Sun Oct 9 07:15:34 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 Sun Oct 9 2011 at 07:15:34 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: 260 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2497 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: 0.5469854 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): -5.020000 41.34400 ymin,ymax (A): 37.25500 89.41100 zmin,zma (A): -3.171000 61.91300 x,y,z range (A): 46.36400 52.15599 65.08400 scale (grids/A): 0.5469854 object centre (A): 18.16200 63.33300 29.37100 number of atom coordinates read : 2497 total number of charged atoms : 2351 net assigned charge : -9.499980 assigned positive charge : 375.4769 centred at (gu) : 90.93556 88.31422 89.39330 assigned negative charge : -384.9774 centred at (gu) : 91.10824 87.92659 89.33389 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 4846 nv = 96 ne = 84 npr = 50056 no. pairs analyzed = 50056 no. exposed pairs = 3511 no. arc points = 24810 no. surface atoms = 1183 nbur = 1314 mkacc time = 0.1100000 writing accessible surface arcs data to file ARCDAT initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.568000 m= 185 mr = 2253 m= 0 mr = 7 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2900000 number of dielectric boundary points 2771 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2446 ## 296 charges are in solution ## iepsmp to db, and charging done at 0.3900000 number of grid points assigned charge 6303 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.0490183E-09 -1.7528098E-10 midg,1,midg; midg,igrid,midg -4.5342268E-09 1.0724852E-09 1,midg,midg; igrid,midg,midg 3.5327874E-10 -2.0139319E-09 gauss-seidel spectral radius is 0.9827359 estimated iterations to convergence 63 setup time was (sec) 0.5100000 now iterating at: 07:15:35 rms-change max change #iterations 6.6999167E-02 15.69118 at 10iterations 4.3043289E-03 0.6736450 at 20iterations 2.9576416E-04 6.4668655E-02 at 30iterations 1.9034151E-05 3.9234161E-03 at 40iterations 1.3203880E-06 3.2758713E-04 at 50iterations finished qdiffx linear iterations at : 07:15:38 total time elapsed so far: 3.130000 # loops : 50 mean,max change (kT/e) : 1.3203880E-06 3.2758713E-04 energy calculations done at 3.130000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.300000 DelPhi exited at 07:15:38 3.301u 0.202s 0:03.78 92.5% 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 Sun Oct 9 2011 at 07:15:38 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: 260 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2497 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: 1.640956 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): -5.020000 41.34400 ymin,ymax (A): 37.25500 89.41100 zmin,zma (A): -3.171000 61.91300 x,y,z range (A): 46.36400 52.15599 65.08400 scale (grids/A): 1.640956 object centre (A): 18.16200 63.33300 29.37100 number of atom coordinates read : 2497 total number of charged atoms : 2351 net assigned charge : -9.499980 assigned positive charge : 375.4769 centred at (gu) : 92.80614 84.94215 88.17908 assigned negative charge : -384.9774 centred at (gu) : 93.32449 83.77956 88.00124 start vw surface at 0.1600000 fill in re-entrant regions at 0.2300000 boundary points on vw surface= 53139 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24810 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 14881 mr = 33472 m= 1358 mr = 9420 m= 28 mr = 564 m= 0 mr = 0 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 166 time to turn everything in is 0.4200000 number of dielectric boundary points 25950 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 258 ## 3 charges are in solution ## iepsmp to db, and charging done at 0.5300000 number of grid points assigned charge 17990 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) : 0.5469854 object centre at (A) : 18.16200 63.33300 29.37100 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -3.1344626E-02 8.4115388E-03 midg,1,midg; midg,igrid,midg -3.1512234E-02 5.0048740E-03 1,midg,midg; igrid,midg,midg -3.7577106E-03 -1.5192945E-02 gauss-seidel spectral radius is 0.9981477 estimated iterations to convergence 185 setup time was (sec) 0.7000000 now iterating at: 07:15:39 rms-change max change #iterations 3.044878 157.0110 at 10iterations 1.256765 52.61369 at 20iterations 0.5157262 25.08159 at 30iterations 0.2120545 8.529321 at 40iterations 8.7802663E-02 4.165533 at 50iterations 3.6147960E-02 1.664192 at 60iterations 1.4972842E-02 0.5682459 at 70iterations 6.1394712E-03 0.2536211 at 80iterations 2.5356309E-03 0.1107635 at 90iterations 1.0444144E-03 4.0038109E-02 at 100iterations 4.3219703E-04 1.7482758E-02 at 110iterations 1.7818234E-04 7.2021484E-03 at 120iterations finished qdiffx linear iterations at : 07:15:45 total time elapsed so far: 7.100000 # loops : 120 mean,max change (kT/e) : 1.7818234E-04 7.2021484E-03 energy calculations done at 7.100000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.280000 DelPhi exited at 07:15:46 7.280u 0.227s 0:07.80 96.1% 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 Sun Oct 9 2011 at 07:15:46 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: 260 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2497 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: 2.461434 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): -5.020000 41.34400 ymin,ymax (A): 37.25500 89.41100 zmin,zma (A): -3.171000 61.91300 x,y,z range (A): 46.36400 52.15599 65.08400 scale (grids/A): 2.461434 object centre (A): 18.16200 63.33300 29.37100 number of atom coordinates read : 2497 total number of charged atoms : 2351 net assigned charge : -9.499980 assigned positive charge : 375.4769 centred at (gu) : 94.20909 82.41308 87.26850 assigned negative charge : -384.9774 centred at (gu) : 94.98673 80.66927 87.00173 start vw surface at 0.1200000 fill in re-entrant regions at 0.3300000 boundary points on vw surface= 123351 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24810 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 51970 mr = 82375 m= 13395 mr = 39163 m= 1984 mr = 9493 m= 128 mr = 1196 m= 1 mr = 46 m= 0 mr = 0 time to grow re-entrant surface = 0.4900000 no. cavity mid-points inaccessible to solvent = 563 time to turn everything in is 0.9200000 number of dielectric boundary points 58556 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 19 iepsmp to db, and charging done at 1.050000 number of grid points assigned charge 18786 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) : 1.640956 object centre at (A) : 18.16200 63.33300 29.37100 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.8294981 8.5073791E-02 midg,1,midg; midg,igrid,midg -0.4479762 8.0292091E-02 1,midg,midg; igrid,midg,midg -5.5958431E-02 -0.1931271 gauss-seidel spectral radius is 0.9991155 estimated iterations to convergence 266 setup time was (sec) 1.230000 now iterating at: 07:15:47 rms-change max change #iterations 8.060769 307.7871 at 10iterations 4.463369 129.0091 at 20iterations 2.471010 73.03895 at 30iterations 1.363406 38.43927 at 40iterations 0.7504208 17.56992 at 50iterations 0.4112603 10.40339 at 60iterations 0.2252784 5.514760 at 70iterations 0.1233337 2.743001 at 80iterations 6.7227520E-02 1.508869 at 90iterations 3.6736213E-02 0.9052734 at 100iterations 2.0089721E-02 0.5068593 at 110iterations 1.0919336E-02 0.2574892 at 120iterations 5.9472155E-03 0.1471519 at 130iterations 3.2402782E-03 8.1317186E-02 at 140iterations 1.7653307E-03 3.8808823E-02 at 150iterations 9.5969252E-04 2.1888733E-02 at 160iterations 5.2468455E-04 1.2702942E-02 at 170iterations 2.8528750E-04 6.5097809E-03 at 180iterations finished qdiffx linear iterations at : 07:15:58 total time elapsed so far: 11.65000 # loops : 180 mean,max change (kT/e) : 2.8528750E-04 6.5097809E-03 energy calculations done at 11.65000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.82000 DelPhi exited at 07:15:58 11.824u 0.250s 0:12.35 97.7% 0+0k 0+0io 0pf+0w