Sun Oct 9 08:20:14 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 Sun Oct 9 2011 at 08:20:14 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: 285 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 6120 !!! WARNING: HIR 702 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= 0.1000000 grid size : 179 scale,in grids/A, set to be: 0.4697933 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): -30.34900 34.18900 ymin,ymax (A): -33.14800 31.13400 zmin,zma (A): -32.75400 43.02400 x,y,z range (A): 64.53800 64.28200 75.77800 scale (grids/A): 0.4697933 object centre (A): 1.920002 -1.007000 5.135000 number of atom coordinates read : 6120 total number of charged atoms : 5950 net assigned charge : -1.985963 assigned positive charge : 923.3887 centred at (gu) : 90.91540 90.01323 90.04115 assigned negative charge : -925.3828 centred at (gu) : 90.86184 90.03870 89.92301 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 8185 nv = 96 ne = 84 npr = 124468 no. pairs analyzed = 124468 no. exposed pairs = 7601 no. arc points = 52546 no. surface atoms = 2552 nbur = 3568 mkacc time = 0.2100000 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 = 1.820000 m= 262 mr = 4124 m= 0 mr = 2 time to grow re-entrant surface = 0.2300000 no. cavity mid-points inaccessible to solvent = 13 time to turn everything in is 0.4000000 number of dielectric boundary points 4321 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4858 ## 868 charges are in solution ## iepsmp to db, and charging done at 0.4700000 number of grid points assigned charge 11283 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -6.4093890E-11 5.5119589E-11 midg,1,midg; midg,igrid,midg 8.6007989E-12 -1.7149853E-11 1,midg,midg; igrid,midg,midg -2.4192898E-11 2.9612836E-11 gauss-seidel spectral radius is 0.9769413 estimated iterations to convergence 55 setup time was (sec) 0.6100000 now iterating at: 08:20:15 rms-change max change #iterations 5.0239339E-02 10.36353 at 10iterations 2.5639925E-03 0.4575119 at 20iterations 2.5165037E-04 5.1116943E-02 at 30iterations 5.0806491E-05 9.8934174E-03 at 40iterations 1.3525668E-05 2.1858215E-03 at 50iterations finished qdiffx linear iterations at : 08:20:18 total time elapsed so far: 3.670000 # loops : 50 mean,max change (kT/e) : 1.3525668E-05 2.1858215E-03 energy calculations done at 3.670000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.810000 DelPhi exited at 08:20:18 3.810u 0.181s 0:04.37 91.3% 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 Sun Oct 9 2011 at 08:20:18 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: 285 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 6120 !!! WARNING: HIR 702 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= 0.1000000 grid size : 179 scale,in grids/A, set to be: 1.409380 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): -30.34900 34.18900 ymin,ymax (A): -33.14800 31.13400 zmin,zma (A): -32.75400 43.02400 x,y,z range (A): 64.53800 64.28200 75.77800 scale (grids/A): 1.409380 object centre (A): 1.920002 -1.007000 5.135000 number of atom coordinates read : 6120 total number of charged atoms : 5950 net assigned charge : -1.985963 assigned positive charge : 923.3887 centred at (gu) : 92.74448 90.03744 90.12165 assigned negative charge : -925.3828 centred at (gu) : 92.58525 90.11578 89.76883 start vw surface at 0.1500000 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 94891 reading accessible surface arcs data from file ARCDAT no. of arc points read = 52546 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.708000 m= 24093 mr = 64479 m= 1508 mr = 15053 m= 14 mr = 463 m= 0 mr = 0 time to grow re-entrant surface = 0.2100000 no. cavity mid-points inaccessible to solvent = 471 time to turn everything in is 0.4800000 number of dielectric boundary points 40511 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 912 ## 23 charges are in solution ## iepsmp to db, and charging done at 0.5700000 number of grid points assigned charge 43267 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) : 0.4697933 object centre at (A) : 1.920002 -1.007000 5.135000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.8171230E-02 