Mon Oct 10 00:03:58 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 Mon Oct 10 2011 at 00:03:58 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3062 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: 0.6337790 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): -19.51700 34.61800 ymin,ymax (A): -38.00000 13.12300 zmin,zma (A): -14.03300 42.13800 x,y,z range (A): 54.13500 51.12300 56.17100 scale (grids/A): 0.6337790 object centre (A): 7.550500 -12.43850 14.05250 number of atom coordinates read : 3062 total number of charged atoms : 2946 net assigned charge : 2.500006 assigned positive charge : 465.1340 centred at (gu) : 89.06561 89.58565 91.51871 assigned negative charge : -462.6353 centred at (gu) : 89.08664 89.67968 91.48379 start vw surface at 0.1600000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 8428 nv = 96 ne = 84 npr = 59607 no. pairs analyzed = 59607 no. exposed pairs = 4112 no. arc points = 29135 no. surface atoms = 1372 nbur = 1690 mkacc time = 0.1200000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 428 mr = 4472 m= 2 mr = 27 m= 0 mr = 0 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 24 time to turn everything in is 0.3200000 number of dielectric boundary points 4359 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2797 ## 267 charges are in solution ## iepsmp to db, and charging done at 0.4200000 number of grid points assigned charge 10055 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -8.2855744E-10 9.6668318E-09 midg,1,midg; midg,igrid,midg 1.5059943E-08 -7.4831048E-09 1,midg,midg; igrid,midg,midg 6.5237220E-09 3.7394177E-10 gauss-seidel spectral radius is 0.9871523 estimated iterations to convergence 72 setup time was (sec) 0.5300000 now iterating at: 00:03:59 rms-change max change #iterations 0.1465308 18.74544 at 10iterations 1.4400152E-02 1.877554 at 20iterations 1.3896957E-03 0.1794586 at 30iterations 1.3622000E-04 1.7371178E-02 at 40iterations 1.3640491E-05 1.7013550E-03 at 50iterations finished qdiffx linear iterations at : 00:04:01 total time elapsed so far: 2.910000 # loops : 50 mean,max change (kT/e) : 1.3640491E-05 1.7013550E-03 energy calculations done at 2.910000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.080000 DelPhi exited at 00:04:02 3.080u 0.148s 0:03.54 90.9% 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 00:04:02 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3062 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: 1.901337 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): -19.51700 34.61800 ymin,ymax (A): -38.00000 13.12300 zmin,zma (A): -14.03300 42.13800 x,y,z range (A): 54.13500 51.12300 56.17100 scale (grids/A): 1.901337 object centre (A): 7.550500 -12.43850 14.05250 number of atom coordinates read : 3062 total number of charged atoms : 2946 net assigned charge : 2.500006 assigned positive charge : 465.1340 centred at (gu) : 87.19617 88.75619 94.55520 assigned negative charge : -462.6353 centred at (gu) : 87.25950 89.03875 94.45092 start vw surface at 0.1500000 fill in re-entrant regions at 0.2700000 boundary points on vw surface= 90517 reading accessible surface arcs data from file ARCDAT no. of arc points read = 29135 grid for indexing accessible points = 1.400000 m= 30974 mr = 61444 m= 4285 mr = 22035 m= 222 mr = 2435 m= 1 mr = 60 m= 0 mr = 0 time to grow re-entrant surface = 0.2800000 no. cavity mid-points inaccessible to solvent = 2171 time to turn everything in is 0.5900000 number of dielectric boundary points 40025 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 191 iepsmp to db, and charging done at 0.7100000 number of grid points assigned charge 23134 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) : 0.6337790 object centre at (A) : 7.550500 -12.43850 14.05250 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.3150293E-02 6.8565400E-04 midg,1,midg; midg,igrid,midg 