Wed Feb 15 08:56:26 PST 2012 #!/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_thinner.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 Wed Feb 15 2012 at 08:56:26 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 ! Automatically converted by prot2crg.py # of charge parameter records: 327 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3809 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1100000 grid size : 179 scale,in grids/A, set to be: 0.5360477 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): -27.48200 38.93000 ymin,ymax (A): 1.444000 55.11700 zmin,zma (A): -33.48600 25.52900 x,y,z range (A): 66.41200 53.67300 59.01500 scale (grids/A): 0.5360477 object centre (A): 5.724000 28.28050 -3.978500 number of atom coordinates read : 3809 total number of charged atoms : 3661 net assigned charge : 1.8358231E-05 assigned positive charge : 566.5783 centred at (gu) : 89.84369 89.33633 91.45123 assigned negative charge : -566.5803 centred at (gu) : 89.79984 89.35248 91.54531 start vw surface at 0.1900000 fill in re-entrant regions at 0.2000000 boundary points on vw surface= 7008 nv = 96 ne = 84 npr = 79603 no. pairs analyzed = 79603 no. exposed pairs = 4838 no. arc points = 34002 no. surface atoms = 1623 nbur = 2186 mkacc time = 0.1900000 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= 294 mr = 3598 m= 0 mr = 8 time to grow re-entrant surface = 0.2200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4200000 number of dielectric boundary points 3696 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3349 ## 373 charges are in solution ## iepsmp to db, and charging done at 0.5500000 number of grid points assigned charge 9290 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 3.7824696E-10 -7.8865237E-10 midg,1,midg; midg,igrid,midg 1.2106771E-10 -7.1479107E-11 1,midg,midg; igrid,midg,midg -2.5625999E-10 2.5090760E-10 gauss-seidel spectral radius is 0.9821296 estimated iterations to convergence 62 setup time was (sec) 0.6900000 now iterating at: 08:56:27 rms-change max change #iterations 7.6389484E-02 10.69844 at 10iterations 4.8735412E-03 0.7595696 at 20iterations 3.4962586E-04 5.7132721E-02 at 30iterations 4.3206335E-05 1.1163712E-02 at 40iterations 9.1164447E-06 2.5291443E-03 at 50iterations finished qdiffx linear iterations at : 08:56:30 total time elapsed so far: 3.590000 # loops : 50 mean,max change (kT/e) : 9.1164447E-06 2.5291443E-03 energy calculations done at 3.590000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.780000 DelPhi exited at 08:56:30 3.784u 0.181s 0:04.72 83.8% 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 Wed Feb 15 2012 at 08:56:31 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 ! Automatically converted by prot2crg.py # of charge parameter records: 327 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3809 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1200000 grid size : 179 scale,in grids/A, set to be: 1.608143 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): -27.48200 38.93000 ymin,ymax (A): 1.444000 55.11700 zmin,zma (A): -33.48600 25.52900 x,y,z range (A): 66.41200 53.67300 59.01500 scale (grids/A): 1.608143 object centre (A): 5.724000 28.28050 -3.978500 number of atom coordinates read : 3809 total number of charged atoms : 3661 net assigned charge : 1.8358231E-05 assigned positive charge : 566.5783 centred at (gu) : 89.53004 88.00789 94.35278 assigned negative charge : -566.5803 centred at (gu) : 89.39914 88.05678 94.63512 start vw surface at 0.2000000 fill in re-entrant regions at 0.3100000 boundary points on vw surface= 78288 reading accessible surface arcs data from file ARCDAT no. of arc points read = 34002 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 24100 mr = 53112 m= 2511 mr = 16451 m= 47 mr = 1240 m= 0 mr = 0 time to grow re-entrant surface = 0.2700000 no. cavity mid-points inaccessible to solvent = 721 time to turn everything in is 0.6200000 number of dielectric boundary points 34143 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 341 ## 4 charges are in solution ## iepsmp to db, and charging done at 0.7400000 number of grid points assigned charge 27943 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) : 0.5360477 object centre at (A) : 