Tue Oct 11 01:45:54 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 01:45:54 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 = 2667 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: 0.5916570 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): 17.92500 78.09500 ymin,ymax (A): -11.47600 44.47300 zmin,zma (A): -7.648000 35.28300 x,y,z range (A): 60.17000 55.94900 42.93100 scale (grids/A): 0.5916570 object centre (A): 48.01000 16.49850 13.81750 number of atom coordinates read : 2667 total number of charged atoms : 2524 net assigned charge : 6.500021 assigned positive charge : 402.6736 centred at (gu) : 88.26382 89.81841 89.75089 assigned negative charge : -396.1744 centred at (gu) : 88.52882 89.96451 89.90295 start vw surface at 0.1700000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 6096 nv = 96 ne = 84 npr = 54228 no. pairs analyzed = 54228 no. exposed pairs = 3215 no. arc points = 22691 no. surface atoms = 1090 nbur = 1577 mkacc time = 0.1500000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 278 mr = 3364 m= 1 mr = 29 m= 0 mr = 0 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 29 time to turn everything in is 0.3600000 number of dielectric boundary points 2982 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2235 ## 245 charges are in solution ## iepsmp to db, and charging done at 0.4800000 number of grid points assigned charge 7664 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 6.5985191E-09 -2.3250830E-09 midg,1,midg; midg,igrid,midg 6.3245822E-09 -2.1944164E-09 1,midg,midg; igrid,midg,midg 1.3966523E-08 -3.8890393E-09 gauss-seidel spectral radius is 0.9852206 estimated iterations to convergence 67 setup time was (sec) 0.6300000 now iterating at: 01:45:55 rms-change max change #iterations 0.1042116 15.77333 at 10iterations 9.2255836E-03 1.589607 at 20iterations 1.0320893E-03 0.2146759 at 30iterations 1.9952175E-04 4.6772003E-02 at 40iterations 4.2588923E-05 1.0623932E-02 at 50iterations finished qdiffx linear iterations at : 01:45:58 total time elapsed so far: 3.970000 # loops : 50 mean,max change (kT/e) : 4.2588923E-05 1.0623932E-02 energy calculations done at 3.970000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.160000 DelPhi exited at 01:45:59 4.165u 0.247s 0:04.92 89.4% 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 Tue Oct 11 2011 at 01:45:59 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 = 2667 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: 1.774971 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): 17.92500 78.09500 ymin,ymax (A): -11.47600 44.47300 zmin,zma (A): -7.648000 35.28300 x,y,z range (A): 60.17000 55.94900 42.93100 scale (grids/A): 1.774971 object centre (A): 48.01000 16.49850 13.81750 number of atom coordinates read : 2667 total number of charged atoms : 2524 net assigned charge : 6.500021 assigned positive charge : 402.6736 centred at (gu) : 84.79071 89.45461 89.25219 assigned negative charge : -396.1744 centred at (gu) : 85.58625 89.89339 89.70866 start vw surface at 0.1700000 fill in re-entrant regions at 0.2900000 boundary points on vw surface= 66449 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22691 grid for indexing accessible points = 1.400000 m= 21830 mr = 46128 m= 2869 mr = 15905 m= 126 mr = 1770 m= 0 mr = 29 time to grow re-entrant surface = 0.2800000 no. cavity mid-points inaccessible to solvent = 3252 time to turn everything in is 0.6000000 number of dielectric boundary points 27442 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 201 iepsmp to db, and charging done at 0.7300000 number of grid points assigned charge 19640 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) : 0.5916570 object centre at (A) : 48.01000 16.49850 13.81750 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.2071486E-02 1.1770276E-03 midg,1,midg; midg,igrid,midg 2.6069161E-02 -2.1481622E-02 