Mon Oct 10 13:56:46 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 Mon Oct 10 2011 at 13:56:46 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 = 2960 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 0.5729092 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): 111.1330 173.2720 ymin,ymax (A): -44.77600 8.509000 zmin,zma (A): 46.06600 103.9290 x,y,z range (A): 62.13898 53.28500 57.86300 scale (grids/A): 0.5729092 object centre (A): 142.2025 -18.13350 74.99750 number of atom coordinates read : 2960 total number of charged atoms : 2808 net assigned charge : 5.000019 assigned positive charge : 431.2477 centred at (gu) : 89.69702 89.03345 88.90929 assigned negative charge : -426.2483 centred at (gu) : 89.70987 89.09983 88.75462 start vw surface at 0.1700000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 6581 nv = 96 ne = 84 npr = 57504 no. pairs analyzed = 57504 no. exposed pairs = 4470 no. arc points = 31871 no. surface atoms = 1496 nbur = 1464 mkacc time = 0.2000000 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 = 1.484000 m= 345 mr = 2947 m= 1 mr = 25 m= 0 mr = 0 time to grow re-entrant surface = 0.2500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4300000 number of dielectric boundary points 3955 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3118 ## 298 charges are in solution ## iepsmp to db, and charging done at 0.5500000 number of grid points assigned charge 8277 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -2.2898314E-09 2.6204197E-09 midg,1,midg; midg,igrid,midg 2.4705562E-09 -1.8278283E-10 1,midg,midg; igrid,midg,midg 1.1627322E-09 6.1372663E-10 gauss-seidel spectral radius is 0.9842960 estimated iterations to convergence 66 setup time was (sec) 0.7200000 now iterating at: 13:56:47 rms-change max change #iterations 9.0185486E-02 13.79767 at 10iterations 6.7068092E-03 1.092340 at 20iterations 5.0516764E-04 7.6065063E-02 at 30iterations 3.9750848E-05 7.2242022E-03 at 40iterations 3.8158619E-06 5.8937073E-04 at 50iterations finished qdiffx linear iterations at : 13:56:51 total time elapsed so far: 4.510000 # loops : 50 mean,max change (kT/e) : 3.8158619E-06 5.8937073E-04 energy calculations done at 4.510000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.720000 DelPhi exited at 13:56:52 4.729u 0.390s 0:05.48 93.2% 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 Mon Oct 10 2011 at 13:56:52 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 = 2960 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 1.718728 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): 111.1330 173.2720 ymin,ymax (A): -44.77600 8.509000 zmin,zma (A): 46.06600 103.9290 x,y,z range (A): 62.13898 53.28500 57.86300 scale (grids/A): 1.718728 object centre (A): 142.2025 -18.13350 74.99750 number of atom coordinates read : 2960 total number of charged atoms : 2808 net assigned charge : 5.000019 assigned positive charge : 431.2477 centred at (gu) : 89.09057 87.10009 86.72736 assigned negative charge : -426.2483 centred at (gu) : 89.12914 87.29910 86.26360 start vw surface at 0.1700000 fill in re-entrant regions at 0.3100000 boundary points on vw surface= 70246 reading accessible surface arcs data from file ARCDAT no. of arc points read = 31871 grid for indexing accessible points = 1.400000 m= 22976 mr = 43277 m= 3309 mr = 14708 m= 122 mr = 1606 m= 1 mr = 12 m= 0 mr = 0 time to grow re-entrant surface = 0.3800000 no. cavity mid-points inaccessible to solvent = 375 time to turn everything in is 0.7500000 number of dielectric boundary points 37051 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 208 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.8900000 number of grid points assigned charge 21741 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) : 0.5729092 object centre at (A) : 142.2025 -18.13350 74.99750 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.8885907E-02 2.1030163E-02 