Sat Oct 8 14:01:38 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 14:01:38 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: 333 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2996 !!! WARNING: HIR 110 has a net charge of 0.5140 !!! WARNING: NAP 500 has a net charge of -2.0000 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: 0.6520266 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): -12.01400 42.28700 ymin,ymax (A): -22.46100 22.17200 zmin,zma (A): -7.835000 46.76400 x,y,z range (A): 54.30100 44.63300 54.59900 scale (grids/A): 0.6520266 object centre (A): 15.13650 -0.1445007 19.46450 number of atom coordinates read : 2996 total number of charged atoms : 2849 net assigned charge : -0.9859920 assigned positive charge : 451.5807 centred at (gu) : 88.94598 89.57158 91.89117 assigned negative charge : -452.5674 centred at (gu) : 88.95975 89.45271 91.81596 start vw surface at 0.1600000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 8416 nv = 96 ne = 84 npr = 63313 no. pairs analyzed = 63313 no. exposed pairs = 3374 no. arc points = 23455 no. surface atoms = 1158 nbur = 1838 mkacc time = 0.1300000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 457 mr = 4976 m= 1 mr = 59 m= 0 mr = 0 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 24 time to turn everything in is 0.3300000 number of dielectric boundary points 3839 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2242 ## 216 charges are in solution ## iepsmp to db, and charging done at 0.4300000 number of grid points assigned charge 10118 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.0982718E-08 1.7743025E-08 midg,1,midg; midg,igrid,midg -2.7061724E-08 1.7969864E-08 1,midg,midg; igrid,midg,midg 4.8348947E-10 -3.8393426E-09 gauss-seidel spectral radius is 0.9878385 estimated iterations to convergence 74 setup time was (sec) 0.5500000 now iterating at: 14:01:39 rms-change max change #iterations 0.1778842 24.09732 at 10iterations 1.8911278E-02 2.651375 at 20iterations 2.0339822E-03 0.2631912 at 30iterations 2.6109267E-04 3.2607079E-02 at 40iterations 4.5690751E-05 6.0405731E-03 at 50iterations finished qdiffx linear iterations at : 14:01:42 total time elapsed so far: 3.080000 # loops : 50 mean,max change (kT/e) : 4.5690751E-05 6.0405731E-03 energy calculations done at 3.080000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.250000 DelPhi exited at 14:01:42 3.254u 0.161s 0:03.67 92.9% 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 14:01:42 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: 333 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2996 !!! WARNING: HIR 110 has a net charge of 0.5140 !!! WARNING: NAP 500 has a net charge of -2.0000 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: 1.956080 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): -12.01400 42.28700 ymin,ymax (A): -22.46100 22.17200 zmin,zma (A): -7.835000 46.76400 x,y,z range (A): 54.30100 44.63300 54.59900 scale (grids/A): 1.956080 object centre (A): 15.13650 -0.1445007 19.46450 number of atom coordinates read : 2996 total number of charged atoms : 2849 net assigned charge : -0.9859920 assigned positive charge : 451.5807 centred at (gu) : 86.83735 88.71436 95.67315 assigned negative charge : -452.5674 centred at (gu) : 86.87902 88.35801 95.44746 start vw surface at 0.1600000 fill in re-entrant regions at 0.2800000 boundary points on vw surface= 91611 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23455 grid for indexing accessible points = 1.400000 m= 34135 mr = 66526 m= 5443 mr = 25832 m= 393 mr = 3553 m= 4 mr = 135 m= 0 mr = 0 time to grow re-entrant surface = 0.3000000 no. cavity mid-points inaccessible to solvent = 855 time to turn everything in is 0.6300000 number of dielectric boundary points 35540 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 136 iepsmp to db, and charging done at 0.7600000 number of grid points assigned charge 22468 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) : 0.6520266 object centre at (A) : 15.13650 -0.1445007 19.46450 