Sun Oct 9 06:43:18 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 06:43:18 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: 284 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1995 !!! WARNING: ASP 186 has a net charge of -2.0000 !!! WARNING: NDP 188 has a net charge of -3.0000 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: 0.6655201 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): -24.25800 25.69300 ymin,ymax (A): 1.938000 46.14900 zmin,zma (A): -23.50500 29.98700 x,y,z range (A): 49.95100 44.21100 53.49200 scale (grids/A): 0.6655201 object centre (A): 0.7174988 24.04350 3.240999 number of atom coordinates read : 1995 total number of charged atoms : 1856 net assigned charge : -1.499990 assigned positive charge : 298.7900 centred at (gu) : 89.24103 89.14632 88.46499 assigned negative charge : -300.2901 centred at (gu) : 89.17901 89.38584 88.43851 start vw surface at 0.1500000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 5905 nv = 96 ne = 84 npr = 42148 no. pairs analyzed = 42148 no. exposed pairs = 2446 no. arc points = 17566 no. surface atoms = 832 nbur = 1163 mkacc time = 8.9999989E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 327 mr = 3259 m= 2 mr = 36 m= 0 mr = 0 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 29 time to turn everything in is 0.2600000 number of dielectric boundary points 2939 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1691 ## 135 charges are in solution ## iepsmp to db, and charging done at 0.3600000 number of grid points assigned charge 6941 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.2694627E-08 -1.3746525E-11 midg,1,midg; midg,igrid,midg 4.3692161E-08 -3.9908784E-08 1,midg,midg; igrid,midg,midg -1.8197014E-08 5.2886016E-09 gauss-seidel spectral radius is 0.9882398 estimated iterations to convergence 75 setup time was (sec) 0.4700000 now iterating at: 06:43:19 rms-change max change #iterations 0.1523485 21.19792 at 10iterations 1.6481675E-02 2.840414 at 20iterations 1.7742272E-03 0.2565613 at 30iterations 1.9313612E-04 2.7562141E-02 at 40iterations 2.0622854E-05 3.1099319E-03 at 50iterations finished qdiffx linear iterations at : 06:43:21 total time elapsed so far: 2.890000 # loops : 50 mean,max change (kT/e) : 2.0622854E-05 3.1099319E-03 energy calculations done at 2.890000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.060000 DelPhi exited at 06:43:22 3.059u 0.150s 0:03.51 91.1% 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 06:43:22 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: 284 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1995 !!! WARNING: ASP 186 has a net charge of -2.0000 !!! WARNING: NDP 188 has a net charge of -3.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.996560 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): -24.25800 25.69300 ymin,ymax (A): 1.938000 46.14900 zmin,zma (A): -23.50500 29.98700 x,y,z range (A): 49.95100 44.21100 53.49200 scale (grids/A): 1.996560 object centre (A): 0.7174988 24.04350 3.240999 number of atom coordinates read : 1995 total number of charged atoms : 1856 net assigned charge : -1.499990 assigned positive charge : 298.7900 centred at (gu) : 87.72317 87.43912 85.39487 assigned negative charge : -300.2901 centred at (gu) : 87.53712 88.15755 85.31573 start vw surface at 0.1400000 fill in re-entrant regions at 0.2200000 boundary points on vw surface= 63572 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17566 grid for indexing accessible points = 1.400000 m= 22426 mr = 43819 m= 3542 mr = 16604 m= 231 mr = 2214 m= 4 mr = 78 m= 0 mr = 0 time to grow re-entrant surface = 0.2000000 no. cavity mid-points inaccessible to solvent = 741 time to turn everything in is 0.4600000 number of dielectric boundary points 27060 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 85 iepsmp to db, and charging done at 0.5700000 number of grid points assigned charge 14688 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) : 0.6655201 object centre at (A) : 0.7174988 24.04350 3.240999 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -5.1435493E-02 