2.4158657E-02 -4.0398641E-05 1,midg,midg; igrid,midg,midg 2.9960675E-03 -1.3674370E-02 gauss-seidel spectral radius is 0.9986889 estimated iterations to convergence 219 setup time was (sec) 0.8600000 now iterating at: 00:04:03 rms-change max change #iterations 4.669114 176.5738 at 10iterations 2.211645 67.86641 at 20iterations 1.050107 37.36058 at 30iterations 0.4982027 15.57416 at 40iterations 0.2366310 7.210958 at 50iterations 0.1127722 3.798749 at 60iterations 5.3404111E-02 1.525153 at 70iterations 2.5280353E-02 0.8092213 at 80iterations 1.2032904E-02 0.3860626 at 90iterations 5.7090009E-03 0.1777768 at 100iterations 2.7159983E-03 8.2864761E-02 at 110iterations 1.2940218E-03 4.0748596E-02 at 120iterations finished qdiffx linear iterations at : 00:04:09 total time elapsed so far: 6.880000 # loops : 120 mean,max change (kT/e) : 1.2940218E-03 4.0748596E-02 energy calculations done at 6.880000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.050000 DelPhi exited at 00:04:09 7.050u 0.162s 0:07.59 94.9% 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 00:04:09 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3062 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: 2.852006 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): -19.51700 34.61800 ymin,ymax (A): -38.00000 13.12300 zmin,zma (A): -14.03300 42.13800 x,y,z range (A): 54.13500 51.12300 56.17100 scale (grids/A): 2.852006 object centre (A): 7.550500 -12.43850 14.05250 number of atom coordinates read : 3062 total number of charged atoms : 2946 net assigned charge : 2.500006 assigned positive charge : 465.1340 centred at (gu) : 85.79420 88.13402 96.83240 assigned negative charge : -462.6353 centred at (gu) : 85.88911 88.55817 96.67628 start vw surface at 0.1600000 fill in re-entrant regions at 0.5100000 boundary points on vw surface= 209502 reading accessible surface arcs data from file ARCDAT no. of arc points read = 29135 grid for indexing accessible points = 1.400000 m= 101651 mr = 149551 m= 34496 mr = 81841 m= 7515 mr = 26708 m= 856 mr = 5206 m= 48 mr = 566 m= 1 mr = 3 m= 0 mr = 0 time to grow re-entrant surface = 0.8900000 no. cavity mid-points inaccessible to solvent = 7471 time to turn everything in is 1.510000 number of dielectric boundary points 90194 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.640000 number of grid points assigned charge 23560 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) : 1.901337 object centre at (A) : 7.550500 -12.43850 14.05250 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1716337 -9.0469494E-02 midg,1,midg; midg,igrid,midg 8.4229223E-02 4.8533238E-02 1,midg,midg; igrid,midg,midg -6.4972393E-02 -0.2866895 gauss-seidel spectral radius is 0.9992990 estimated iterations to convergence 298 setup time was (sec) 1.790000 now iterating at: 00:04:11 rms-change max change #iterations 11.12891 334.2117 at 10iterations 6.724345 142.8720 at 20iterations 4.015668 108.0065 at 30iterations 2.386958 49.53174 at 40iterations 1.414695 25.09790 at 50iterations 0.8327535 15.07710 at 60iterations 0.4903382 9.154572 at 70iterations 0.2879717 5.024851 at 80iterations 0.1691064 2.744524 at 90iterations 9.8935261E-02 1.659065 at 100iterations 5.7865608E-02 0.9527804 at 110iterations 3.3866782E-02 0.5646648 at 120iterations 1.9797653E-02 0.3409083 at 130iterations 1.1554830E-02 0.2041740 at 140iterations 6.7546307E-03 0.1175461 at 150iterations 3.9410326E-03 6.0161591E-02 at 160iterations 2.3024525E-03 3.7077904E-02 at 170iterations 1.3428587E-03 2.2633553E-02 at 180iterations finished qdiffx linear iterations at : 00:04:21 total time elapsed so far: 11.45000 # loops : 180 mean,max change (kT/e) : 1.3428587E-03 2.2633553E-02 energy calculations done at 11.45000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.63000 DelPhi exited at 00:04:22 11.633u 0.172s 0:12.16 97.0% 0+0k 0+0io 0pf+0w