Mon Oct 10 14:01:55 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 Mon Oct 10 2011 at 14:01:55 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 = 2068 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 0.6164289 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): 28.16000 74.14600 ymin,ymax (A): 8.404000 66.15600 zmin,zma (A): 57.52200 100.5670 x,y,z range (A): 45.98600 57.75200 43.04500 scale (grids/A): 0.6164289 object centre (A): 51.15300 37.28000 79.04450 number of atom coordinates read : 2068 total number of charged atoms : 2002 net assigned charge : 0.5000049 assigned positive charge : 303.9917 centred at (gu) : 89.42651 90.96691 88.99391 assigned negative charge : -303.4923 centred at (gu) : 89.32303 90.88231 89.08276 start vw surface at 0.1400000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 5540 nv = 96 ne = 84 npr = 39716 no. pairs analyzed = 39716 no. exposed pairs = 2892 no. arc points = 20462 no. surface atoms = 964 nbur = 1104 mkacc time = 0.1100000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 316 mr = 2815 m= 1 mr = 26 m= 0 mr = 0 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2800000 number of dielectric boundary points 3016 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1976 ## 163 charges are in solution ## iepsmp to db, and charging done at 0.4100000 number of grid points assigned charge 6646 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 5.5485381E-09 -3.0984688E-09 midg,1,midg; midg,igrid,midg -2.9630536E-09 5.2572622E-09 1,midg,midg; igrid,midg,midg -5.2273204E-09 4.4759378E-09 gauss-seidel spectral radius is 0.9863404 estimated iterations to convergence 70 setup time was (sec) 0.5500000 now iterating at: 14:01:56 rms-change max change #iterations 0.1003835 18.90849 at 10iterations 9.1034304E-03 1.693371 at 20iterations 8.2304282E-04 0.1325417 at 30iterations 7.4822347E-05 1.2601852E-02 at 40iterations 6.8565696E-06 9.9754333E-04 at 50iterations finished qdiffx linear iterations at : 14:01:59 total time elapsed so far: 3.850000 # loops : 50 mean,max change (kT/e) : 6.8565696E-06 9.9754333E-04 energy calculations done at 3.850000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.020000 DelPhi exited at 14:02:00 4.024u 0.268s 0:04.88 87.7% 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 Mon Oct 10 2011 at 14:02:00 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 = 2068 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 1.849287 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): 28.16000 74.14600 ymin,ymax (A): 8.404000 66.15600 zmin,zma (A): 57.52200 100.5670 x,y,z range (A): 45.98600 57.75200 43.04500 scale (grids/A): 1.849287 object centre (A): 51.15300 37.28000 79.04450 number of atom coordinates read : 2068 total number of charged atoms : 2002 net assigned charge : 0.5000049 assigned positive charge : 303.9917 centred at (gu) : 88.27924 92.90051 86.98136 assigned negative charge : -303.4923 centred at (gu) : 87.96908 92.64689 87.24841 start vw surface at 0.1300000 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 59975 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20462 grid for indexing accessible points = 1.400000 m= 20938 mr = 39796 m= 3343 mr = 14863 m= 189 mr = 1974 m= 4 mr = 59 m= 0 mr = 0 time to grow re-entrant surface = 0.2700000 no. cavity mid-points inaccessible to solvent = 283 time to turn everything in is 0.5500000 number of dielectric boundary points 27757 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 125 iepsmp to db, and charging done at 0.6700000 number of grid points assigned charge 15720 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) : 0.6164289 object centre at (A) : 51.15300 37.28000 79.04450 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.0163723E-02 -6.4284475E-05 midg,1,midg; midg,igrid,midg -1.3178963E-02 6.1989427E-03 