Mon Oct 10 09:20:56 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 Mon Oct 10 2011 at 09:20:56 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: 300 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2745 !!! WARNING: HIT 229 has a net charge of 0.5140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 0.5800313 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): -18.31600 34.37200 ymin,ymax (A): -61.08100 -0.6420001 zmin,zma (A): -0.6259999 60.75000 x,y,z range (A): 52.68800 60.43900 61.37600 scale (grids/A): 0.5800313 object centre (A): 8.027999 -30.86150 30.06200 number of atom coordinates read : 2745 total number of charged atoms : 2598 net assigned charge : 8.014017 assigned positive charge : 401.5191 centred at (gu) : 88.31060 88.28064 88.13865 assigned negative charge : -393.5055 centred at (gu) : 88.31358 88.12576 88.05980 start vw surface at 0.1800000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 6410 nv = 96 ne = 84 npr = 51584 no. pairs analyzed = 51584 no. exposed pairs = 4305 no. arc points = 32071 no. surface atoms = 1415 nbur = 1330 mkacc time = 0.1200000 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 = 1.512000 m= 336 mr = 2735 m= 0 mr = 19 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3300000 number of dielectric boundary points 3992 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3073 ## 314 charges are in solution ## iepsmp to db, and charging done at 0.4600000 number of grid points assigned charge 7908 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 3.9665624E-10 2.1722000E-09 midg,1,midg; midg,igrid,midg -1.8928981E-09 3.1937042E-09 1,midg,midg; igrid,midg,midg 2.7759111E-09 1.2097221E-09 gauss-seidel spectral radius is 0.9846665 estimated iterations to convergence 66 setup time was (sec) 0.6000000 now iterating at: 09:20:56 rms-change max change #iterations 9.5294409E-02 14.88155 at 10iterations 7.3094307E-03 1.205776 at 20iterations 5.6718505E-04 9.3105316E-02 at 30iterations 5.3065603E-05 8.6784363E-03 at 40iterations 7.5707940E-06 1.0185242E-03 at 50iterations finished qdiffx linear iterations at : 09:20:59 total time elapsed so far: 3.480000 # loops : 50 mean,max change (kT/e) : 7.5707940E-06 1.0185242E-03 energy calculations done at 3.480000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.680000 DelPhi exited at 09:21:00 3.683u 0.202s 0:04.22 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 09:21:00 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: 300 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2745 !!! WARNING: HIT 229 has a net charge of 0.5140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 1.740094 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): -18.31600 34.37200 ymin,ymax (A): -61.08100 -0.6420001 zmin,zma (A): -0.6259999 60.75000 x,y,z range (A): 52.68800 60.43900 61.37600 scale (grids/A): 1.740094 object centre (A): 8.027999 -30.86150 30.06200 number of atom coordinates read : 2745 total number of charged atoms : 2598 net assigned charge : 8.014017 assigned positive charge : 401.5191 centred at (gu) : 84.93129 84.84174 84.41547 assigned negative charge : -393.5055 centred at (gu) : 84.94049 84.37678 84.17941 start vw surface at 0.1600000 fill in re-entrant regions at 0.2600000 boundary points on vw surface= 68319 reading accessible surface arcs data from file ARCDAT no. of arc points read = 32071 grid for indexing accessible points = 1.400000 m= 21770 mr = 40618 m= 2943 mr = 13866 m= 106 mr = 1421 m= 0 mr = 20 time to grow re-entrant surface = 0.2400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5500000 number of dielectric boundary points 37213 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 248 iepsmp to db, and charging done at 0.6800000 number of grid points assigned charge 20214 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) : 0.5800313 object centre at (A) : 8.027999 -30.86150 30.06200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.1806002E-02 7.3966729E-03 