Sun Oct 9 19:44:03 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 19:44:03 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: 267 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5425 !!! WARNING: LLP 1 has a net charge of 1.7400 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1300000 grid size : 179 scale,in grids/A, set to be: 0.5221396 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): 3.069000 67.20700 ymin,ymax (A): -9.254000 53.09600 zmin,zma (A): -1.850000 66.33100 x,y,z range (A): 64.13800 62.35000 68.18100 scale (grids/A): 0.5221396 object centre (A): 35.13800 21.92100 32.24050 number of atom coordinates read : 5425 total number of charged atoms : 5247 net assigned charge : 4.740028 assigned positive charge : 828.8291 centred at (gu) : 88.17505 89.36907 88.76015 assigned negative charge : -824.0952 centred at (gu) : 88.09488 89.38062 88.66882 start vw surface at 0.2200000 fill in re-entrant regions at 0.2300000 boundary points on vw surface= 9181 nv = 96 ne = 84 npr = 113140 no. pairs analyzed = 113140 no. exposed pairs = 6013 no. arc points = 41711 no. surface atoms = 2061 nbur = 3364 mkacc time = 0.2400000 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 = 1.652000 m= 356 mr = 5191 m= 1 mr = 16 m= 0 mr = 0 time to grow re-entrant surface = 0.2600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5000000 number of dielectric boundary points 4331 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4183 ## 575 charges are in solution ## iepsmp to db, and charging done at 0.6100000 number of grid points assigned charge 12480 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -4.4699899E-10 4.0601045E-10 midg,1,midg; midg,igrid,midg 2.1157455E-10 5.9109932E-11 1,midg,midg; igrid,midg,midg -4.3477991E-10 3.1698325E-10 gauss-seidel spectral radius is 0.9812703 estimated iterations to convergence 60 setup time was (sec) 0.7200000 now iterating at: 19:44:03 rms-change max change #iterations 8.8371672E-02 14.75132 at 10iterations 1.0080891E-02 1.673161 at 20iterations 3.6793507E-03 0.6607475 at 30iterations 1.5752716E-03 0.2783928 at 40iterations 6.8462512E-04 0.1174698 at 50iterations finished qdiffx linear iterations at : 19:44:06 total time elapsed so far: 3.130000 # loops : 50 mean,max change (kT/e) : 6.8462512E-04 0.1174698 energy calculations done at 3.130000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.300000 DelPhi exited at 19:44:06 3.306u 0.133s 0:03.73 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 Sun Oct 9 2011 at 19:44:06 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: 267 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5425 !!! WARNING: LLP 1 has a net charge of 1.7400 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1300000 grid size : 179 scale,in grids/A, set to be: 1.566419 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): 3.069000 67.20700 ymin,ymax (A): -9.254000 53.09600 zmin,zma (A): -1.850000 66.33100 x,y,z range (A): 64.13800 62.35000 68.18100 scale (grids/A): 1.566419 object centre (A): 35.13800 21.92100 32.24050 number of atom coordinates read : 5425 total number of charged atoms : 5247 net assigned charge : 4.740028 assigned positive charge : 828.8291 centred at (gu) : 84.52321 88.10588 86.27904 assigned negative charge : -824.0952 centred at (gu) : 84.28429 88.14152 86.00623 start vw surface at 0.2000000 fill in re-entrant regions at 0.3200000 boundary points on vw surface= 105438 reading accessible surface arcs data from file ARCDAT no. of arc points read = 41711 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.540000 m= 31720 mr = 76386 m= 2947 mr = 22016 m= 61 mr = 1330 m= 0 mr = 6 time to grow re-entrant surface = 0.3100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.6800000 number of dielectric boundary points 40428 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 520 ## 4 charges are in solution ## iepsmp to db, and charging done at 0.8000000 number of grid points assigned charge 39566 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) : 0.5221396 object centre at (A) : 35.13800 21.92100 