8.3380975E-03 midg,1,midg; midg,igrid,midg -4.6392441E-05 -1.1544573E-03 1,midg,midg; igrid,midg,midg -6.7491238E-03 2.7800133E-04 gauss-seidel spectral radius is 0.9978464 estimated iterations to convergence 171 setup time was (sec) 0.7200000 now iterating at: 08:20:19 rms-change max change #iterations 3.604465 160.4651 at 10iterations 1.389229 44.81142 at 20iterations 0.5368876 17.69151 at 30iterations 0.2079457 6.828732 at 40iterations 8.0249675E-02 2.619850 at 50iterations 3.1129776E-02 0.9975815 at 60iterations 1.2044056E-02 0.3821278 at 70iterations 4.7080144E-03 0.1623955 at 80iterations 1.8588066E-03 6.1115265E-02 at 90iterations 7.4988574E-04 2.5321960E-02 at 100iterations 3.1895895E-04 1.0194778E-02 at 110iterations 1.5128606E-04 5.6381226E-03 at 120iterations finished qdiffx linear iterations at : 08:20:27 total time elapsed so far: 8.260000 # loops : 120 mean,max change (kT/e) : 1.5128606E-04 5.6381226E-03 energy calculations done at 8.260000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.400000 DelPhi exited at 08:20:27 8.405u 0.210s 0:08.93 96.4% 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 08:20:27 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: 285 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 6120 !!! WARNING: HIR 702 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= 0.1000000 grid size : 179 scale,in grids/A, set to be: 2.114070 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): -30.34900 34.18900 ymin,ymax (A): -33.14800 31.13400 zmin,zma (A): -32.75400 43.02400 x,y,z range (A): 64.53800 64.28200 75.77800 scale (grids/A): 2.114070 object centre (A): 1.920002 -1.007000 5.135000 number of atom coordinates read : 6120 total number of charged atoms : 5950 net assigned charge : -1.985963 assigned positive charge : 923.3887 centred at (gu) : 94.11628 90.05593 90.18188 assigned negative charge : -925.3828 centred at (gu) : 93.87791 90.17370 89.65325 start vw surface at 0.1500000 fill in re-entrant regions at 0.4200000 boundary points on vw surface= 222026 reading accessible surface arcs data from file ARCDAT no. of arc points read = 52546 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.680000 m= 91397 mr = 159587 m= 18790 mr = 69228 m= 1767 mr = 12682 m= 42 mr = 893 m= 0 mr = 2 time to grow re-entrant surface = 0.6600000 no. cavity mid-points inaccessible to solvent = 1808 time to turn everything in is 1.170000 number of dielectric boundary points 91630 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 170 iepsmp to db, and charging done at 1.300000 number of grid points assigned charge 47260 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) : 1.409380 object centre at (A) : 1.920002 -1.007000 5.135000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.6143717 -2.7458582E-02 midg,1,midg; midg,igrid,midg 7.8080925E-03 -7.0530842E-03 1,midg,midg; igrid,midg,midg -0.1577768 -2.2380300E-02 gauss-seidel spectral radius is 0.9991170 estimated iterations to convergence 266 setup time was (sec) 1.480000 now iterating at: 08:20:29 rms-change max change #iterations 10.39888 295.7403 at 10iterations 5.928114 137.1414 at 20iterations 3.350865 78.39380 at 30iterations 1.882140 53.33564 at 40iterations 1.056200 24.41268 at 50iterations 0.5887887 14.81283 at 60iterations 0.3275392 7.094965 at 70iterations 0.1818417 3.687551 at 80iterations 0.1006779 2.303307 at 90iterations 5.5713639E-02 1.069025 at 100iterations 3.0731229E-02 0.6443462 at 110iterations 1.6982138E-02 0.3286381 at 120iterations 9.3645826E-03 0.2036819 at 130iterations 5.1581971E-03 0.1027241 at 140iterations 2.8444547E-03 5.8506966E-02 at 150iterations 1.5737634E-03 2.8839111E-02 at 160iterations 8.6854590E-04 1.6395569E-02 at 170iterations 4.8292705E-04 9.1466904E-03 at 180iterations finished qdiffx linear iterations at : 08:20:44 total time elapsed so far: 15.96000 # loops : 180 mean,max change (kT/e) : 4.8292705E-04 9.1466904E-03 energy calculations done at 15.96000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 16.09000 DelPhi exited at 08:20:44 16.087u 0.304s 0:16.67 98.2% 0+0k 0+0io 0pf+0w