Sun Oct 9 06:52:03 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 Sun Oct 9 2011 at 06:52:03 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: 284 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2002 !!! WARNING: ASP 186 has a net charge of -2.0000 !!! WARNING: NDP 188 has a net charge of -3.0000 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: 0.6696135 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): -40.85700 3.197000 ymin,ymax (A): -32.56600 12.60400 zmin,zma (A): -23.47200 29.69300 x,y,z range (A): 44.05400 45.17000 53.16500 scale (grids/A): 0.6696135 object centre (A): -18.83000 -9.980999 3.110499 number of atom coordinates read : 2002 total number of charged atoms : 1863 net assigned charge : -1.499990 assigned positive charge : 299.5480 centred at (gu) : 89.43742 88.78522 88.56579 assigned negative charge : -301.0481 centred at (gu) : 89.24884 88.59859 88.53686 start vw surface at 9.0000004E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 5912 nv = 96 ne = 84 npr = 42334 no. pairs analyzed = 42334 no. exposed pairs = 2505 no. arc points = 17608 no. surface atoms = 842 nbur = 1160 mkacc time = 7.0000000E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 351 mr = 3209 m= 0 mr = 47 time to grow re-entrant surface = 8.0000006E-02 no. cavity mid-points inaccessible to solvent = 18 time to turn everything in is 0.1800000 number of dielectric boundary points 3007 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1698 ## 151 charges are in solution ## iepsmp to db, and charging done at 0.2400000 number of grid points assigned charge 7026 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.2973637E-08 1.1293341E-09 midg,1,midg; midg,igrid,midg -5.3013004E-08 2.4514724E-08 1,midg,midg; igrid,midg,midg -4.6645990E-08 2.8417592E-08 gauss-seidel spectral radius is 0.9883822 estimated iterations to convergence 76 setup time was (sec) 0.3700000 now iterating at: 06:52:03 rms-change max change #iterations 0.1556790 27.15196 at 10iterations 1.7232709E-02 2.717514 at 20iterations 1.8309038E-03 0.2904205 at 30iterations 2.0316699E-04 3.2455325E-02 at 40iterations 2.2044294E-05 2.9830933E-03 at 50iterations finished qdiffx linear iterations at : 06:52:06 total time elapsed so far: 3.270000 # loops : 50 mean,max change (kT/e) : 2.2044294E-05 2.9830933E-03 energy calculations done at 3.270000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.420000 DelPhi exited at 06:52:07 3.421u 0.382s 0:04.08 93.1% 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 06:52:07 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: 284 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2002 !!! WARNING: ASP 186 has a net charge of -2.0000 !!! WARNING: NDP 188 has a net charge of -3.0000 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: 2.008840 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): -40.85700 3.197000 ymin,ymax (A): -32.56600 12.60400 zmin,zma (A): -23.47200 29.69300 x,y,z range (A): 44.05400 45.17000 53.16500 scale (grids/A): 2.008840 object centre (A): -18.83000 -9.980999 3.110499 number of atom coordinates read : 2002 total number of charged atoms : 1863 net assigned charge : -1.499990 assigned positive charge : 299.5480 centred at (gu) : 88.31232 86.35581 85.69757 assigned negative charge : -301.0481 centred at (gu) : 87.74648 85.79579 85.61040 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 64222 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17608 grid for indexing accessible points = 1.400000 m= 22644 mr = 44195 m= 3764 mr = 16497 m= 266 mr = 2370 m= 6 mr = 109 m= 0 mr = 0 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 583 time to turn everything in is 0.3400000 number of dielectric boundary points 27731 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 99 iepsmp to db, and charging done at 0.4100000 number of grid points assigned charge 14743 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) : 0.6696135 object centre at (A) : -18.83000 -9.980999 3.110499 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -4.0679004E-02 