Tue Oct 11 07:37:35 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 Tue Oct 11 2011 at 07:37:35 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: 258 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3304 !!! WARNING: UMP 1125 has a net charge of -0.1000 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: 0.6034614 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): 1.431000 52.53800 ymin,ymax (A): 0.8570000 59.85000 zmin,zma (A): -22.35700 35.72700 x,y,z range (A): 51.10700 58.99300 58.08400 scale (grids/A): 0.6034614 object centre (A): 26.98450 30.35350 6.684999 number of atom coordinates read : 3304 total number of charged atoms : 3162 net assigned charge : 6.900036 assigned positive charge : 499.6456 centred at (gu) : 90.18298 90.57380 89.24559 assigned negative charge : -492.7471 centred at (gu) : 90.20747 90.52905 89.12985 start vw surface at 0.1400000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 8188 nv = 96 ne = 84 npr = 66280 no. pairs analyzed = 66280 no. exposed pairs = 4043 no. arc points = 28105 no. surface atoms = 1361 nbur = 1943 mkacc time = 0.1800000 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 = 1.456000 m= 425 mr = 4605 m= 2 mr = 43 m= 0 mr = 0 time to grow re-entrant surface = 0.2300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3800000 number of dielectric boundary points 3967 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2896 ## 314 charges are in solution ## iepsmp to db, and charging done at 0.5200000 number of grid points assigned charge 10102 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -3.2449878E-09 7.7911739E-09 midg,1,midg; midg,igrid,midg 9.2235825E-10 6.4144197E-09 1,midg,midg; igrid,midg,midg 4.4220489E-09 2.1645166E-09 gauss-seidel spectral radius is 0.9858485 estimated iterations to convergence 69 setup time was (sec) 0.6800000 now iterating at: 07:37:36 rms-change max change #iterations 0.1270735 23.81281 at 10iterations 1.1400632E-02 1.450277 at 20iterations 1.6430792E-03 0.2413559 at 30iterations 4.8800337E-04 7.7086449E-02 at 40iterations 1.7709909E-04 2.8118134E-02 at 50iterations finished qdiffx linear iterations at : 07:37:39 total time elapsed so far: 4.390000 # loops : 50 mean,max change (kT/e) : 1.7709909E-04 2.8118134E-02 energy calculations done at 4.390000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.560000 DelPhi exited at 07:37:40 4.567u 0.392s 0:05.27 93.9% 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 Tue Oct 11 2011 at 07:37:40 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: 258 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3304 !!! WARNING: UMP 1125 has a net charge of -0.1000 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: 1.810384 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): 1.431000 52.53800 ymin,ymax (A): 0.8570000 59.85000 zmin,zma (A): -22.35700 35.72700 x,y,z range (A): 51.10700 58.99300 58.08400 scale (grids/A): 1.810384 object centre (A): 26.98450 30.35350 6.684999 number of atom coordinates read : 3304 total number of charged atoms : 3162 net assigned charge : 6.900036 assigned positive charge : 499.6456 centred at (gu) : 90.54759 91.72041 87.73618 assigned negative charge : -492.7471 centred at (gu) : 90.62193 91.58694 87.38921 start vw surface at 0.1300000 fill in re-entrant regions at 0.2700000 boundary points on vw surface= 89460 reading accessible surface arcs data from file ARCDAT no. of arc points read = 28105 grid for indexing accessible points = 1.400000 m= 33729 mr = 63280 m= 5065 mr = 25327 m= 211 mr = 3169 m= 0 mr = 42 time to grow re-entrant surface = 0.3900000 no. cavity mid-points inaccessible to solvent = 362 time to turn everything in is 0.7200000 number of dielectric boundary points 36647 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 235 iepsmp to db, and charging done at 0.8400000 number of grid points assigned charge 24711 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) : 0.6034614 object centre at (A) : 26.98450 30.35350 6.684999 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -3.5131063E-02 