Mon Oct 10 00:40:33 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 00:40:33 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 = 2156 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: 0.6944038 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): -9.444000 40.42800 ymin,ymax (A): -54.37400 -11.23500 zmin,zma (A): -28.29200 22.97500 x,y,z range (A): 49.87200 43.13900 51.26700 scale (grids/A): 0.6944038 object centre (A): 15.49200 -32.80450 -2.658500 number of atom coordinates read : 2156 total number of charged atoms : 2014 net assigned charge : 3.000004 assigned positive charge : 319.0787 centred at (gu) : 89.93275 89.78608 88.60684 assigned negative charge : -316.0790 centred at (gu) : 89.98142 89.77805 88.49936 start vw surface at 0.1400000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 7377 nv = 96 ne = 84 npr = 42210 no. pairs analyzed = 42210 no. exposed pairs = 2964 no. arc points = 20613 no. surface atoms = 995 nbur = 1161 mkacc time = 9.9999994E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 490 mr = 3964 m= 2 mr = 107 m= 0 mr = 0 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2700000 number of dielectric boundary points 3798 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1785 ## 136 charges are in solution ## iepsmp to db, and charging done at 0.3800000 number of grid points assigned charge 7993 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -2.8740283E-08 4.4527280E-08 midg,1,midg; midg,igrid,midg 1.6790814E-08 2.1196755E-08 1,midg,midg; igrid,midg,midg 3.7608860E-08 9.2598657E-10 gauss-seidel spectral radius is 0.9892160 estimated iterations to convergence 78 setup time was (sec) 0.4900000 now iterating at: 00:40:34 rms-change max change #iterations 0.1869054 30.05784 at 10iterations 2.1987142E-02 2.994702 at 20iterations 2.6078434E-03 0.3330288 at 30iterations 3.2066469E-04 4.8536301E-02 at 40iterations 4.5471261E-05 6.0901642E-03 at 50iterations finished qdiffx linear iterations at : 00:40:37 total time elapsed so far: 3.080000 # loops : 50 mean,max change (kT/e) : 4.5471261E-05 6.0901642E-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) 3.270000 DelPhi exited at 00:40:37 3.277u 0.164s 0:03.73 91.9% 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 Mon Oct 10 2011 at 00:40:37 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 = 2156 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: 2.083211 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): -9.444000 40.42800 ymin,ymax (A): -54.37400 -11.23500 zmin,zma (A): -28.29200 22.97500 x,y,z range (A): 49.87200 43.13900 51.26700 scale (grids/A): 2.083211 object centre (A): 15.49200 -32.80450 -2.658500 number of atom coordinates read : 2156 total number of charged atoms : 2014 net assigned charge : 3.000004 assigned positive charge : 319.0787 centred at (gu) : 89.79834 89.35810 85.82014 assigned negative charge : -316.0790 centred at (gu) : 89.94441 89.33419 85.49803 start vw surface at 0.1500000 fill in re-entrant regions at 0.2700000 boundary points on vw surface= 77745 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20613 grid for indexing accessible points = 1.400000 m= 29974 mr = 52764 m= 6469 mr = 22190 m= 644 mr = 4600 m= 12 mr = 348 m= 0 mr = 2 time to grow re-entrant surface = 0.2900000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.6000000 number of dielectric boundary points 34940 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 53 iepsmp to db, and charging done at 0.7100000 number of grid points assigned charge 15970 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) : 0.6944038 object centre at (A) : 15.49200 -32.80450 -2.658500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.5698567E-02 6.7564897E-02 midg,1,midg; midg,igrid,midg 9.3932071E-04 9.3940357E-03 