Sat Oct 15 12:23:43 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 Sat Oct 15 2011 at 12:23:43 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 = 4673 !!! WARNING: HIZ 356 has a net charge of 0.2000 !!! WARNING: HEM 1103 has a net charge of 1.4000 !!! WARNING: FE 3 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= 0.1400000 grid size : 179 scale,in grids/A, set to be: 0.4322381 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): -5.024000 77.33801 ymin,ymax (A): 0.5030001 67.25800 zmin,zma (A): 173.9150 235.3110 x,y,z range (A): 82.36201 66.75500 61.39600 scale (grids/A): 0.4322381 object centre (A): 36.15700 33.88050 204.6130 number of atom coordinates read : 4673 total number of charged atoms : 4436 net assigned charge : 19.00001 assigned positive charge : 686.3787 centred at (gu) : 86.79589 91.11196 88.66925 assigned negative charge : -667.3835 centred at (gu) : 86.72596 91.09570 88.69216 start vw surface at 0.2500000 fill in re-entrant regions at 0.2600000 boundary points on vw surface= 5078 nv = 96 ne = 84 npr = 95518 no. pairs analyzed = 95518 no. exposed pairs = 6050 no. arc points = 41390 no. surface atoms = 2048 nbur = 2625 mkacc time = 0.2800000 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 = 1.932000 m= 134 mr = 2323 m= 0 mr = 1 time to grow re-entrant surface = 0.3100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5800000 number of dielectric boundary points 2888 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3377 ## 709 charges are in solution ## iepsmp to db, and charging done at 0.7300000 number of grid points assigned charge 7010 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 8.1493545E-12 2.2654157E-12 midg,1,midg; midg,igrid,midg 2.6304688E-12 7.1950198E-12 1,midg,midg; igrid,midg,midg 2.8359975E-12 2.8863949E-12 gauss-seidel spectral radius is 0.9727088 estimated iterations to convergence 51 setup time was (sec) 0.8800000 now iterating at: 12:23:45 rms-change max change #iterations 2.7795454E-02 5.636347 at 10iterations 3.2193898E-03 0.4920864 at 20iterations 9.3989092E-04 0.1499958 at 30iterations 2.8320184E-04 4.6190262E-02 at 40iterations 8.5486659E-05 1.4139175E-02 at 50iterations finished qdiffx linear iterations at : 12:23:48 total time elapsed so far: 4.180000 # loops : 50 mean,max change (kT/e) : 8.5486659E-05 1.4139175E-02 energy calculations done at 4.180000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.400000 DelPhi exited at 12:23:48 4.408u 0.210s 0:04.91 93.8% 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 15 2011 at 12:23:48 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 = 4673 !!! WARNING: HIZ 356 has a net charge of 0.2000 !!! WARNING: HEM 1103 has a net charge of 1.4000 !!! WARNING: FE 3 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= 0.1400000 grid size : 179 scale,in grids/A, set to be: 1.296714 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): -5.024000 77.33801 ymin,ymax (A): 0.5030001 67.25800 zmin,zma (A): 173.9150 235.3110 x,y,z range (A): 82.36201 66.75500 61.39600 scale (grids/A): 1.296714 object centre (A): 36.15700 33.88050 204.6130 number of atom coordinates read : 4673 total number of charged atoms : 4436 net assigned charge : 19.00001 assigned positive charge : 686.3787 centred at (gu) : 80.38616 93.33405 86.00632 assigned negative charge : -667.3835 centred at (gu) : 80.17773 93.28648 86.07590 start vw surface at 0.2500000 fill in re-entrant regions at 0.3400000 boundary points on vw surface= 59393 reading accessible surface arcs data from file ARCDAT no. of arc points read = 41390 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.820000 m= 14143 mr = 38516 m= 712 mr = 8331 m= 8 mr = 128 m= 0 mr = 0 time to grow re-entrant surface = 0.2600000 no. cavity mid-points inaccessible to solvent = 160 time to turn everything in is 0.6400000 number of dielectric boundary points 27281 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 740 ## 33 charges are in solution ## iepsmp to db, and charging done at 0.8000000 number of grid points assigned charge 30939 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) : 0.4322381 object centre at (A) : 36.15700 33.88050 204.6130 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.7499827E-03 