Sat Oct 8 20:40:20 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 Sat Oct 8 2011 at 20:40:20 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: 262 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2573 !!! WARNING: HIZ 94 has a net charge of 0.2000 !!! WARNING: HIZ 96 has a net charge of 0.2000 !!! WARNING: HIY 119 has a net charge of 0.2000 !!! WARNING: ZN4 472 has a net charge of 1.4000 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: 0.6261322 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): -31.90500 17.46400 ymin,ymax (A): -24.11400 22.84500 zmin,zma (A): -12.00900 44.84800 x,y,z range (A): 49.36900 46.95900 56.85700 scale (grids/A): 0.6261322 object centre (A): -7.220500 -0.6345005 16.41950 number of atom coordinates read : 2573 total number of charged atoms : 2457 net assigned charge : 4.000009 assigned positive charge : 391.9970 centred at (gu) : 88.53532 89.42736 89.57963 assigned negative charge : -387.9975 centred at (gu) : 88.44711 89.47017 89.48146 start vw surface at 0.1600000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 6656 nv = 96 ne = 84 npr = 53180 no. pairs analyzed = 53180 no. exposed pairs = 2980 no. arc points = 21360 no. surface atoms = 1004 nbur = 1569 mkacc time = 0.1500000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 322 mr = 3754 m= 2 mr = 46 m= 0 mr = 0 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 106 time to turn everything in is 0.3500000 number of dielectric boundary points 3180 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2142 ## 209 charges are in solution ## iepsmp to db, and charging done at 0.4800000 number of grid points assigned charge 8223 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -4.2387902E-09 1.0655875E-08 midg,1,midg; midg,igrid,midg 8.3478326E-09 5.5601584E-10 1,midg,midg; igrid,midg,midg -4.3138804E-09 7.9445046E-09 gauss-seidel spectral radius is 0.9867834 estimated iterations to convergence 71 setup time was (sec) 0.6200000 now iterating at: 20:40:20 rms-change max change #iterations 0.1321553 18.85808 at 10iterations 1.2161591E-02 1.711725 at 20iterations 1.1616595E-03 0.1672287 at 30iterations 1.0975605E-04 1.6273499E-02 at 40iterations 1.0464139E-05 1.4419556E-03 at 50iterations finished qdiffx linear iterations at : 20:40:24 total time elapsed so far: 3.890000 # loops : 50 mean,max change (kT/e) : 1.0464139E-05 1.4419556E-03 energy calculations done at 3.890000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.070000 DelPhi exited at 20:40:24 4.072u 0.249s 0:04.63 93.0% 0+0k 0+0io 6pf+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 20:40:24 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: 262 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2573 !!! WARNING: HIZ 94 has a net charge of 0.2000 !!! WARNING: HIZ 96 has a net charge of 0.2000 !!! WARNING: HIY 119 has a net charge of 0.2000 !!! WARNING: ZN4 472 has a net charge of 1.4000 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: 1.878397 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): -31.90500 17.46400 ymin,ymax (A): -24.11400 22.84500 zmin,zma (A): -12.00900 44.84800 x,y,z range (A): 49.36900 46.95900 56.85700 scale (grids/A): 1.878397 object centre (A): -7.220500 -0.6345005 16.41950 number of atom coordinates read : 2573 total number of charged atoms : 2457 net assigned charge : 4.000009 assigned positive charge : 391.9970 centred at (gu) : 85.60577 88.28178 88.73820 assigned negative charge : -387.9975 centred at (gu) : 85.34123 88.41023 88.44431 start vw surface at 0.1600000 fill in re-entrant regions at 0.2900000 boundary points on vw surface= 72193 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21360 grid for indexing accessible points = 1.400000 m= 25909 mr = 50690 m= 3940 mr = 19474 m= 239 mr = 2540 m= 0 mr = 93 time to grow re-entrant surface = 0.3100000 no. cavity mid-points inaccessible to solvent = 3011 time to turn everything in is 0.6400000 number of dielectric boundary points 29484 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 165 iepsmp to db, and charging done at 0.7800000 number of grid points assigned charge 19265 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) : 0.6261322 object centre at (A) : -7.220500 -0.6345005 