Sun Oct 9 15:48:44 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 15:48:44 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 = 5280 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: 0.5216041 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): 24.24700 85.69000 ymin,ymax (A): 13.80500 82.05600 zmin,zma (A): -33.32900 31.22100 x,y,z range (A): 61.44300 68.25100 64.55000 scale (grids/A): 0.5216041 object centre (A): 54.96850 47.93050 -1.054001 number of atom coordinates read : 5280 total number of charged atoms : 5110 net assigned charge : -4.499960 assigned positive charge : 805.6577 centred at (gu) : 90.44147 89.69911 90.55079 assigned negative charge : -810.1641 centred at (gu) : 90.32637 89.70166 90.62934 start vw surface at 0.2200000 fill in re-entrant regions at 0.2300000 boundary points on vw surface= 8884 nv = 96 ne = 84 npr = 108740 no. pairs analyzed = 108740 no. exposed pairs = 6175 no. arc points = 42392 no. surface atoms = 2088 nbur = 3192 mkacc time = 0.2600000 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 = 1.624000 m= 322 mr = 4877 m= 2 mr = 10 m= 0 mr = 0 time to grow re-entrant surface = 0.2800000 no. cavity mid-points inaccessible to solvent = 48 time to turn everything in is 0.5200000 number of dielectric boundary points 4321 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4062 ## 545 charges are in solution ## iepsmp to db, and charging done at 0.6300000 number of grid points assigned charge 11834 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.2397433E-10 -5.4689997E-10 midg,1,midg; midg,igrid,midg -9.8644495E-11 -1.0687843E-10 1,midg,midg; igrid,midg,midg -5.7820093E-10 4.7855825E-10 gauss-seidel spectral radius is 0.9812232 estimated iterations to convergence 60 setup time was (sec) 0.7600000 now iterating at: 15:48:45 rms-change max change #iterations 8.2182266E-02 10.32475 at 10iterations 8.4231915E-03 1.503525 at 20iterations 2.9821524E-03 0.5475006 at 30iterations 1.2790085E-03 0.2364883 at 40iterations 5.5146258E-04 0.1023293 at 50iterations finished qdiffx linear iterations at : 15:48:48 total time elapsed so far: 3.400000 # loops : 50 mean,max change (kT/e) : 5.5146258E-04 0.1023293 energy calculations done at 3.400000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.600000 DelPhi exited at 15:48:48 3.599u 0.155s 0:04.24 88.2% 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 Sun Oct 9 2011 at 15:48:48 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 = 5280 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1400000 grid size : 179 scale,in grids/A, set to be: 1.564812 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): 24.24700 85.69000 ymin,ymax (A): 13.80500 82.05600 zmin,zma (A): -33.32900 31.22100 x,y,z range (A): 61.44300 68.25100 64.55000 scale (grids/A): 1.564812 object centre (A): 54.96850 47.93050 -1.054001 number of atom coordinates read : 5280 total number of charged atoms : 5110 net assigned charge : -4.499960 assigned positive charge : 805.6577 centred at (gu) : 91.32245 89.09590 91.65054 assigned negative charge : -810.1641 centred at (gu) : 90.97845 89.10452 91.88810 start vw surface at 0.2200000 fill in re-entrant regions at 0.3500000 boundary points on vw surface= 99835 reading accessible surface arcs data from file ARCDAT no. of arc points read = 42392 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.512000 m= 31084 mr = 70611 m= 3013 mr = 21797 m= 73 mr = 1402 m= 3 mr = 5 m= 0 mr = 0 time to grow re-entrant surface = 0.3300000 no. cavity mid-points inaccessible to solvent = 1786 time to turn everything in is 0.7300000 number of dielectric boundary points 40193 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 493 ## 5 charges are in solution ## iepsmp to db, and charging done at 0.8500000 number of grid points assigned charge 38635 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) : 0.5216041 object centre at (A) : 54.96850 47.93050 -1.054001 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -3.4443177E-03 -1.6377155E-02 midg,1,midg; midg,igrid,midg 6.0637211E-03 -1.5188274E-02 1,midg,midg; igrid,midg,midg -9.9516073E-03 1.9311789E-02 gauss-seidel spectral radius is 0.9982278 estimated iterations to convergence 189 setup time was (sec) 1.010000 now iterating at: 15:48:50 rms-change max change #iterations 4.274627 156.6789 at 10iterations 1.799172 57.71500 at 20iterations 0.7596015 24.33897 at 30iterations 0.3209616 10.01348 at 40iterations 0.1364397 4.087080 at 50iterations 5.8171436E-02 1.807159 at 60iterations 2.5487129E-02 0.7706871 at 70iterations 1.1774030E-02 0.3725433 at 80iterations 6.0505755E-03 0.2235718 at 90iterations 3.6373027E-03 0.1345901 at 100iterations 2.4318222E-03 8.6082458E-02 at 110iterations 1.7294337E-03 6.2919617E-02 at 120iterations finished qdiffx linear iterations at : 15:48:56 total time elapsed so far: 7.610000 # loops : 120 mean,max change (kT/e) : 1.7294337E-03 6.2919617E-02 energy calculations done at 7.610000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.800000 DelPhi exited at 15:48:57 7.804u 0.166s 0:08.34 95.4% 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 15:48:57 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 = 5280 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: 2.347218 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): 24.24700 85.69000 ymin,ymax (A): 13.80500 82.05600 zmin,zma (A): -33.32900 31.22100 x,y,z range (A): 61.44300 68.25100 64.55000 scale (grids/A): 2.347218 object centre (A): 54.96850 47.93050 -1.054001 number of atom coordinates read : 5280 total number of charged atoms : 5110 net assigned charge : -4.499960 assigned positive charge : 805.6577 centred at (gu) : 91.98303 88.64363 92.47521 assigned negative charge : -810.1641 centred at (gu) : 91.46791 88.65665 92.83233 start vw surface at 0.2200000 fill in re-entrant regions at 0.6000000 boundary points on vw surface= 232571 reading accessible surface arcs data from file ARCDAT no. of arc points read = 42392 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.512000 m= 108739 mr = 172671 m= 30374 mr = 87338 m= 4510 mr = 22861 m= 251 mr = 2889 m= 3 mr = 81 m= 0 mr = 0 time to grow re-entrant surface = 1.030000 no. cavity mid-points inaccessible to solvent = 5778 time to turn everything in is 1.760000 number of dielectric boundary points 90608 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 43 iepsmp to db, and charging done at 1.900000 number of grid points assigned charge 40811 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) : 1.564812 object centre at (A) : 54.96850 47.93050 -1.054001 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -9.5994309E-02 -0.1905089 midg,1,midg; midg,igrid,midg 0.1433154 -0.2701926 1,midg,midg; igrid,midg,midg -0.1206155 0.4034507 gauss-seidel spectral radius is 0.9991982 estimated iterations to convergence 279 setup time was (sec) 2.060000 now iterating at: 15:48:59 rms-change max change #iterations 11.27741 279.0855 at 10iterations 6.503798 144.9157 at 20iterations 3.718902 74.18373 at 30iterations 2.120977 43.05468 at 40iterations 1.205634 22.63948 at 50iterations 0.6833242 14.09092 at 60iterations 0.3863007 7.393803 at 70iterations 0.2185721 3.758472 at 80iterations 0.1233868 2.369999 at 90iterations 6.9698609E-02 1.293282 at 100iterations 3.9464451E-02 0.6660233 at 110iterations 2.2454714E-02 0.3867664 at 120iterations 1.2892569E-02 0.2637367 at 130iterations 7.5333770E-03 0.1518307 at 140iterations 4.5840796E-03 8.8462830E-02 at 150iterations 2.9357073E-03 6.0295105E-02 at 160iterations 2.0025442E-03 4.5581818E-02 at 170iterations 1.4656087E-03 3.1703949E-02 at 180iterations finished qdiffx linear iterations at : 15:49:10 total time elapsed so far: 12.60000 # loops : 180 mean,max change (kT/e) : 1.4656087E-03 3.1703949E-02 energy calculations done at 12.60000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.79000 DelPhi exited at 15:49:10 12.794u 0.201s 0:13.27 97.8% 0+0k 0+0io 0pf+0w