Sun Oct 9 03:46:23 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 03:46:23 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 = 4926 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: 0.5078677 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): -4.152000 65.94500 ymin,ymax (A): -11.83300 58.07000 zmin,zma (A): 16.36300 73.17600 x,y,z range (A): 70.09700 69.90300 56.81300 scale (grids/A): 0.5078677 object centre (A): 30.89650 23.11850 44.76950 number of atom coordinates read : 4926 total number of charged atoms : 4773 net assigned charge : 12.00001 assigned positive charge : 742.2743 centred at (gu) : 89.48421 92.03254 88.70541 assigned negative charge : -730.2808 centred at (gu) : 89.40671 92.12833 88.66830 start vw surface at 0.1200000 fill in re-entrant regions at 0.1300000 boundary points on vw surface= 7905 nv = 96 ne = 84 npr = 99611 no. pairs analyzed = 99611 no. exposed pairs = 6397 no. arc points = 43991 no. surface atoms = 2142 nbur = 2784 mkacc time = 0.1700000 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 = 1.680000 m= 261 mr = 3872 m= 2 mr = 2 m= 0 mr = 0 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3200000 number of dielectric boundary points 4294 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4253 ## 605 charges are in solution ## iepsmp to db, and charging done at 0.4000000 number of grid points assigned charge 10692 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 9.5964410E-11 1.7390686E-10 midg,1,midg; midg,igrid,midg 2.2246627E-10 -1.2778724E-10 1,midg,midg; igrid,midg,midg -3.0968211E-11 2.9372935E-10 gauss-seidel spectral radius is 0.9801840 estimated iterations to convergence 59 setup time was (sec) 0.5200000 now iterating at: 03:46:24 rms-change max change #iterations 6.5974675E-02 10.29977 at 10iterations 4.8868316E-03 0.6736679 at 20iterations 1.0682289E-03 0.1488686 at 30iterations 3.3024445E-04 4.0653229E-02 at 40iterations 1.0465951E-04 1.2119293E-02 at 50iterations finished qdiffx linear iterations at : 03:46:27 total time elapsed so far: 3.560000 # loops : 50 mean,max change (kT/e) : 1.0465951E-04 1.2119293E-02 energy calculations done at 3.560000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.680000 DelPhi exited at 03:46:28 3.688u 0.201s 0:04.26 91.0% 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 03:46:28 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 = 4926 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: 1.523603 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): -4.152000 65.94500 ymin,ymax (A): -11.83300 58.07000 zmin,zma (A): 16.36300 73.17600 x,y,z range (A): 70.09700 69.90300 56.81300 scale (grids/A): 1.523603 object centre (A): 30.89650 23.11850 44.76950 number of atom coordinates read : 4926 total number of charged atoms : 4773 net assigned charge : 12.00001 assigned positive charge : 742.2743 centred at (gu) : 88.45070 96.09605 86.11433 assigned negative charge : -730.2808 centred at (gu) : 88.22009 96.38441 86.00453 start vw surface at 0.1200000 fill in re-entrant regions at 0.2100000 boundary points on vw surface= 88977 reading accessible surface arcs data from file ARCDAT no. of arc points read = 43991 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.596000 m= 24355 mr = 59448 m= 2024 mr = 15260 m= 43 mr = 758 m= 0 mr = 0 time to grow re-entrant surface = 0.2000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4400000 number of dielectric boundary points 39933 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 563 ## 8 charges are in solution ## iepsmp to db, and charging done at 0.5400000 number of grid points assigned charge 35829 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) : 0.5078677 object centre at (A) : 30.89650 23.11850 44.76950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 9.6137626E-03 7.7938596E-03 midg,1,midg; midg,igrid,midg 