5.8889785E-04 midg,1,midg; midg,igrid,midg 3.0393091E-03 2.6689093E-03 1,midg,midg; igrid,midg,midg 7.6654907E-03 3.1358709E-03 gauss-seidel spectral radius is 0.9972215 estimated iterations to convergence 151 setup time was (sec) 1.000000 now iterating at: 12:23:50 rms-change max change #iterations 2.422043 136.8051 at 10iterations 0.8226272 34.70842 at 20iterations 0.2787903 13.11822 at 30iterations 9.5318273E-02 3.924677 at 40iterations 3.2875139E-02 1.436737 at 50iterations 1.1774880E-02 0.4955730 at 60iterations 4.7527943E-03 0.2102013 at 70iterations 2.3333989E-03 9.7721100E-02 at 80iterations 1.4062593E-03 5.3174973E-02 at 90iterations 9.3763327E-04 3.4429550E-02 at 100iterations 6.4231956E-04 2.3857117E-02 at 110iterations 4.4467824E-04 1.6641617E-02 at 120iterations finished qdiffx linear iterations at : 12:23:58 total time elapsed so far: 9.580000 # loops : 120 mean,max change (kT/e) : 4.4467824E-04 1.6641617E-02 energy calculations done at 9.580000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.810000 DelPhi exited at 12:23:59 9.812u 0.262s 0:10.64 94.6% 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 15 2011 at 12:23:59 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: 291 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4673 !!! WARNING: HIZ 356 has a net charge of 0.2000 !!! WARNING: HEM 1103 has a net charge of 1.4000 !!! WARNING: FE 3 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= 0.1500000 grid size : 179 scale,in grids/A, set to be: 1.945072 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): -5.024000 77.33801 ymin,ymax (A): 0.5030001 67.25800 zmin,zma (A): 173.9150 235.3110 x,y,z range (A): 82.36201 66.75500 61.39600 scale (grids/A): 1.945072 object centre (A): 36.15700 33.88050 204.6130 number of atom coordinates read : 4673 total number of charged atoms : 4436 net assigned charge : 19.00001 assigned positive charge : 686.3787 centred at (gu) : 75.57869 95.00066 84.00908 assigned negative charge : -667.3835 centred at (gu) : 75.26630 94.92965 84.11376 start vw surface at 0.2600000 fill in re-entrant regions at 0.5200000 boundary points on vw surface= 139544 reading accessible surface arcs data from file ARCDAT no. of arc points read = 41390 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.792000 m= 53891 mr = 96512 m= 10204 mr = 39531 m= 708 mr = 6390 m= 12 mr = 256 m= 0 mr = 0 time to grow re-entrant surface = 0.8000000 no. cavity mid-points inaccessible to solvent = 466 time to turn everything in is 1.420000 number of dielectric boundary points 61670 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 234 ## 1 charges are in solution ## iepsmp to db, and charging done at 1.590000 number of grid points assigned charge 35006 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) : 1.296714 object centre at (A) : 36.15700 33.88050 204.6130 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 7.7994198E-02 8.8557946E-03 midg,1,midg; midg,igrid,midg 8.3650470E-02 5.7602189E-02 1,midg,midg; igrid,midg,midg 0.1905810 4.0045492E-02 gauss-seidel spectral radius is 0.9988505 estimated iterations to convergence 233 setup time was (sec) 1.800000 now iterating at: 12:24:01 rms-change max change #iterations 7.325264 253.5854 at 10iterations 3.783109 109.2557 at 20iterations 1.938635 52.16425 at 30iterations 0.9913902 26.82476 at 40iterations 0.5037758 14.13490 at 50iterations 0.2553518 7.313431 at 60iterations 0.1290673 3.325954 at 70iterations 6.5245457E-02 1.541416 at 80iterations 3.2858700E-02 0.7893600 at 90iterations 1.6651789E-02 0.3938446 at 100iterations 8.4453989E-03 0.2003975 at 110iterations 4.3509086E-03 0.1109982 at 120iterations 2.2910463E-03 6.0544968E-02 at 130iterations 1.2686579E-03 3.4461975E-02 at 140iterations 7.5963471E-04 1.7668810E-02 at 150iterations 4.9744989E-04 1.2516022E-02 at 160iterations 3.4973188E-04 8.0871582E-03 at 170iterations 2.5814882E-04 5.8422089E-03 at 180iterations finished qdiffx linear iterations at : 12:24:15 total time elapsed so far: 15.46000 # loops : 180 mean,max change (kT/e) : 2.5814882E-04 5.8422089E-03 energy calculations done at 15.46000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.70000 DelPhi exited at 12:24:16 15.697u 0.275s 0:16.46 96.9% 0+0k 0+0io 0pf+0w