1.7431846E-02 midg,1,midg; midg,igrid,midg 1.8441578E-02 5.5992655E-03 1,midg,midg; igrid,midg,midg 2.8176486E-02 1.2280701E-02 gauss-seidel spectral radius is 0.9985722 estimated iterations to convergence 210 setup time was (sec) 1.030000 now iterating at: 07:37:41 rms-change max change #iterations 4.431438 200.3969 at 10iterations 2.036743 63.09009 at 20iterations 0.9418321 30.23550 at 30iterations 0.4353302 13.15087 at 40iterations 0.2005791 6.311394 at 50iterations 9.2912659E-02 3.030552 at 60iterations 4.3097723E-02 1.335247 at 70iterations 2.0089643E-02 0.6192527 at 80iterations 9.4377119E-03 0.2747202 at 90iterations 4.5330417E-03 0.1503410 at 100iterations 2.2801338E-03 7.9053879E-02 at 110iterations 1.2341135E-03 4.7203064E-02 at 120iterations finished qdiffx linear iterations at : 07:37:51 total time elapsed so far: 11.09000 # loops : 120 mean,max change (kT/e) : 1.2341135E-03 4.7203064E-02 energy calculations done at 11.09000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.25000 DelPhi exited at 07:37:52 11.257u 0.472s 0:12.29 95.3% 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 Tue Oct 11 2011 at 07:37:52 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: 258 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3304 !!! WARNING: UMP 1125 has a net charge of -0.1000 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: 2.715576 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): 1.431000 52.53800 ymin,ymax (A): 0.8570000 59.85000 zmin,zma (A): -22.35700 35.72700 x,y,z range (A): 51.10700 58.99300 58.08400 scale (grids/A): 2.715576 object centre (A): 26.98450 30.35350 6.684999 number of atom coordinates read : 3304 total number of charged atoms : 3162 net assigned charge : 6.900036 assigned positive charge : 499.6456 centred at (gu) : 90.82119 92.58046 86.60400 assigned negative charge : -492.7471 centred at (gu) : 90.93279 92.38027 86.08385 start vw surface at 0.1400000 fill in re-entrant regions at 0.5700000 boundary points on vw surface= 206705 reading accessible surface arcs data from file ARCDAT no. of arc points read = 28105 grid for indexing accessible points = 1.400000 m= 108641 mr = 152965 m= 39629 mr = 89880 m= 8874 mr = 32326 m= 928 mr = 6608 m= 35 mr = 528 m= 0 mr = 0 time to grow re-entrant surface = 1.200000 no. cavity mid-points inaccessible to solvent = 1203 time to turn everything in is 1.910000 number of dielectric boundary points 82505 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 2.050000 number of grid points assigned charge 25288 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) : 1.810384 object centre at (A) : 26.98450 30.35350 6.684999 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.5388929 0.2125929 midg,1,midg; midg,igrid,midg 0.1121033 -8.3403580E-02 1,midg,midg; igrid,midg,midg 0.3681342 0.1401562 gauss-seidel spectral radius is 0.9992563 estimated iterations to convergence 289 setup time was (sec) 2.240000 now iterating at: 07:37:55 rms-change max change #iterations 10.63483 272.2120 at 10iterations 6.247780 121.7505 at 20iterations 3.632977 70.28625 at 30iterations 2.112571 37.39993 at 40iterations 1.219913 21.99257 at 50iterations 0.7041042 13.68668 at 60iterations 0.4057951 7.309353 at 70iterations 0.2337914 3.992731 at 80iterations 0.1347734 2.313553 at 90iterations 7.7271067E-02 1.333281 at 100iterations 4.4398624E-02 0.7776880 at 110iterations 2.5550302E-02 0.4400940 at 120iterations 1.4704277E-02 0.2532921 at 130iterations 8.4863575E-03 0.1478345 at 140iterations 4.9080956E-03 9.4276428E-02 at 150iterations 2.8674938E-03 5.0786972E-02 at 160iterations 1.7021677E-03 2.9521942E-02 at 170iterations 1.0376049E-03 2.0084381E-02 at 180iterations finished qdiffx linear iterations at : 07:38:11 total time elapsed so far: 18.73000 # loops : 180 mean,max change (kT/e) : 1.0376049E-03 2.0084381E-02 energy calculations done at 18.73000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 18.89000 DelPhi exited at 07:38:12 18.898u 0.495s 0:20.00 96.9% 0+0k 0+0io 0pf+0w