Sun Oct 9 04:09:14 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 04:09:14 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: 291 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4836 !!! WARNING: HIZ 357 has a net charge of 0.2000 !!! WARNING: HEM 2209 has a net charge of 1.4000 !!! WARNING: FE 5 has a net charge of 1.4000 !!! WARNING: FE 6 has a net charge of 1.4000 !!! WARNING: FE 7 has a net charge of 1.4000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1100000 grid size : 179 scale,in grids/A, set to be: 0.4213965 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): -2.133000 79.36700 ymin,ymax (A): -11.56100 55.76500 zmin,zma (A): -17.15800 67.32300 x,y,z range (A): 81.50001 67.32600 84.48100 scale (grids/A): 0.4213965 object centre (A): 38.61700 22.10200 25.08250 number of atom coordinates read : 4836 total number of charged atoms : 4517 net assigned charge : 20.80000 assigned positive charge : 707.1354 centred at (gu) : 85.26241 91.62067 83.92692 assigned negative charge : -686.3409 centred at (gu) : 85.10643 91.66718 83.83616 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 5019 nv = 96 ne = 84 npr = 98653 no. pairs analyzed = 98653 no. exposed pairs = 6224 no. arc points = 44113 no. surface atoms = 2072 nbur = 2764 mkacc time = 0.2600000 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 = 1.988000 m= 124 mr = 2252 m= 0 mr = 0 time to grow re-entrant surface = 0.3000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4700000 number of dielectric boundary points 2891 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3250 ## 690 charges are in solution ## iepsmp to db, and charging done at 0.5700000 number of grid points assigned charge 6673 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.5331690E-12 7.1639412E-13 midg,1,midg; midg,igrid,midg 2.1436650E-12 2.4417118E-12 1,midg,midg; igrid,midg,midg -5.2613161E-12 1.3790018E-12 gauss-seidel spectral radius is 0.9713216 estimated iterations to convergence 49 setup time was (sec) 0.7400000 now iterating at: 04:09:15 rms-change max change #iterations 2.5810923E-02 10.47134 at 10iterations 3.2610486E-03 0.5462666 at 20iterations 1.0819754E-03 0.2056503 at 30iterations 3.7673765E-04 7.5950623E-02 at 40iterations 1.3313572E-04 2.7536392E-02 at 50iterations finished qdiffx linear iterations at : 04:09:19 total time elapsed so far: 4.810000 # loops : 50 mean,max change (kT/e) : 1.3313572E-04 2.7536392E-02 energy calculations done at 4.810000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.990000 DelPhi exited at 04:09:20 4.992u 0.422s 0:05.69 95.0% 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 04:09:20 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: 291 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4836 !!! WARNING: HIZ 357 has a net charge of 0.2000 !!! WARNING: HEM 2209 has a net charge of 1.4000 !!! WARNING: FE 5 has a net charge of 1.4000 !!! WARNING: FE 6 has a net charge of 1.4000 !!! WARNING: FE 7 has a net charge of 1.4000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1100000 grid size : 179 scale,in grids/A, set to be: 1.264189 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): -2.133000 79.36700 ymin,ymax (A): -11.56100 55.76500 zmin,zma (A): -17.15800 67.32300 x,y,z range (A): 81.50001 67.32600 84.48100 scale (grids/A): 1.264189 object centre (A): 38.61700 22.10200 25.08250 number of atom coordinates read : 4836 total number of charged atoms : 4517 net assigned charge : 20.80000 assigned positive charge : 707.1354 centred at (gu) : 75.78555 94.86031 71.77908 assigned negative charge : -686.3409 centred at (gu) : 75.31905 95.00137 71.50818 start vw surface at 0.1700000 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 58826 reading accessible surface arcs data from file ARCDAT no. of arc points read = 44113 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.848000 m= 12267 mr = 37475 m= 503 mr = 6939 m= 5 mr = 97 m= 0 mr = 0 time to grow re-entrant surface = 0.2500000 no. cavity mid-points inaccessible to solvent = 720 time to turn everything in is 0.5500000 number of dielectric boundary points 27090 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 689 ## 21 charges are in solution ## iepsmp to db, and charging done at 0.6600000 number of grid points assigned charge 30976 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) : 0.4213965 object centre