1,midg,midg; igrid,midg,midg 2.4224490E-02 -1.4393233E-02 gauss-seidel spectral radius is 0.9988223 estimated iterations to convergence 231 setup time was (sec) 0.8700000 now iterating at: 00:40:38 rms-change max change #iterations 4.568238 187.1375 at 10iterations 2.256612 76.27730 at 20iterations 1.123655 34.96128 at 30iterations 0.5595944 17.60830 at 40iterations 0.2778161 8.696532 at 50iterations 0.1379083 4.251625 at 60iterations 6.7959704E-02 1.983967 at 70iterations 3.3820868E-02 1.075603 at 80iterations 1.6828332E-02 0.5322431 at 90iterations 8.3109429E-03 0.2828026 at 100iterations 4.1411757E-03 0.1228104 at 110iterations 2.0466708E-03 6.0741425E-02 at 120iterations finished qdiffx linear iterations at : 00:40:45 total time elapsed so far: 7.280000 # loops : 120 mean,max change (kT/e) : 2.0466708E-03 6.0741425E-02 energy calculations done at 7.280000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.470000 DelPhi exited at 00:40:45 7.474u 0.163s 0:08.02 95.1% 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 Mon Oct 10 2011 at 00:40:45 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 = 2156 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: 3.124817 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): -9.444000 40.42800 ymin,ymax (A): -54.37400 -11.23500 zmin,zma (A): -28.29200 22.97500 x,y,z range (A): 49.87200 43.13900 51.26700 scale (grids/A): 3.124817 object centre (A): 15.49200 -32.80450 -2.658500 number of atom coordinates read : 2156 total number of charged atoms : 2014 net assigned charge : 3.000004 assigned positive charge : 319.0787 centred at (gu) : 89.69743 89.03711 83.73009 assigned negative charge : -316.0790 centred at (gu) : 89.91660 89.00140 83.24695 start vw surface at 0.1400000 fill in re-entrant regions at 0.8000000 boundary points on vw surface= 179234 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20613 grid for indexing accessible points = 1.400000 m= 92383 mr = 127657 m= 38562 mr = 75056 m= 12700 mr = 31741 m= 2845 mr = 10286 m= 327 mr = 2213 m= 16 mr = 226 m= 0 mr = 6 time to grow re-entrant surface = 0.9300001 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.840000 number of dielectric boundary points 78882 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.970000 number of grid points assigned charge 16112 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) : 2.083211 object centre at (A) : 15.49200 -32.80450 -2.658500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.6444416 0.9848901 midg,1,midg; midg,igrid,midg -3.9441675E-02 6.9305547E-02 1,midg,midg; igrid,midg,midg 0.4283231 -4.1897196E-02 gauss-seidel spectral radius is 0.9993149 estimated iterations to convergence 301 setup time was (sec) 2.140000 now iterating at: 00:40:47 rms-change max change #iterations 10.33986 397.1308 at 10iterations 6.169723 144.8440 at 20iterations 3.677926 77.07941 at 30iterations 2.189636 41.66010 at 40iterations 1.296474 25.01657 at 50iterations 0.7687458 13.96618 at 60iterations 0.4540415 7.697453 at 70iterations 0.2679225 5.008653 at 80iterations 0.1578887 3.288528 at 90iterations 9.3021251E-02 1.671274 at 100iterations 5.4701291E-02 1.014195 at 110iterations 3.2221362E-02 0.5725613 at 120iterations 1.8929785E-02 0.3143525 at 130iterations 1.1140357E-02 0.1797972 at 140iterations 6.5502636E-03 0.1080780 at 150iterations 3.8459499E-03 6.2460899E-02 at 160iterations 2.2636564E-03 4.0573120E-02 at 170iterations 1.3322377E-03 2.2581100E-02 at 180iterations finished qdiffx linear iterations at : 00:40:58 total time elapsed so far: 12.26000 # loops : 180 mean,max change (kT/e) : 1.3322377E-03 2.2581100E-02 energy calculations done at 12.26000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.45000 DelPhi exited at 00:40:58 12.450u 0.155s 0:12.88 97.8% 0+0k 0+0io 0pf+0w