1,midg,midg; igrid,midg,midg 5.5706236E-03 -4.2786412E-03 gauss-seidel spectral radius is 0.9984335 estimated iterations to convergence 200 setup time was (sec) 0.8900000 now iterating at: 01:46:00 rms-change max change #iterations 3.709655 155.4999 at 10iterations 1.649963 68.08614 at 20iterations 0.7308152 29.57753 at 30iterations 0.3225893 12.46093 at 40iterations 0.1433312 4.862822 at 50iterations 6.3802861E-02 2.275640 at 60iterations 2.8460123E-02 1.006445 at 70iterations 1.2716870E-02 0.4416580 at 80iterations 5.7538692E-03 0.2050495 at 90iterations 2.6551746E-03 9.8335266E-02 at 100iterations 1.2742708E-03 4.7288895E-02 at 110iterations 6.4032758E-04 2.9197693E-02 at 120iterations finished qdiffx linear iterations at : 01:46:08 total time elapsed so far: 9.250000 # loops : 120 mean,max change (kT/e) : 6.4032758E-04 2.9197693E-02 energy calculations done at 9.250000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.430000 DelPhi exited at 01:46:09 9.434u 0.302s 0:10.18 95.5% 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 Tue Oct 11 2011 at 01:46:09 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 = 2667 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: 2.662457 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): 17.92500 78.09500 ymin,ymax (A): -11.47600 44.47300 zmin,zma (A): -7.648000 35.28300 x,y,z range (A): 60.17000 55.94900 42.93100 scale (grids/A): 2.662457 object centre (A): 48.01000 16.49850 13.81750 number of atom coordinates read : 2667 total number of charged atoms : 2524 net assigned charge : 6.500021 assigned positive charge : 402.6736 centred at (gu) : 82.18596 89.18170 88.87807 assigned negative charge : -396.1744 centred at (gu) : 83.37939 89.84012 89.56293 start vw surface at 0.1600000 fill in re-entrant regions at 0.5100000 boundary points on vw surface= 154372 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22691 grid for indexing accessible points = 1.400000 m= 73338 mr = 112247 m= 23763 mr = 59675 m= 5084 mr = 19058 m= 549 mr = 3813 m= 17 mr = 370 m= 0 mr = 4 time to grow re-entrant surface = 0.8600001 no. cavity mid-points inaccessible to solvent = 10603 time to turn everything in is 1.470000 number of dielectric boundary points 61956 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 7 iepsmp to db, and charging done at 1.620000 number of grid points assigned charge 20188 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) : 1.774971 object centre at (A) : 48.01000 16.49850 13.81750 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2378490 2.1544790E-02 midg,1,midg; midg,igrid,midg 0.3120475 -0.4464039 1,midg,midg; igrid,midg,midg 1.2131427E-02 0.1043714 gauss-seidel spectral radius is 0.9991999 estimated iterations to convergence 279 setup time was (sec) 1.790000 now iterating at: 01:46:11 rms-change max change #iterations 8.961542 282.8401 at 10iterations 5.098903 111.9570 at 20iterations 2.870769 62.95392 at 30iterations 1.614850 32.46948 at 40iterations 0.9094554 18.57765 at 50iterations 0.5107343 10.33153 at 60iterations 0.2874524 5.555641 at 70iterations 0.1610486 3.281440 at 80iterations 9.0691641E-02 1.964796 at 90iterations 5.0959319E-02 1.007687 at 100iterations 2.8685894E-02 0.7080746 at 110iterations 1.6208386E-02 0.3709186 at 120iterations 9.2032198E-03 0.1971989 at 130iterations 5.2671027E-03 0.1135025 at 140iterations 3.0630082E-03 7.1697235E-02 at 150iterations 1.8336887E-03 4.7090530E-02 at 160iterations 1.1447914E-03 3.0757904E-02 at 170iterations 7.4788654E-04 2.0538330E-02 at 180iterations finished qdiffx linear iterations at : 01:46:25 total time elapsed so far: 15.34000 # loops : 180 mean,max change (kT/e) : 7.4788654E-04 2.0538330E-02 energy calculations done at 15.34000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.52000 DelPhi exited at 01:46:25 15.522u 0.326s 0:16.21 97.7% 0+0k 0+0io 0pf+0w