at (A) : 38.61700 22.10200 25.08250 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.3201308E-02 1.9678643E-03 midg,1,midg; midg,igrid,midg 2.9085532E-03 2.0657973E-03 1,midg,midg; igrid,midg,midg -1.0972001E-03 1.6611827E-03 gauss-seidel spectral radius is 0.9970112 estimated iterations to convergence 146 setup time was (sec) 0.8400000 now iterating at: 04:09:21 rms-change max change #iterations 2.278942 122.7462 at 10iterations 0.7407666 32.30435 at 20iterations 0.2417235 10.73095 at 30iterations 7.9207726E-02 3.344063 at 40iterations 2.6837198E-02 1.102480 at 50iterations 9.8605780E-03 0.4570770 at 60iterations 4.5817164E-03 0.1909981 at 70iterations 2.6503822E-03 0.1053963 at 80iterations 1.7311089E-03 6.9015503E-02 at 90iterations 1.1691154E-03 4.5093536E-02 at 100iterations 7.9693703E-04 3.0490875E-02 at 110iterations 5.4424262E-04 2.0694733E-02 at 120iterations finished qdiffx linear iterations at : 04:09:30 total time elapsed so far: 10.11000 # loops : 120 mean,max change (kT/e) : 5.4424262E-04 2.0694733E-02 energy calculations done at 10.11000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.28000 DelPhi exited at 04:09:31 10.281u 0.467s 0:11.10 96.7% 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 04:09:31 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: 291 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4836 !!! WARNING: HIZ 357 has a net charge of 0.2000 !!! WARNING: HEM 2209 has a net charge of 1.4000 !!! WARNING: FE 5 has a net charge of 1.4000 !!! WARNING: FE 6 has a net charge of 1.4000 !!! WARNING: FE 7 has a net charge of 1.4000 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: 1.896284 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): -2.133000 79.36700 ymin,ymax (A): -11.56100 55.76500 zmin,zma (A): -17.15800 67.32300 x,y,z range (A): 81.50001 67.32600 84.48100 scale (grids/A): 1.896284 object centre (A): 38.61700 22.10200 25.08250 number of atom coordinates read : 4836 total number of charged atoms : 4517 net assigned charge : 20.80000 assigned positive charge : 707.1354 centred at (gu) : 68.67787 97.29006 62.66818 assigned negative charge : -686.3409 centred at (gu) : 67.97855 97.50213 62.26218 start vw surface at 0.1700000 fill in re-entrant regions at 0.4100000 boundary points on vw surface= 138301 reading accessible surface arcs data from file ARCDAT no. of arc points read = 44113 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.820000 m= 49057 mr = 94040 m= 7740 mr = 35277 m= 482 mr = 4794 m= 5 mr = 168 m= 0 mr = 0 time to grow re-entrant surface = 0.6999999 no. cavity mid-points inaccessible to solvent = 2392 time to turn everything in is 1.210000 number of dielectric boundary points 61306 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 198 iepsmp to db, and charging done at 1.340000 number of grid points assigned charge 35478 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) : 1.264189 object centre at (A) : 38.61700 22.10200 25.08250 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.4507430 2.6272647E-02 midg,1,midg; midg,igrid,midg 6.8040401E-02 3.0697221E-02 1,midg,midg; igrid,midg,midg -1.8980473E-02 2.1291541E-02 gauss-seidel spectral radius is 0.9987088 estimated iterations to convergence 220 setup time was (sec) 1.530000 now iterating at: 04:09:33 rms-change max change #iterations 7.001824 242.3802 at 10iterations 3.485343 102.9279 at 20iterations 1.719867 51.47051 at 30iterations 0.8407944 21.75152 at 40iterations 0.4113697 10.69428 at 50iterations 0.2003183 5.091730 at 60iterations 9.7128883E-02 2.376625 at 70iterations 4.7065794E-02 1.110912 at 80iterations 2.2915723E-02 0.5646400 at 90iterations 1.1163964E-02 0.3186978 at 100iterations 5.5527077E-03 0.1840744 at 110iterations 2.8321489E-03 7.5141907E-02 at 120iterations 1.5449437E-03 4.7672272E-02 at 130iterations 9.2188612E-04 2.9518127E-02 at 140iterations 6.0700078E-04 2.0153046E-02 at 150iterations 4.3074411E-04 1.3427734E-02 at 160iterations 3.1980980E-04 9.5939636E-03 at 170iterations 2.4166201E-04 7.0190430E-03 at 180iterations finished qdiffx linear iterations at : 04:09:48 total time elapsed so far: 16.71000 # loops : 180 mean,max change (kT/e) : 2.4166201E-04 7.0190430E-03 energy calculations done at 16.71000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 16.89000 DelPhi exited at 04:09:49 16.893u 0.509s 0:17.67 98.4% 0+0k 0+0io 0pf+0w