Tue Nov 22 14:12:35 PST 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 Tue Nov 22 2011 at 14:12:41 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: 259 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1964 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6054113 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): 1.731000 44.49200 ymin,ymax (A): -24.29800 24.43900 zmin,zma (A): -29.16900 29.63400 x,y,z range (A): 42.76100 48.73700 58.80300 scale (grids/A): 0.6054113 object centre (A): 23.11150 7.0499420E-02 0.2325001 number of atom coordinates read : 1964 total number of charged atoms : 1832 net assigned charge : 3.000004 assigned positive charge : 290.6260 centred at (gu) : 90.19792 89.94307 89.86597 assigned negative charge : -287.6263 centred at (gu) : 90.37570 89.94651 89.85168 start vw surface at 0.1100000 fill in re-entrant regions at 0.1100000 boundary points on vw surface= 4901 nv = 96 ne = 84 npr = 39881 no. pairs analyzed = 39881 no. exposed pairs = 2439 no. arc points = 17222 no. surface atoms = 822 nbur = 1142 mkacc time = 9.0000004E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 235 mr = 2709 m= 3 mr = 26 m= 0 mr = 0 time to grow re-entrant surface = 9.9999994E-02 no. cavity mid-points inaccessible to solvent = 20 time to turn everything in is 0.2100000 number of dielectric boundary points 2404 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1754 ## 177 charges are in solution ## iepsmp to db, and charging done at 0.3200000 number of grid points assigned charge 5913 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.1245010E-09 1.9476374E-09 midg,1,midg; midg,igrid,midg 1.6809247E-09 1.4225431E-09 1,midg,midg; igrid,midg,midg 6.8046515E-09 -4.4496300E-09 gauss-seidel spectral radius is 0.9858239 estimated iterations to convergence 69 setup time was (sec) 0.4300000 now iterating at: 14:12:45 rms-change max change #iterations 9.9405959E-02 17.55290 at 10iterations 8.3735939E-03 1.799339 at 20iterations 7.2244648E-04 0.1235695 at 30iterations 6.4203967E-05 1.1009693E-02 at 40iterations 5.5439455E-06 9.2124939E-04 at 50iterations finished qdiffx linear iterations at : 14:12:53 total time elapsed so far: 2.970000 # loops : 50 mean,max change (kT/e) : 5.5439455E-06 9.2124939E-04 energy calculations done at 2.970000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.140000 DelPhi exited at 14:12:54 3.145u 0.164s 0:13.70 24.0% 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 Tue Nov 22 2011 at 14:12:57 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: 259 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1964 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.816234 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): 1.731000 44.49200 ymin,ymax (A): -24.29800 24.43900 zmin,zma (A): -29.16900 29.63400 x,y,z range (A): 42.76100 48.73700 58.80300 scale (grids/A): 1.816234 object centre (A): 23.11150 7.0499420E-02 0.2325001 number of atom coordinates read : 1964 total number of charged atoms : 1832 net assigned charge : 3.000004 assigned positive charge : 290.6260 centred at (gu) : 90.59381 89.82914 89.59754 assigned negative charge : -287.6263 centred at (gu) : 91.12727 89.83968 89.55537 start vw surface at 0.1000000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 52920 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17222 grid for indexing accessible points = 1.400000 m= 19093 mr = 36483 m= 2489 mr = 14480 m= 85 mr = 1462 m= 2 mr = 18 m= 0 mr = 0 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 522 time to turn everything in is 0.3600000 number of dielectric boundary points 22146 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 156 iepsmp to db, and charging done at 0.4700000 number of grid points assigned charge 14296 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) : 0.6054113 object centre at (A) : 23.11150 7.0499420E-02 0.2325001 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.0042943E-02 