2.6230566E-02 2.0107822E-02 1,midg,midg; igrid,midg,midg -1.8236626E-02 7.3861857E-03 gauss-seidel spectral radius is 0.9981051 estimated iterations to convergence 183 setup time was (sec) 0.6900000 now iterating at: 03:46:29 rms-change max change #iterations 3.784361 159.6875 at 10iterations 1.537733 52.54979 at 20iterations 0.6282070 21.34709 at 30iterations 0.2558671 8.197563 at 40iterations 0.1052444 4.490040 at 50iterations 4.3128956E-02 1.402472 at 60iterations 1.7803179E-02 0.6439133 at 70iterations 7.4835406E-03 0.2483006 at 80iterations 3.2128242E-03 0.1076508 at 90iterations 1.4539213E-03 4.4288635E-02 at 100iterations 7.1255228E-04 2.3513317E-02 at 110iterations 3.8619523E-04 1.1178970E-02 at 120iterations finished qdiffx linear iterations at : 03:46:37 total time elapsed so far: 8.790000 # loops : 120 mean,max change (kT/e) : 3.8619523E-04 1.1178970E-02 energy calculations done at 8.790000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.920000 DelPhi exited at 03:46:37 8.922u 0.263s 0:09.53 96.3% 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 03:46:37 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 = 4926 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: 2.285404 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): -4.152000 65.94500 ymin,ymax (A): -11.83300 58.07000 zmin,zma (A): 16.36300 73.17600 x,y,z range (A): 70.09700 69.90300 56.81300 scale (grids/A): 2.285404 object centre (A): 30.89650 23.11850 44.76950 number of atom coordinates read : 4926 total number of charged atoms : 4773 net assigned charge : 12.00001 assigned positive charge : 742.2743 centred at (gu) : 87.67581 99.14361 84.17113 assigned negative charge : -730.2808 centred at (gu) : 87.32989 99.57666 84.00661 start vw surface at 0.1200000 fill in re-entrant regions at 0.3900000 boundary points on vw surface= 207412 reading accessible surface arcs data from file ARCDAT no. of arc points read = 43991 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.568000 m= 88392 mr = 146868 m= 21076 mr = 66717 m= 2840 mr = 14562 m= 138 mr = 1529 m= 3 mr = 32 m= 0 mr = 0 time to grow re-entrant surface = 0.6100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.100000 number of dielectric boundary points 90153 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 66 iepsmp to db, and charging done at 1.220000 number of grid points assigned charge 38071 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) : 1.523603 object centre at (A) : 30.89650 23.11850 44.76950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1358636 0.1342703 midg,1,midg; midg,igrid,midg 0.8916502 0.4553367 1,midg,midg; igrid,midg,midg -0.3188108 0.1145115 gauss-seidel spectral radius is 0.9991670 estimated iterations to convergence 274 setup time was (sec) 1.400000 now iterating at: 03:46:39 rms-change max change #iterations 10.31601 316.4802 at 10iterations 5.925786 129.1896 at 20iterations 3.370420 71.99105 at 30iterations 1.911378 39.67421 at 40iterations 1.078730 22.74789 at 50iterations 0.6064466 18.03245 at 60iterations 0.3398263 6.723606 at 70iterations 0.1902555 3.735313 at 80iterations 0.1064156 2.202473 at 90iterations 5.9410706E-02 1.127960 at 100iterations 3.3209790E-02 0.6797180 at 110iterations 1.8530831E-02 0.3699608 at 120iterations 1.0328176E-02 0.1989517 at 130iterations 5.7709510E-03 0.1126232 at 140iterations 3.2390165E-03 6.3871384E-02 at 150iterations 1.8254903E-03 3.5907745E-02 at 160iterations 1.0385838E-03 1.9744873E-02 at 170iterations 5.9925212E-04 1.1154175E-02 at 180iterations finished qdiffx linear iterations at : 03:46:52 total time elapsed so far: 14.76000 # loops : 180 mean,max change (kT/e) : 5.9925212E-04 1.1154175E-02 energy calculations done at 14.76000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 14.90000 DelPhi exited at 03:46:53 14.897u 0.264s 0:15.44 98.1% 0+0k 0+0io 0pf+0w