5.724000 28.28050 -3.978500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 7.2494731E-03 -1.5696414E-02 midg,1,midg; midg,igrid,midg 1.0706603E-02 4.5817192E-03 1,midg,midg; igrid,midg,midg 4.8446457E-04 -7.6816767E-03 gauss-seidel spectral radius is 0.9982221 estimated iterations to convergence 188 setup time was (sec) 0.9000000 now iterating at: 08:56:32 rms-change max change #iterations 3.716558 220.6071 at 10iterations 1.560204 52.59796 at 20iterations 0.6544831 21.60243 at 30iterations 0.2759544 9.473895 at 40iterations 0.1158266 4.275078 at 50iterations 4.8770294E-02 1.720039 at 60iterations 2.0624338E-02 0.7010193 at 70iterations 8.6788228E-03 0.3088360 at 80iterations 3.6597510E-03 0.1236668 at 90iterations 1.5402359E-03 5.3711891E-02 at 100iterations 6.5160106E-04 2.2256136E-02 at 110iterations 2.7512206E-04 9.0360641E-03 at 120iterations finished qdiffx linear iterations at : 08:56:38 total time elapsed so far: 7.410000 # loops : 120 mean,max change (kT/e) : 2.7512206E-04 9.0360641E-03 energy calculations done at 7.410000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.630000 DelPhi exited at 08:56:39 7.634u 0.188s 0:08.36 93.4% 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 Wed Feb 15 2012 at 08:56:39 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 ! Automatically converted by prot2crg.py # of charge parameter records: 327 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3809 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1000000 grid size : 179 scale,in grids/A, set to be: 2.412215 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): -27.48200 38.93000 ymin,ymax (A): 1.444000 55.11700 zmin,zma (A): -33.48600 25.52900 x,y,z range (A): 66.41200 53.67300 59.01500 scale (grids/A): 2.412215 object centre (A): 5.724000 28.28050 -3.978500 number of atom coordinates read : 3809 total number of charged atoms : 3661 net assigned charge : 1.8358231E-05 assigned positive charge : 566.5783 centred at (gu) : 89.29481 87.01134 96.52877 assigned negative charge : -566.5803 centred at (gu) : 89.09878 87.08507 96.95235 start vw surface at 0.1800000 fill in re-entrant regions at 0.4800000 boundary points on vw surface= 182393 reading accessible surface arcs data from file ARCDAT no. of arc points read = 34002 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 83116 mr = 130462 m= 23805 mr = 65248 m= 3875 mr = 17922 m= 229 mr = 2531 m= 1 mr = 107 m= 0 mr = 0 time to grow re-entrant surface = 0.8000000 no. cavity mid-points inaccessible to solvent = 2733 time to turn everything in is 1.420000 number of dielectric boundary points 77149 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 27 iepsmp to db, and charging done at 1.560000 number of grid points assigned charge 29247 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) : 1.608143 object centre at (A) : 5.724000 28.28050 -3.978500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1440035 -0.2247494 midg,1,midg; midg,igrid,midg 0.1755486 9.2198201E-02 1,midg,midg; igrid,midg,midg 0.1515838 -6.5453127E-02 gauss-seidel spectral radius is 0.9991741 estimated iterations to convergence 275 setup time was (sec) 1.730000 now iterating at: 08:56:41 rms-change max change #iterations 9.640936 382.1837 at 10iterations 5.477063 139.0168 at 20iterations 3.085472 63.24947 at 30iterations 1.735170 33.39225 at 40iterations 0.9738446 23.05786 at 50iterations 0.5465240 10.83344 at 60iterations 0.3053728 7.009356 at 70iterations 0.1708766 3.346686 at 80iterations 9.5141910E-02 1.825506 at 90iterations 5.3034160E-02 1.134825 at 100iterations 2.9550975E-02 0.5486791 at 110iterations 1.6443726E-02 0.2945633 at 120iterations 9.1762654E-03 0.1686554 at 130iterations 5.1058321E-03 9.8344803E-02 at 140iterations 2.8387054E-03 5.4645061E-02 at 150iterations 1.5815860E-03 3.1731606E-02 at 160iterations 8.7951659E-04 1.6412497E-02 at 170iterations 4.8976252E-04 9.5767975E-03 at 180iterations finished qdiffx linear iterations at : 08:56:53 total time elapsed so far: 13.82000 # loops : 180 mean,max change (kT/e) : 4.8976252E-04 9.5767975E-03 energy calculations done at 13.82000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 14.02000 DelPhi exited at 08:56:54 14.024u 0.224s 0:14.69 96.9% 0+0k 0+0io 0pf+0w