Wed Dec 28 11:07:34 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 Wed Dec 28 2011 at 11:07:34 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: 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= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6534148 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): -5.651000 34.30600 ymin,ymax (A): -3.454000 49.28300 zmin,zma (A): -23.69700 30.78600 x,y,z range (A): 39.95700 52.73700 54.48300 scale (grids/A): 0.6534148 object centre (A): 14.32750 22.91450 3.544500 number of atom coordinates read : 1964 total number of charged atoms : 1832 net assigned charge : 2.000005 assigned positive charge : 292.2259 centred at (gu) : 90.68240 92.32056 90.09456 assigned negative charge : -290.2262 centred at (gu) : 90.80504 92.45908 90.01817 start vw surface at 0.1400000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 5682 nv = 96 ne = 84 npr = 40586 no. pairs analyzed = 40586 no. exposed pairs = 2483 no. arc points = 17625 no. surface atoms = 846 nbur = 1118 mkacc time = 0.1400000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 303 mr = 3154 m= 1 mr = 34 m= 0 mr = 0 time to grow re-entrant surface = 0.2000000 no. cavity mid-points inaccessible to solvent = 6 time to turn everything in is 0.3500000 number of dielectric boundary points 2798 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1765 ## 195 charges are in solution ## iepsmp to db, and charging done at 0.5300000 number of grid points assigned charge 6716 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -4.6380224E-09 1.4473895E-08 midg,1,midg; midg,igrid,midg 1.3371158E-08 -2.1099146E-08 1,midg,midg; igrid,midg,midg 1.7143600E-08 -1.2305524E-08 gauss-seidel spectral radius is 0.9878058 estimated iterations to convergence 74 setup time was (sec) 0.7200000 now iterating at: 11:07:35 rms-change max change #iterations 0.1389437 23.43346 at 10iterations 1.4272376E-02 2.320198 at 20iterations 1.4740453E-03 0.2773628 at 30iterations 1.5177109E-04 2.4950027E-02 at 40iterations 1.5719274E-05 2.6118755E-03 at 50iterations finished qdiffx linear iterations at : 11:07:41 total time elapsed so far: 6.290000 # loops : 50 mean,max change (kT/e) : 1.5719274E-05 2.6118755E-03 energy calculations done at 6.290000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 6.510000 DelPhi exited at 11:07:41 6.519u 0.608s 0:07.43 95.6% 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 Wed Dec 28 2011 at 11:07:41 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= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.960244 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): -5.651000 34.30600 ymin,ymax (A): -3.454000 49.28300 zmin,zma (A): -23.69700 30.78600 x,y,z range (A): 39.95700 52.73700 54.48300 scale (grids/A): 1.960244 object centre (A): 14.32750 22.91450 3.544500 number of atom coordinates read : 1964 total number of charged atoms : 1832 net assigned charge : 2.000005 assigned positive charge : 292.2259 centred at (gu) : 92.04720 96.96144 90.28359 assigned negative charge : -290.2262 centred at (gu) : 92.41524 97.37734 90.05461 start vw surface at 0.1500000 fill in re-entrant regions at 0.2900000 boundary points on vw surface= 61079 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17625 grid for indexing accessible points = 1.400000 m= 22070 mr = 41814 m= 3299 mr = 16688 m= 142 mr = 2143 m= 0 mr = 62 time to grow re-entrant surface = 0.3400000 no. cavity mid-points inaccessible to solvent = 2509 time to turn everything in is 0.7200000 number of dielectric boundary points 25883 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 107 iepsmp to db, and charging done at 0.9000000 number of grid points assigned charge 14456 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) : 0.6534148 object centre at (A) : 14.32750 22.91450 3.544500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.8879234E-02 