2.8592279E-02 midg,1,midg; midg,igrid,midg -3.1629514E-02 1.1993594E-02 1,midg,midg; igrid,midg,midg -3.5995238E-02 2.4283212E-02 gauss-seidel spectral radius is 0.9987040 estimated iterations to convergence 220 setup time was (sec) 0.5500000 now iterating at: 06:52:08 rms-change max change #iterations 4.124463 224.0927 at 10iterations 1.963101 68.66849 at 20iterations 0.9363174 31.41753 at 30iterations 0.4455159 14.50969 at 40iterations 0.2129401 7.180882 at 50iterations 0.1016756 3.443261 at 60iterations 4.8557624E-02 1.696462 at 70iterations 2.3111859E-02 0.7876968 at 80iterations 1.1029607E-02 0.3615627 at 90iterations 5.2550104E-03 0.1754761 at 100iterations 2.5138955E-03 8.3160400E-02 at 110iterations 1.1999272E-03 3.9834976E-02 at 120iterations finished qdiffx linear iterations at : 06:52:16 total time elapsed so far: 7.660000 # loops : 120 mean,max change (kT/e) : 1.1999272E-03 3.9834976E-02 energy calculations done at 7.660000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.800000 DelPhi exited at 06:52:16 7.801u 1.026s 0:09.09 97.0% 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 Sun Oct 9 2011 at 06:52:16 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: 284 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2002 !!! WARNING: ASP 186 has a net charge of -2.0000 !!! WARNING: NDP 188 has a net charge of -3.0000 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: 3.013261 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): -40.85700 3.197000 ymin,ymax (A): -32.56600 12.60400 zmin,zma (A): -23.47200 29.69300 x,y,z range (A): 44.05400 45.17000 53.16500 scale (grids/A): 3.013261 object centre (A): -18.83000 -9.980999 3.110499 number of atom coordinates read : 2002 total number of charged atoms : 1863 net assigned charge : -1.499990 assigned positive charge : 299.5480 centred at (gu) : 87.46844 84.53363 83.54626 assigned negative charge : -301.0481 centred at (gu) : 86.61974 83.69373 83.41560 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.3100000 boundary points on vw surface= 148489 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17608 grid for indexing accessible points = 1.400000 m= 73684 mr = 107114 m= 25939 mr = 59994 m= 6833 mr = 20678 m= 1151 mr = 5200 m= 79 mr = 744 m= 2 mr = 35 m= 0 mr = 0 time to grow re-entrant surface = 0.4800000 no. cavity mid-points inaccessible to solvent = 1885 time to turn everything in is 0.8800000 number of dielectric boundary points 62412 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 0.9800000 number of grid points assigned charge 14900 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) : 2.008840 object centre at (A) : -18.83000 -9.980999 3.110499 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.4781068 0.8443607 midg,1,midg; midg,igrid,midg -0.2276476 0.1348357 1,midg,midg; igrid,midg,midg -0.3336577 0.1984693 gauss-seidel spectral radius is 0.9992603 estimated iterations to convergence 290 setup time was (sec) 1.120000 now iterating at: 06:52:18 rms-change max change #iterations 9.414467 447.2068 at 10iterations 5.394221 130.3452 at 20iterations 3.108549 64.49807 at 30iterations 1.787912 35.31941 at 40iterations 1.024573 20.05495 at 50iterations 0.5888882 12.51109 at 60iterations 0.3374672 6.323265 at 70iterations 0.1932079 3.689335 at 80iterations 0.1111308 2.094055 at 90iterations 6.3955493E-02 1.241159 at 100iterations 3.6568213E-02 0.7904778 at 110iterations 2.0935386E-02 0.4177017 at 120iterations 1.2030923E-02 0.2116637 at 130iterations 6.8778694E-03 0.1303434 at 140iterations 3.9605396E-03 7.3600769E-02 at 150iterations 2.2727579E-03 4.7666430E-02 at 160iterations 1.3037885E-03 2.7498245E-02 at 170iterations 7.4801873E-04 1.4600754E-02 at 180iterations finished qdiffx linear iterations at : 06:52:30 total time elapsed so far: 13.42000 # loops : 180 mean,max change (kT/e) : 7.4801873E-04 1.4600754E-02 energy calculations done at 13.42000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.58000 DelPhi exited at 06:52:30 13.584u 0.256s 0:14.24 97.1% 0+0k 0+0io 0pf+0w