midg,1,midg; midg,igrid,midg 2.3861293E-02 1.1129049E-02 1,midg,midg; igrid,midg,midg 8.8384803E-03 1.0152817E-02 gauss-seidel spectral radius is 0.9983926 estimated iterations to convergence 198 setup time was (sec) 1.090000 now iterating at: 13:56:53 rms-change max change #iterations 3.652433 163.3715 at 10iterations 1.587863 59.25482 at 20iterations 0.6929893 24.90902 at 30iterations 0.3036482 10.37418 at 40iterations 0.1326954 4.831457 at 50iterations 5.8171932E-02 2.091514 at 60iterations 2.5521083E-02 0.8324137 at 70iterations 1.1213131E-02 0.4111328 at 80iterations 4.9090725E-03 0.2006035 at 90iterations 2.1513936E-03 7.2926641E-02 at 100iterations 9.4609731E-04 3.2951355E-02 at 110iterations 4.1503273E-04 1.5541077E-02 at 120iterations finished qdiffx linear iterations at : 13:57:03 total time elapsed so far: 11.01000 # loops : 120 mean,max change (kT/e) : 4.1503273E-04 1.5541077E-02 energy calculations done at 11.01000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.25000 DelPhi exited at 13:57:04 11.250u 0.446s 0:12.19 95.8% 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 Mon Oct 10 2011 at 13:57:04 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 = 2960 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 2.578092 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): 111.1330 173.2720 ymin,ymax (A): -44.77600 8.509000 zmin,zma (A): 46.06600 103.9290 x,y,z range (A): 62.13898 53.28500 57.86300 scale (grids/A): 2.578092 object centre (A): 142.2025 -18.13350 74.99750 number of atom coordinates read : 2960 total number of charged atoms : 2808 net assigned charge : 5.000019 assigned positive charge : 431.2477 centred at (gu) : 88.63586 85.65017 85.09065 assigned negative charge : -426.2483 centred at (gu) : 88.69370 85.94856 84.39526 start vw surface at 0.1600000 fill in re-entrant regions at 0.6000000 boundary points on vw surface= 162146 reading accessible surface arcs data from file ARCDAT no. of arc points read = 31871 grid for indexing accessible points = 1.400000 m= 74111 mr = 106707 m= 25567 mr = 55285 m= 5404 mr = 18502 m= 509 mr = 3457 m= 10 mr = 227 m= 0 mr = 0 time to grow re-entrant surface = 1.150000 no. cavity mid-points inaccessible to solvent = 1144 time to turn everything in is 1.890000 number of dielectric boundary points 83569 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 7 iepsmp to db, and charging done at 2.050000 number of grid points assigned charge 22441 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) : 1.718728 object centre at (A) : 142.2025 -18.13350 74.99750 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.2350399 0.2811392 midg,1,midg; midg,igrid,midg 0.3153848 0.1963128 1,midg,midg; igrid,midg,midg 0.1833100 0.1197828 gauss-seidel spectral radius is 0.9992191 estimated iterations to convergence 283 setup time was (sec) 2.270000 now iterating at: 13:57:07 rms-change max change #iterations 9.398246 390.2677 at 10iterations 5.533525 152.0678 at 20iterations 3.212523 71.02263 at 30iterations 1.854083 43.18418 at 40iterations 1.063411 25.91441 at 50iterations 0.6084902 12.80719 at 60iterations 0.3476655 8.267467 at 70iterations 0.1981648 4.445556 at 80iterations 0.1128829 2.380388 at 90iterations 6.4265721E-02 1.601766 at 100iterations 3.6333140E-02 0.8112946 at 110iterations 2.0639423E-02 0.4551983 at 120iterations 1.1716222E-02 0.2628365 at 130iterations 6.6221282E-03 0.1360683 at 140iterations 3.7546055E-03 7.6641560E-02 at 150iterations 2.1257624E-03 4.1961670E-02 at 160iterations 1.2030232E-03 2.2332191E-02 at 170iterations 6.8128842E-04 1.3494492E-02 at 180iterations finished qdiffx linear iterations at : 13:57:23 total time elapsed so far: 18.86000 # loops : 180 mean,max change (kT/e) : 6.8128842E-04 1.3494492E-02 energy calculations done at 18.86000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 19.09000 DelPhi exited at 13:57:24 19.096u 0.444s 0:20.05 97.4% 0+0k 0+0io 0pf+0w