32.24050 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.9283390E-02 2.4477832E-02 midg,1,midg; midg,igrid,midg 1.7405109E-02 7.2482359E-03 1,midg,midg; igrid,midg,midg -1.3246462E-02 -9.1155368E-04 gauss-seidel spectral radius is 0.9982379 estimated iterations to convergence 189 setup time was (sec) 0.9500000 now iterating at: 19:44:07 rms-change max change #iterations 4.341034 161.7396 at 10iterations 1.837614 55.20656 at 20iterations 0.7759647 22.61389 at 30iterations 0.3299963 11.12744 at 40iterations 0.1405509 4.131737 at 50iterations 6.0916021E-02 1.922199 at 60iterations 2.7094694E-02 0.8850212 at 70iterations 1.3015664E-02 0.4215622 at 80iterations 7.1316133E-03 0.2382965 at 90iterations 4.4421600E-03 0.1622925 at 100iterations 3.0232286E-03 0.1050110 at 110iterations 2.1482699E-03 7.2608948E-02 at 120iterations finished qdiffx linear iterations at : 19:44:14 total time elapsed so far: 6.970000 # loops : 120 mean,max change (kT/e) : 2.1482699E-03 7.2608948E-02 energy calculations done at 6.970000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.150000 DelPhi exited at 19:44:14 7.156u 0.154s 0:07.63 95.6% 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 19:44:14 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: 267 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5425 !!! WARNING: LLP 1 has a net charge of 1.7400 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: 2.349628 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): 3.069000 67.20700 ymin,ymax (A): -9.254000 53.09600 zmin,zma (A): -1.850000 66.33100 x,y,z range (A): 64.13800 62.35000 68.18100 scale (grids/A): 2.349628 object centre (A): 35.13800 21.92100 32.24050 number of atom coordinates read : 5425 total number of charged atoms : 5247 net assigned charge : 4.740028 assigned positive charge : 828.8291 centred at (gu) : 81.78453 87.15836 84.41815 assigned negative charge : -824.0952 centred at (gu) : 81.42651 87.21234 84.00933 start vw surface at 0.2000000 fill in re-entrant regions at 0.5500000 boundary points on vw surface= 246271 reading accessible surface arcs data from file ARCDAT no. of arc points read = 41711 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.540000 m= 112990 mr = 186688 m= 30288 mr = 90728 m= 4303 mr = 22455 m= 261 mr = 2738 m= 3 mr = 111 m= 0 mr = 0 time to grow re-entrant surface = 0.9900000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.660000 number of dielectric boundary points 91396 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 52 iepsmp to db, and charging done at 1.790000 number of grid points assigned charge 41861 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) : 1.566419 object centre at (A) : 35.13800 21.92100 32.24050 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.4555883 0.7061763 midg,1,midg; midg,igrid,midg 0.3070707 5.2441660E-02 1,midg,midg; igrid,midg,midg -0.3341333 -7.3533109E-03 gauss-seidel spectral radius is 0.9991976 estimated iterations to convergence 279 setup time was (sec) 1.950000 now iterating at: 19:44:16 rms-change max change #iterations 11.34449 271.6788 at 10iterations 6.519109 145.2278 at 20iterations 3.729009 79.64262 at 30iterations 2.118102 41.49082 at 40iterations 1.202807 24.87336 at 50iterations 0.6809541 11.36666 at 60iterations 0.3849420 6.835930 at 70iterations 0.2180050 3.856407 at 80iterations 0.1230088 2.133993 at 90iterations 6.9822967E-02 1.175560 at 100iterations 3.9814673E-02 0.8119965 at 110iterations 2.2908850E-02 0.4397469 at 120iterations 1.3581767E-02 0.2639999 at 130iterations 8.3330395E-03 0.1767349 at 140iterations 5.4013222E-03 0.1134644 at 150iterations 3.7353558E-03 7.8125000E-02 at 160iterations 2.7508023E-03 5.6686401E-02 at 170iterations 2.1195065E-03 4.4853210E-02 at 180iterations finished qdiffx linear iterations at : 19:44:26 total time elapsed so far: 11.49000 # loops : 180 mean,max change (kT/e) : 2.1195065E-03 4.4853210E-02 energy calculations done at 11.49000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.66000 DelPhi exited at 19:44:26 11.662u 0.177s 0:12.11 97.6% 0+0k 0+0io 0pf+0w