midg,1,midg; midg,igrid,midg 1.5863776E-02 2.9127572E-02 1,midg,midg; igrid,midg,midg 1.2073826E-02 1.0132366E-02 gauss-seidel spectral radius is 0.9984167 estimated iterations to convergence 199 setup time was (sec) 0.8600000 now iterating at: 09:21:01 rms-change max change #iterations 3.590962 156.8843 at 10iterations 1.581181 66.86730 at 20iterations 0.6942480 29.74920 at 30iterations 0.3062751 11.82092 at 40iterations 0.1344490 5.909780 at 50iterations 5.9374511E-02 2.044086 at 60iterations 2.6154483E-02 0.9457626 at 70iterations 1.1563020E-02 0.4077644 at 80iterations 5.0905524E-03 0.1933804 at 90iterations 2.2400061E-03 7.9853058E-02 at 100iterations 9.8495884E-04 3.7456512E-02 at 110iterations 4.3525887E-04 1.5681267E-02 at 120iterations finished qdiffx linear iterations at : 09:21:08 total time elapsed so far: 8.070000 # loops : 120 mean,max change (kT/e) : 4.3525887E-04 1.5681267E-02 energy calculations done at 8.070000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.270000 DelPhi exited at 09:21:09 8.268u 0.233s 0:08.82 96.2% 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 09:21:09 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: 300 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2745 !!! WARNING: HIT 229 has a net charge of 0.5140 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: 2.610141 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): -18.31600 34.37200 ymin,ymax (A): -61.08100 -0.6420001 zmin,zma (A): -0.6259999 60.75000 x,y,z range (A): 52.68800 60.43900 61.37600 scale (grids/A): 2.610141 object centre (A): 8.027999 -30.86150 30.06200 number of atom coordinates read : 2745 total number of charged atoms : 2598 net assigned charge : 8.014017 assigned positive charge : 401.5191 centred at (gu) : 82.39681 82.26254 81.62306 assigned negative charge : -393.5055 centred at (gu) : 82.41074 81.56521 81.26907 start vw surface at 0.1500000 fill in re-entrant regions at 0.4300000 boundary points on vw surface= 157404 reading accessible surface arcs data from file ARCDAT no. of arc points read = 32071 grid for indexing accessible points = 1.400000 m= 70553 mr = 100225 m= 23422 mr = 52228 m= 4722 mr = 17081 m= 525 mr = 2949 m= 12 mr = 282 m= 0 mr = 3 time to grow re-entrant surface = 0.7499999 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.320000 number of dielectric boundary points 83870 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 9 iepsmp to db, and charging done at 1.470000 number of grid points assigned charge 20772 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) : 1.740094 object centre at (A) : 8.027999 -30.86150 30.06200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.4922346 -2.8766203E-03 midg,1,midg; midg,igrid,midg 0.4232768 0.3621229 1,midg,midg; igrid,midg,midg 6.8770632E-02 0.1497616 gauss-seidel spectral radius is 0.9992274 estimated iterations to convergence 284 setup time was (sec) 1.650000 now iterating at: 09:21:11 rms-change max change #iterations 9.299087 293.6611 at 10iterations 5.519669 131.7928 at 20iterations 3.244800 90.16983 at 30iterations 1.885869 48.43919 at 40iterations 1.089331 25.98370 at 50iterations 0.6268265 20.19202 at 60iterations 0.3602577 9.123034 at 70iterations 0.2063377 6.086738 at 80iterations 0.1177714 3.356509 at 90iterations 6.7216165E-02 1.626070 at 100iterations 3.8340416E-02 1.022219 at 110iterations 2.1823904E-02 0.4769287 at 120iterations 1.2430068E-02 0.3035283 at 130iterations 7.0474818E-03 0.1625748 at 140iterations 4.0135989E-03 0.1022835 at 150iterations 2.2807368E-03 4.9995422E-02 at 160iterations 1.2901324E-03 2.6156425E-02 at 170iterations 7.3308172E-04 1.6894817E-02 at 180iterations finished qdiffx linear iterations at : 09:21:22 total time elapsed so far: 13.30000 # loops : 180 mean,max change (kT/e) : 7.3308172E-04 1.6894817E-02 energy calculations done at 13.30000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.49000 DelPhi exited at 09:21:23 13.492u 0.259s 0:14.07 97.6% 0+0k 0+0io 0pf+0w