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.2269387E-02 2.3534028E-02 midg,1,midg; midg,igrid,midg -3.2490711E-03 2.2215677E-02 1,midg,midg; igrid,midg,midg -4.1494582E-02 2.0054285E-03 gauss-seidel spectral radius is 0.9987313 estimated iterations to convergence 222 setup time was (sec) 0.9200000 now iterating at: 14:01:43 rms-change max change #iterations 4.903014 200.8053 at 10iterations 2.371575 74.68900 at 20iterations 1.141640 32.66830 at 30iterations 0.5516038 17.11116 at 40iterations 0.2654534 7.599037 at 50iterations 0.1277389 3.529466 at 60iterations 6.1658219E-02 1.989599 at 70iterations 2.9790200E-02 0.8185606 at 80iterations 1.4378339E-02 0.4277763 at 90iterations 6.9499724E-03 0.2017584 at 100iterations 3.3648091E-03 0.1013184 at 110iterations 1.6310163E-03 4.2074203E-02 at 120iterations finished qdiffx linear iterations at : 14:01:50 total time elapsed so far: 7.390000 # loops : 120 mean,max change (kT/e) : 1.6310163E-03 4.2074203E-02 energy calculations done at 7.390000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.560000 DelPhi exited at 14:01:50 7.563u 0.194s 0:08.03 96.5% 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 8 2011 at 14:01:50 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: 333 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2996 !!! WARNING: HIR 110 has a net charge of 0.5140 !!! WARNING: NAP 500 has a net charge of -2.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 2.934120 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): -12.01400 42.28700 ymin,ymax (A): -22.46100 22.17200 zmin,zma (A): -7.835000 46.76400 x,y,z range (A): 54.30100 44.63300 54.59900 scale (grids/A): 2.934120 object centre (A): 15.13650 -0.1445007 19.46450 number of atom coordinates read : 2996 total number of charged atoms : 2849 net assigned charge : -0.9859920 assigned positive charge : 451.5807 centred at (gu) : 85.25586 88.07134 98.50951 assigned negative charge : -452.5674 centred at (gu) : 85.31852 87.53691 98.17117 start vw surface at 0.1400000 fill in re-entrant regions at 0.5300000 boundary points on vw surface= 211908 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23455 grid for indexing accessible points = 1.400000 m= 110340 mr = 160187 m= 40461 mr = 92207 m= 10009 mr = 33164 m= 1554 mr = 7666 m= 105 mr = 1072 m= 1 mr = 43 m= 0 mr = 0 time to grow re-entrant surface = 0.9499999 no. cavity mid-points inaccessible to solvent = 2951 time to turn everything in is 1.590000 number of dielectric boundary points 80039 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.730000 number of grid points assigned charge 22791 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) : 1.956080 object centre at (A) : 15.13650 -0.1445007 19.46450 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -9.1860056E-02 0.3460450 midg,1,midg; midg,igrid,midg -2.5559930E-02 0.2477780 1,midg,midg; igrid,midg,midg -0.6131915 0.2794346 gauss-seidel spectral radius is 0.9992867 estimated iterations to convergence 295 setup time was (sec) 1.890000 now iterating at: 14:01:52 rms-change max change #iterations 11.30203 368.4750 at 10iterations 6.638877 136.9933 at 20iterations 3.897991 80.92116 at 30iterations 2.281006 43.34629 at 40iterations 1.332494 23.63715 at 50iterations 0.7769517 14.30502 at 60iterations 0.4517694 7.375061 at 70iterations 0.2633619 4.642477 at 80iterations 0.1532582 2.460821 at 90iterations 8.9232020E-02 1.435720 at 100iterations 5.1942591E-02 0.8636031 at 110iterations 3.0156037E-02 0.4786277 at 120iterations 1.7563784E-02 0.3000902 at 130iterations 1.0197341E-02 0.1609029 at 140iterations 5.9571257E-03 9.7459793E-02 at 150iterations 3.4782283E-03 5.9574127E-02 at 160iterations 2.0460195E-03 3.2510757E-02 at 170iterations 1.2032884E-03 2.1551132E-02 at 180iterations finished qdiffx linear iterations at : 14:02:03 total time elapsed so far: 12.52000 # loops : 180 mean,max change (kT/e) : 1.2032884E-03 2.1551132E-02 energy calculations done at 12.52000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.70000 DelPhi exited at 14:02:04 12.700u 0.237s 0:13.24 97.6% 0+0k 0+0io 0pf+0w