1,midg,midg; igrid,midg,midg -6.3868877E-03 9.9292304E-03 gauss-seidel spectral radius is 0.9985186 estimated iterations to convergence 206 setup time was (sec) 0.8200000 now iterating at: 14:02:01 rms-change max change #iterations 3.494503 226.3076 at 10iterations 1.580111 65.67357 at 20iterations 0.7141862 28.56669 at 30iterations 0.3253299 12.51567 at 40iterations 0.1471862 5.203491 at 50iterations 6.6761732E-02 2.522752 at 60iterations 3.0260283E-02 1.030392 at 70iterations 1.3737555E-02 0.4942678 at 80iterations 6.2056463E-03 0.2204657 at 90iterations 2.8278879E-03 0.1112226 at 100iterations 1.2785663E-03 4.4755936E-02 at 110iterations 5.8044947E-04 2.0998001E-02 at 120iterations finished qdiffx linear iterations at : 14:02:10 total time elapsed so far: 9.140000 # loops : 120 mean,max change (kT/e) : 5.8044947E-04 2.0998001E-02 energy calculations done at 9.140000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.320000 DelPhi exited at 14:02:11 9.327u 0.326s 0:10.88 88.6% 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 Mon Oct 10 2011 at 14:02:12 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 = 2068 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 2.773930 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): 28.16000 74.14600 ymin,ymax (A): 8.404000 66.15600 zmin,zma (A): 57.52200 100.5670 x,y,z range (A): 45.98600 57.75200 43.04500 scale (grids/A): 2.773930 object centre (A): 51.15300 37.28000 79.04450 number of atom coordinates read : 2068 total number of charged atoms : 2002 net assigned charge : 0.5000049 assigned positive charge : 303.9917 centred at (gu) : 87.41888 94.35077 85.47198 assigned negative charge : -303.4923 centred at (gu) : 86.95380 93.97043 85.87273 start vw surface at 0.1400000 fill in re-entrant regions at 0.4600000 boundary points on vw surface= 138902 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20462 grid for indexing accessible points = 1.400000 m= 67213 mr = 97490 m= 24700 mr = 53348 m= 5972 mr = 19354 m= 828 mr = 4352 m= 69 mr = 511 m= 1 mr = 29 m= 0 mr = 0 time to grow re-entrant surface = 0.8300000 no. cavity mid-points inaccessible to solvent = 918 time to turn everything in is 1.380000 number of dielectric boundary points 62601 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2 iepsmp to db, and charging done at 1.520000 number of grid points assigned charge 16015 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) : 1.849287 object centre at (A) : 51.15300 37.28000 79.04450 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1374773 2.6077058E-02 midg,1,midg; midg,igrid,midg -0.1298759 6.1265342E-02 1,midg,midg; igrid,midg,midg -8.9370571E-02 7.3181160E-02 gauss-seidel spectral radius is 0.9992272 estimated iterations to convergence 284 setup time was (sec) 1.690000 now iterating at: 14:02:14 rms-change max change #iterations 8.400971 251.1892 at 10iterations 4.923168 131.4126 at 20iterations 2.854796 72.07427 at 30iterations 1.649398 40.02759 at 40iterations 0.9493867 21.52530 at 50iterations 0.5438738 11.29836 at 60iterations 0.3106049 6.418714 at 70iterations 0.1777064 4.521053 at 80iterations 0.1013814 2.372608 at 90iterations 5.7777759E-02 1.208481 at 100iterations 3.2828063E-02 0.7053432 at 110iterations 1.8676551E-02 0.3715210 at 120iterations 1.0623566E-02 0.2185252 at 130iterations 6.0393666E-03 0.1204138 at 140iterations 3.4257940E-03 7.3852539E-02 at 150iterations 1.9456875E-03 3.9113998E-02 at 160iterations 1.1054254E-03 2.2385597E-02 at 170iterations 6.2729348E-04 1.2516022E-02 at 180iterations finished qdiffx linear iterations at : 14:02:27 total time elapsed so far: 15.19000 # loops : 180 mean,max change (kT/e) : 6.2729348E-04 1.2516022E-02 energy calculations done at 15.19000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.35000 DelPhi exited at 14:02:28 15.352u 0.331s 0:16.16 97.0% 0+0k 0+0io 0pf+0w