E-03 3.6708832E-02 at 170iterations 1.4010560E-03 2.1822214E-02 at 180iterations finished qdiffx linear iterations at : 14:25:38 total time elapsed so far: 24.54000 # loops : 180 mean,max change (kT/e) : 1.4010560E-03 2.1822214E-02 energy calculations done at 24.54000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 24.70000 DelPhi exited at 14:25:39 24.708u 0.585s 0:25.64 98.5% 0+0k 0+0io 0pf+0w