16.41950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.1837283E-02 1.8293915E-02 midg,1,midg; midg,igrid,midg 1.4524688E-02 3.3397770E-03 1,midg,midg; igrid,midg,midg -2.7307272E-03 3.0703286E-02 gauss-seidel spectral radius is 0.9985934 estimated iterations to convergence 211 setup time was (sec) 0.9400000 now iterating at: 20:40:25 rms-change max change #iterations 4.098053 164.4440 at 10iterations 1.893996 68.58939 at 20iterations 0.8778090 28.50463 at 30iterations 0.4057081 13.85596 at 40iterations 0.1885290 6.036737 at 50iterations 8.7193079E-02 2.770261 at 60iterations 4.0400758E-02 1.279630 at 70iterations 1.8756643E-02 0.5715256 at 80iterations 8.6778607E-03 0.2741089 at 90iterations 4.0132059E-03 0.1309547 at 100iterations 1.8598303E-03 6.5684319E-02 at 110iterations 8.6199708E-04 2.5932312E-02 at 120iterations finished qdiffx linear iterations at : 20:40:34 total time elapsed so far: 9.180000 # loops : 120 mean,max change (kT/e) : 8.6199708E-04 2.5932312E-02 energy calculations done at 9.180000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.360000 DelPhi exited at 20:40:34 9.368u 0.289s 0:09.92 97.1% 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 20:40:34 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: 262 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2573 !!! WARNING: HIZ 94 has a net charge of 0.2000 !!! WARNING: HIZ 96 has a net charge of 0.2000 !!! WARNING: HIY 119 has a net charge of 0.2000 !!! WARNING: ZN4 472 has a net charge of 1.4000 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: 2.817595 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): -31.90500 17.46400 ymin,ymax (A): -24.11400 22.84500 zmin,zma (A): -12.00900 44.84800 x,y,z range (A): 49.36900 46.95900 56.85700 scale (grids/A): 2.817595 object centre (A): -7.220500 -0.6345005 16.41950 number of atom coordinates read : 2573 total number of charged atoms : 2457 net assigned charge : 4.000009 assigned positive charge : 391.9970 centred at (gu) : 83.40872 87.42264 88.10718 assigned negative charge : -387.9975 centred at (gu) : 83.01189 87.61543 87.66645 start vw surface at 0.1600000 fill in re-entrant regions at 0.5500000 boundary points on vw surface= 167020 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21360 grid for indexing accessible points = 1.400000 m= 85008 mr = 122421 m= 29905 mr = 70506 m= 7094 mr = 24389 m= 965 mr = 5449 m= 43 mr = 683 m= 0 mr = 13 time to grow re-entrant surface = 0.9600000 no. cavity mid-points inaccessible to solvent = 10528 time to turn everything in is 1.620000 number of dielectric boundary points 66574 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2 iepsmp to db, and charging done at 1.770000 number of grid points assigned charge 19651 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) : 1.878397 object centre at (A) : -7.220500 -0.6345005 16.41950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.2538512 0.2195575 midg,1,midg; midg,igrid,midg 0.1799769 3.7185762E-02 1,midg,midg; igrid,midg,midg -3.2807026E-02 0.4061257 gauss-seidel spectral radius is 0.9992427 estimated iterations to convergence 287 setup time was (sec) 1.940000 now iterating at: 20:40:36 rms-change max change #iterations 9.589622 393.7981 at 10iterations 5.510307 110.3452 at 20iterations 3.148729 60.03784 at 30iterations 1.799246 33.73967 at 40iterations 1.026711 19.84463 at 50iterations 0.5841134 10.28142 at 60iterations 0.3340366 5.817881 at 70iterations 0.1907843 3.600304 at 80iterations 0.1085369 1.900306 at 90iterations 6.1822835E-02 1.109348 at 100iterations 3.5269137E-02 0.6705170 at 110iterations 2.0071499E-02 0.3542328 at 120iterations 1.1467084E-02 0.2016602 at 130iterations 6.5427548E-03 0.1264696 at 140iterations 3.7140674E-03 6.6314697E-02 at 150iterations 2.1256602E-03 4.2113781E-02 at 160iterations 1.2089330E-03 2.1766663E-02 at 170iterations 6.8969693E-04 1.3141632E-02 at 180iterations finished qdiffx linear iterations at : 20:40:50 total time elapsed so far: 15.45000 # loops : 180 mean,max change (kT/e) : 6.8969693E-04 1.3141632E-02 energy calculations done at 15.45000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.62000 DelPhi exited at 20:40:50 15.620u 0.310s 0:16.22 98.2% 0+0k 0+0io 0pf+0w