2.1132642E-02 midg,1,midg; midg,igrid,midg 6.1549693E-02 -3.3040371E-02 1,midg,midg; igrid,midg,midg -3.9100114E-02 -3.4035959E-03 gauss-seidel spectral radius is 0.9986889 estimated iterations to convergence 219 setup time was (sec) 0.7200000 now iterating at: 06:43:23 rms-change max change #iterations 4.062584 204.4505 at 10iterations 1.925611 84.76367 at 20iterations 0.9133170 31.31226 at 30iterations 0.4365447 17.52845 at 40iterations 0.2065220 6.742488 at 50iterations 9.8053813E-02 3.493164 at 60iterations 4.6487540E-02 1.536774 at 70iterations 2.2196067E-02 0.8566856 at 80iterations 1.0505675E-02 0.3540058 at 90iterations 4.9989256E-03 0.1604400 at 100iterations 2.3849928E-03 8.4359169E-02 at 110iterations 1.1353631E-03 3.5957336E-02 at 120iterations finished qdiffx linear iterations at : 06:43:29 total time elapsed so far: 6.620000 # loops : 120 mean,max change (kT/e) : 1.1353631E-03 3.5957336E-02 energy calculations done at 6.620000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 6.800000 DelPhi exited at 06:43:29 6.798u 0.154s 0:07.27 95.4% 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 Sun Oct 9 2011 at 06:43:29 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: 284 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1995 !!! WARNING: ASP 186 has a net charge of -2.0000 !!! WARNING: NDP 188 has a net charge of -3.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.994840 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): -24.25800 25.69300 ymin,ymax (A): 1.938000 46.14900 zmin,zma (A): -23.50500 29.98700 x,y,z range (A): 49.95100 44.21100 53.49200 scale (grids/A): 2.994840 object centre (A): 0.7174988 24.04350 3.240999 number of atom coordinates read : 1995 total number of charged atoms : 1856 net assigned charge : -1.499990 assigned positive charge : 298.7900 centred at (gu) : 86.58479 86.15864 83.09234 assigned negative charge : -300.2901 centred at (gu) : 86.30575 87.23628 82.97362 start vw surface at 0.1400000 fill in re-entrant regions at 0.4000000 boundary points on vw surface= 147098 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17566 grid for indexing accessible points = 1.400000 m= 73213 mr = 106350 m= 25972 mr = 59983 m= 6394 mr = 20953 m= 1002 mr = 4808 m= 68 mr = 649 m= 4 mr = 40 m= 0 mr = 0 time to grow re-entrant surface = 0.6400000 no. cavity mid-points inaccessible to solvent = 2712 time to turn everything in is 1.130000 number of dielectric boundary points 60968 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.250000 number of grid points assigned charge 14848 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) : 1.996560 object centre at (A) : 0.7174988 24.04350 3.240999 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.8105219 0.6993453 midg,1,midg; midg,igrid,midg 0.6955395 -0.3360227 1,midg,midg; igrid,midg,midg -0.3628179 3.0378744E-02 gauss-seidel spectral radius is 0.9992617 estimated iterations to convergence 290 setup time was (sec) 1.410000 now iterating at: 06:43:31 rms-change max change #iterations 9.313795 437.2863 at 10iterations 5.366390 126.4589 at 20iterations 3.089192 68.15222 at 30iterations 1.775374 33.77184 at 40iterations 1.024070 21.16188 at 50iterations 0.5884642 12.90973 at 60iterations 0.3371722 6.635366 at 70iterations 0.1934747 3.576935 at 80iterations 0.1110756 2.116445 at 90iterations 6.3796706E-02 1.196381 at 100iterations 3.6548678E-02 0.7358017 at 110iterations 2.0999892E-02 0.4304779 at 120iterations 1.2093621E-02 0.2332401 at 130iterations 6.9449032E-03 0.1326470 at 140iterations 3.9840303E-03 8.0794334E-02 at 150iterations 2.2982825E-03 4.3983459E-02 at 160iterations 1.3236555E-03 2.4486542E-02 at 170iterations 7.6897017E-04 1.4252186E-02 at 180iterations finished qdiffx linear iterations at : 06:43:40 total time elapsed so far: 10.92000 # loops : 180 mean,max change (kT/e) : 7.6897017E-04 1.4252186E-02 energy calculations done at 10.92000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.09000 DelPhi exited at 06:43:41 11.095u 0.164s 0:11.55 97.4% 0+0k 0+0io 0pf+0w