2.3838533E-02 midg,1,midg; midg,igrid,midg -7.2143658E-04 -1.5849182E-03 1,midg,midg; igrid,midg,midg 9.3265548E-03 -1.3646456E-02 gauss-seidel spectral radius is 0.9984254 estimated iterations to convergence 200 setup time was (sec) 0.6200000 now iterating at: 14:13:02 rms-change max change #iterations 3.279680 143.3866 at 10iterations 1.448826 59.28591 at 20iterations 0.6435752 25.11807 at 30iterations 0.2844995 12.22881 at 40iterations 0.1260358 4.766583 at 50iterations 5.5695944E-02 2.349192 at 60iterations 2.4643274E-02 0.9527740 at 70iterations 1.0875540E-02 0.4072495 at 80iterations 4.8282789E-03 0.1824036 at 90iterations 2.1315978E-03 7.5982094E-02 at 100iterations 9.4431324E-04 3.4017086E-02 at 110iterations 4.1896448E-04 1.5953064E-02 at 120iterations finished qdiffx linear iterations at : 14:13:20 total time elapsed so far: 6.630000 # loops : 120 mean,max change (kT/e) : 4.1896448E-04 1.5953064E-02 energy calculations done at 6.630000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 6.810000 DelPhi exited at 14:13:25 6.808u 0.211s 0:28.48 24.6% 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 Tue Nov 22 2011 at 14:13:26 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: 259 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1964 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.724351 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): 1.731000 44.49200 ymin,ymax (A): -24.29800 24.43900 zmin,zma (A): -29.16900 29.63400 x,y,z range (A): 42.76100 48.73700 58.80300 scale (grids/A): 2.724351 object centre (A): 23.11150 7.0499420E-02 0.2325001 number of atom coordinates read : 1964 total number of charged atoms : 1832 net assigned charge : 3.000004 assigned positive charge : 290.6260 centred at (gu) : 90.89069 89.74366 89.39637 assigned negative charge : -287.6263 centred at (gu) : 91.69091 89.75965 89.33298 start vw surface at 0.1100000 fill in re-entrant regions at 0.3100000 boundary points on vw surface= 122095 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17222 grid for indexing accessible points = 1.400000 m= 62293 mr = 87945 m= 21917 mr = 51896 m= 4200 mr = 17917 m= 327 mr = 3078 m= 10 mr = 163 m= 0 mr = 0 time to grow re-entrant surface = 0.5100000 no. cavity mid-points inaccessible to solvent = 1671 time to turn everything in is 0.9100000 number of dielectric boundary points 49843 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.030000 number of grid points assigned charge 14648 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) : 1.816234 object centre at (A) : 23.11150 7.0499420E-02 0.2325001 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1108372 0.1113089 midg,1,midg; midg,igrid,midg -4.8051152E-02 -5.1249038E-02 1,midg,midg; igrid,midg,midg 6.7342117E-02 -0.1802667 gauss-seidel spectral radius is 0.9991815 estimated iterations to convergence 276 setup time was (sec) 1.180000 now iterating at: 14:13:36 rms-change max change #iterations 7.844317 243.5797 at 10iterations 4.412301 139.2408 at 20iterations 2.465804 57.34208 at 30iterations 1.373966 37.10556 at 40iterations 0.7676407 16.57911 at 50iterations 0.4261093 9.531748 at 60iterations 0.2369722 5.105083 at 70iterations 0.1315906 2.937283 at 80iterations 7.3411755E-02 1.535091 at 90iterations 4.0876869E-02 0.8070869 at 100iterations 2.2716435E-02 0.4975023 at 110iterations 1.2677189E-02 0.2602921 at 120iterations 7.0385383E-03 0.1547089 at 130iterations 3.9158626E-03 8.6455345E-02 at 140iterations 2.1796788E-03 5.0193787E-02 at 150iterations 1.2146290E-03 2.7113914E-02 at 160iterations 6.7481410E-04 1.4947772E-02 at 170iterations 3.7647513E-04 9.8922849E-03 at 180iterations finished qdiffx linear iterations at : 14:14:06 total time elapsed so far: 10.54000 # loops : 180 mean,max change (kT/e) : 3.7647513E-04 9.8922849E-03 energy calculations done at 10.54000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.72000 DelPhi exited at 14:14:11 10.727u 0.194s 0:45.22 24.1% 0+0k 0+0io 0pf+0w