Sat Oct 8 14:29:34 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+sph2.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 = amb2.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 Sat Oct 8 2011 at 14:29:34 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: 319 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3052 !!! WARNING: HIR 110 has a net charge of 0.5140 !!! WARNING: NAP 500 has a net charge of -2.0000 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: 0.6323830 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): -11.85100 43.45100 ymin,ymax (A): -22.32000 22.28700 zmin,zma (A): -8.093000 48.20200 x,y,z range (A): 55.30200 44.60700 56.29500 scale (grids/A): 0.6323830 object centre (A): 15.80000 -1.6500473E-02 20.05450 number of atom coordinates read : 3052 total number of charged atoms : 2905 net assigned charge : 1.014007 assigned positive charge : 459.6776 centred at (gu) : 88.71591 89.56285 91.59902 assigned negative charge : -458.6643 centred at (gu) : 88.70430 89.49267 91.52486 start vw surface at 0.1400000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 7927 nv = 96 ne = 84 npr = 64674 no. pairs analyzed = 64674 no. exposed pairs = 3426 no. arc points = 24041 no. surface atoms = 1169 nbur = 1883 mkacc time = 0.1500000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 446 mr = 4637 m= 1 mr = 52 m= 0 mr = 0 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3200000 number of dielectric boundary points 3685 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2379 ## 241 charges are in solution ## iepsmp to db, and charging done at 0.4500000 number of grid points assigned charge 9955 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -5.0783084E-09 1.3211208E-08 midg,1,midg; midg,igrid,midg -7.4711268E-09 8.0347311E-09 1,midg,midg; igrid,midg,midg -2.9147693E-10 1.8119553E-09 gauss-seidel spectral radius is 0.9870778 estimated iterations to convergence 72 setup time was (sec) 0.5900000 now iterating at: 14:29:35 rms-change max change #iterations 0.1547857 25.80839 at 10iterations 1.5241234E-02 2.093682 at 20iterations 1.5635991E-03 0.2084246 at 30iterations 1.9494204E-04 2.3498535E-02 at 40iterations 3.1986434E-05 4.0664673E-03 at 50iterations finished qdiffx linear iterations at : 14:29:39 total time elapsed so far: 4.020000 # loops : 50 mean,max change (kT/e) : 3.1986434E-05 4.0664673E-03 energy calculations done at 4.020000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.210000 DelPhi exited at 14:29:39 4.209u 0.241s 0:04.75 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 Sat Oct 8 2011 at 14:29:39 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 # of charge parameter records: 319 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3052 !!! WARNING: HIR 110 has a net charge of 0.5140 !!! WARNING: NAP 500 has a net charge of -2.0000 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: 1.897149 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): -11.85100 43.45100 ymin,ymax (A): -22.32000 22.28700 zmin,zma (A): -8.093000 48.20200 x,y,z range (A): 55.30200 44.60700 56.29500 scale (grids/A): 1.897149 object centre (A): 15.80000 -1.6500473E-02 20.05450 number of atom coordinates read : 3052 total number of charged atoms : 2905 net assigned charge : 1.014007 assigned positive charge : 459.6776 centred at (gu) : 86.14741 88.68808 94.79674 assigned negative charge : -458.6643 centred at (gu) : 86.11263 88.47773 94.57420 start vw surface at 0.1500000 fill in re-entrant regions at 0.2700000 boundary points on vw surface= 86910 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24041 grid for indexing accessible points = 1.400000 m= 31373 mr = 62688 m= 4700 mr = 23577 m= 290 mr = 2865 m= 2 mr = 77 m= 0 mr = 0 time to grow re-entrant surface = 0.3100000 no. cavity mid-points inaccessible to solvent = 394 time to turn everything in is 0.6300000 number of dielectric boundary points 34068 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 161 iepsmp to db, and charging done at 0.7600000 number of grid points assigned charge 22865 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) : 0.6323830 object centre at (A) : 15.80000 -1.6500473E-02 20.05450 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.7028492E-02 2.7396213E-02 midg,1,midg; midg,igrid,midg 6.6371770E-03 1.7215528E-02 1,midg,midg; igrid,midg,midg -4.8880808E-02 3.9367932E-03 gauss-seidel spectral radius is 0.9986582 estimated iterations to convergence 216 setup time was (sec) 0.9500000 now iterating at: 14:29:40 rms-change max change #iterations 4.656785 204.9067 at 10iterations 2.203710 69.46866 at 20iterations 1.040496 30.04720 at 30iterations 0.4902029 14.64919 at 40iterations 0.2320598 7.186377 at 50iterations 0.1097800 3.154185 at 60iterations 5.1798224E-02 1.535370 at 70iterations 2.4395615E-02 0.7536182 at 80iterations 1.1582352E-02 0.3254862 at 90iterations 5.4822112E-03 0.1654053 at 100iterations 2.6127945E-03 7.7026367E-02 at 110iterations 1.2322509E-03 3.3920288E-02 at 120iterations finished qdiffx linear iterations at : 14:29:49 total time elapsed so far: 9.460000 # loops : 120 mean,max change (kT/e) : 1.2322509E-03 3.3920288E-02 energy calculations done at 9.460000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.640000 DelPhi exited at 14:29:49 9.646u 0.277s 0:10.26 96.5% 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 Sat Oct 8 2011 at 14:29:50 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: 319 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3052 !!! WARNING: HIR 110 has a net charge of 0.5140 !!! WARNING: NAP 500 has a net charge of -2.0000 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: 2.845724 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): -11.85100 43.45100 ymin,ymax (A): -22.32000 22.28700 zmin,zma (A): -8.093000 48.20200 x,y,z range (A): 55.30200 44.60700 56.29500 scale (grids/A): 2.845724 object centre (A): 15.80000 -1.6500473E-02 20.05450 number of atom coordinates read : 3052 total number of charged atoms : 2905 net assigned charge : 1.014007 assigned positive charge : 459.6776 centred at (gu) : 84.22099 88.03184 97.19497 assigned negative charge : -458.6643 centred at (gu) : 84.16900 87.71651 96.86120 start vw surface at 0.1600000 fill in re-entrant regions at 0.5800000 boundary points on vw surface= 201465 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24041 grid for indexing accessible points = 1.400000 m= 102583 mr = 151679 m= 36226 mr = 85257 m= 8381 mr = 29219 m= 1179 mr = 6127 m= 62 mr = 764 m= 0 mr = 17 time to grow re-entrant surface = 0.9899999 no. cavity mid-points inaccessible to solvent = 1296 time to turn everything in is 1.710000 number of dielectric boundary points 76833 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.880000 number of grid points assigned charge 23239 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) : 1.897149 object centre at (A) : 15.80000 -1.6500473E-02 20.05450 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -8.0295332E-02 0.5222720 midg,1,midg; midg,igrid,midg 7.3970333E-02 0.1999395 1,midg,midg; igrid,midg,midg -0.8307903 0.1070349 gauss-seidel spectral radius is 0.9992680 estimated iterations to convergence 292 setup time was (sec) 2.090000 now iterating at: 14:29:52 rms-change max change #iterations 10.88626 381.3107 at 10iterations 6.381706 145.4831 at 20iterations 3.719630 68.12705 at 30iterations 2.162110 40.44454 at 40iterations 1.254298 25.38552 at 50iterations 0.7260491 13.15526 at 60iterations 0.4205639 7.317314 at 70iterations 0.2433540 4.649083 at 80iterations 0.1405341 2.315456 at 90iterations 8.1190497E-02 1.373182 at 100iterations 4.7024567E-02 0.8123560 at 110iterations 2.7106032E-02 0.4627314 at 120iterations 1.5659045E-02 0.2864532 at 130iterations 9.0646651E-03 0.1681528 at 140iterations 5.2389330E-03 9.1186523E-02 at 150iterations 3.0389950E-03 5.0247192E-02 at 160iterations 1.7658127E-03 2.8795242E-02 at 170iterations 1.0349093E-03 1.7086029E-02 at 180iterations finished qdiffx linear iterations at : 14:30:06 total time elapsed so far: 16.56000 # loops : 180 mean,max change (kT/e) : 1.0349093E-03 1.7086029E-02 energy calculations done at 16.56000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 16.75000 DelPhi exited at 14:30:07 16.754u 0.322s 0:17.41 98.0% 0+0k 0+0io 0pf+0w