1.3841991E-02 midg,1,midg; midg,igrid,midg 3.5252616E-02 -2.1831559E-02 1,midg,midg; igrid,midg,midg 7.6692672E-03 -6.8991510E-03 gauss-seidel spectral radius is 0.9986336 estimated iterations to convergence 214 setup time was (sec) 1.200000 now iterating at: 11:07:43 rms-change max change #iterations 3.822129 185.0825 at 10iterations 1.794728 70.13831 at 20iterations 0.8411700 33.95794 at 30iterations 0.3929251 13.97406 at 40iterations 0.1835532 6.624000 at 50iterations 8.6020961E-02 2.914619 at 60iterations 4.0049445E-02 1.408388 at 70iterations 1.8806439E-02 0.6063995 at 80iterations 8.7572578E-03 0.2727928 at 90iterations 4.0977444E-03 0.1713028 at 100iterations 1.9276738E-03 6.5475464E-02 at 110iterations 9.0154534E-04 3.5030365E-02 at 120iterations finished qdiffx linear iterations at : 11:07:58 total time elapsed so far: 16.04000 # loops : 120 mean,max change (kT/e) : 9.0154534E-04 3.5030365E-02 energy calculations done at 16.04000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 16.26000 DelPhi exited at 11:07:58 16.268u 0.744s 0:17.29 98.3% 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 Wed Dec 28 2011 at 11:07:59 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= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 2.940367 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): -5.651000 34.30600 ymin,ymax (A): -3.454000 49.28300 zmin,zma (A): -23.69700 30.78600 x,y,z range (A): 39.95700 52.73700 54.48300 scale (grids/A): 2.940367 object centre (A): 14.32750 22.91450 3.544500 number of atom coordinates read : 1964 total number of charged atoms : 1832 net assigned charge : 2.000005 assigned positive charge : 292.2259 centred at (gu) : 93.07079 100.4422 90.42544 assigned negative charge : -290.2262 centred at (gu) : 93.62273 101.0661 90.08186 start vw surface at 0.1400000 fill in re-entrant regions at 0.6100000 boundary points on vw surface= 141309 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17625 grid for indexing accessible points = 1.400000 m= 71285 mr = 101285 m= 25601 mr = 58831 m= 5768 mr = 21189 m= 720 mr = 4493 m= 38 mr = 520 m= 0 mr = 17 time to grow re-entrant surface = 1.040000 no. cavity mid-points inaccessible to solvent = 8444 time to turn everything in is 1.850000 number of dielectric boundary points 58386 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.060000 number of grid points assigned charge 14656 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) : 1.960244 object centre at (A) : 14.32750 22.91450 3.544500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.8689979 2.5842113E-02 midg,1,midg; midg,igrid,midg 0.3415583 -0.2473601 1,midg,midg; igrid,midg,midg 4.7931686E-02 -4.1961212E-02 gauss-seidel spectral radius is 0.9992465 estimated iterations to convergence 288 setup time was (sec) 2.380000 now iterating at: 11:08:02 rms-change max change #iterations 8.907473 386.3242 at 10iterations 5.115421 130.4099 at 20iterations 2.920575 62.17823 at 30iterations 1.667367 30.99939 at 40iterations 0.9528863 18.40530 at 50iterations 0.5436701 11.10679 at 60iterations 0.3089702 6.439606 at 70iterations 0.1766180 3.541126 at 80iterations 0.1004059 2.074664 at 90iterations 5.7215948E-02 1.163012 at 100iterations 3.2684021E-02 0.6373901 at 110iterations 1.8719561E-02 0.3590870 at 120iterations 1.0628888E-02 0.2037230 at 130iterations 6.0574659E-03 0.1224823 at 140iterations 3.4589805E-03 6.8966389E-02 at 150iterations 1.9696278E-03 3.9764881E-02 at 160iterations 1.1232968E-03 2.0809174E-02 at 170iterations 6.4092100E-04 1.3596296E-02 at 180iterations finished qdiffx linear iterations at : 11:08:30 total time elapsed so far: 30.56000 # loops : 180 mean,max change (kT/e) : 6.4092100E-04 1.3596296E-02 energy calculations done at 30.56000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 30.77000 DelPhi exited at 11:08:31 30.777u 0.810s 0:32.10 98.3% 0+0k 0+0io 0pf+0w