Sun Oct 9 23:07:10 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 23:07:10 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 = 3142 !!! WARNING: GLY 516 has a net charge of 0.5000 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: 0.5668248 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): -25.58100 37.22500 ymin,ymax (A): 6.964000 63.28300 zmin,zma (A): -26.85200 28.09500 x,y,z range (A): 62.80600 56.31900 54.94700 scale (grids/A): 0.5668248 object centre (A): 5.822001 35.12350 0.6214991 number of atom coordinates read : 3142 total number of charged atoms : 2994 net assigned charge : 4.000006 assigned positive charge : 476.7271 centred at (gu) : 92.38419 91.40690 89.38741 assigned negative charge : -472.7279 centred at (gu) : 92.44227 91.46185 89.35605 start vw surface at 0.1600000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 6643 nv = 96 ne = 84 npr = 61459 no. pairs analyzed = 61459 no. exposed pairs = 4110 no. arc points = 30053 no. surface atoms = 1387 nbur = 1755 mkacc time = 0.1300000 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 = 1.512000 m= 268 mr = 3299 m= 1 mr = 16 m= 0 mr = 0 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 10 time to turn everything in is 0.3200000 number of dielectric boundary points 3597 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3127 ## 413 charges are in solution ## iepsmp to db, and charging done at 0.4400000 number of grid points assigned charge 8667 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.2882283E-10 9.0353408E-10 midg,1,midg; midg,igrid,midg 9.9634034E-10 -3.4939002E-10 1,midg,midg; igrid,midg,midg 8.1902413E-10 -5.4231664E-10 gauss-seidel spectral radius is 0.9839626 estimated iterations to convergence 65 setup time was (sec) 0.5500000 now iterating at: 23:07:11 rms-change max change #iterations 9.0048648E-02 16.11341 at 10iterations 6.5603987E-03 1.067192 at 20iterations 4.8490742E-04 7.8123093E-02 at 30iterations 3.6656606E-05 5.7268143E-03 at 40iterations 3.2463556E-06 4.5776367E-04 at 50iterations finished qdiffx linear iterations at : 23:07:14 total time elapsed so far: 3.060000 # loops : 50 mean,max change (kT/e) : 3.2463556E-06 4.5776367E-04 energy calculations done at 3.060000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.230000 DelPhi exited at 23:07:14 3.229u 0.182s 0:03.72 91.3% 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 23:07:14 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3142 !!! WARNING: GLY 516 has a net charge of 0.5000 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: 1.700474 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): -25.58100 37.22500 ymin,ymax (A): 6.964000 63.28300 zmin,zma (A): -26.85200 28.09500 x,y,z range (A): 62.80600 56.31900 54.94700 scale (grids/A): 1.700474 object centre (A): 5.822001 35.12350 0.6214991 number of atom coordinates read : 3142 total number of charged atoms : 2994 net assigned charge : 4.000006 assigned positive charge : 476.7271 centred at (gu) : 97.15200 94.21980 88.16138 assigned negative charge : -472.7279 centred at (gu) : 97.32639 94.38510 88.06779 start vw surface at 0.1900000 fill in re-entrant regions at 0.2800000 boundary points on vw surface= 73686 reading accessible surface arcs data from file ARCDAT no. of arc points read = 30053 grid for indexing accessible points = 1.400000 m= 21979 mr = 48708 m= 2495 mr = 14704 m= 103 mr = 1311 m= 1 mr = 18 m= 1 mr = 0 m= 0 mr = 0 time to grow re-entrant surface = 0.2300000 no. cavity mid-points inaccessible to solvent = 459 time to turn everything in is 0.5600000 number of dielectric boundary points 33524 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 336 ## 2 charges are in solution ## iepsmp to db, and charging done at 0.6700000 number of grid points assigned charge 23153 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) : 0.5668248 object centre at (A) : 5.822001 35.12350 0.6214991 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.2478709E-03 1.2797236E-02 midg,1,midg; midg,igrid,midg 3.1330512E-04 7.6117651E-03 1,midg,midg; igrid,midg,midg -1.8839419E-02 1.2148226E-02 gauss-seidel spectral radius is 0.9983547 estimated iterations to convergence 196 setup time was (sec) 0.8400000 now iterating at: 23:07:15 rms-change max change #iterations 3.716817 174.9269 at 10iterations 1.604488 56.37162 at 20iterations 0.6972977 23.02360 at 30iterations 0.3016720 10.15093 at 40iterations 0.1309572 4.496025 at 50iterations 5.6809813E-02 1.877152 at 60iterations 2.4615249E-02 0.7907963 at 70iterations 1.0708565E-02 0.3814497 at 80iterations 4.6671098E-03 0.1574242 at 90iterations 2.0222336E-03 7.8013420E-02 at 100iterations 8.8047516E-04 3.2535553E-02 at 110iterations 3.8453392E-04 1.2954712E-02 at 120iterations finished qdiffx linear iterations at : 23:07:22 total time elapsed so far: 7.560000 # loops : 120 mean,max change (kT/e) : 3.8453392E-04 1.2954712E-02 energy calculations done at 7.560000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.740000 DelPhi exited at 23:07:22 7.747u 0.211s 0:08.32 95.5% 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 23:07:22 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3142 !!! WARNING: GLY 516 has a net charge of 0.5000 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: 2.550712 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): -25.58100 37.22500 ymin,ymax (A): 6.964000 63.28300 zmin,zma (A): -26.85200 28.09500 x,y,z range (A): 62.80600 56.31900 54.94700 scale (grids/A): 2.550712 object centre (A): 5.822001 35.12350 0.6214991 number of atom coordinates read : 3142 total number of charged atoms : 2994 net assigned charge : 4.000006 assigned positive charge : 476.7271 centred at (gu) : 100.7278 96.32976 87.24184 assigned negative charge : -472.7279 centred at (gu) : 100.9894 96.57755 87.10163 start vw surface at 0.1500000 fill in re-entrant regions at 0.4100000 boundary points on vw surface= 171005 reading accessible surface arcs data from file ARCDAT no. of arc points read = 30053 grid for indexing accessible points = 1.400000 m= 76251 mr = 119399 m= 21643 mr = 59389 m= 4065 mr = 15912 m= 407 mr = 2818 m= 10 mr = 210 m= 0 mr = 3 time to grow re-entrant surface = 0.6700000 no. cavity mid-points inaccessible to solvent = 1538 time to turn everything in is 1.190000 number of dielectric boundary points 75650 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 13 iepsmp to db, and charging done at 1.340000 number of grid points assigned charge 23931 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) : 1.700474 object centre at (A) : 5.822001 35.12350 0.6214991 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -5.0883379E-02 0.2034993 midg,1,midg; midg,igrid,midg 4.1342370E-02 8.6458594E-02 1,midg,midg; igrid,midg,midg -0.5961657 0.7040575 gauss-seidel spectral radius is 0.9991984 estimated iterations to convergence 279 setup time was (sec) 1.510000 now iterating at: 23:07:24 rms-change max change #iterations 9.513355 307.6681 at 10iterations 5.467627 142.6201 at 20iterations 3.136543 79.91446 at 30iterations 1.785914 50.73309 at 40iterations 1.017270 23.25535 at 50iterations 0.5758067 12.17789 at 60iterations 0.3266321 6.679603 at 70iterations 0.1842379 3.773992 at 80iterations 0.1041263 2.326010 at 90iterations 5.8735039E-02 1.191643 at 100iterations 3.3082195E-02 0.6478157 at 110iterations 1.8659376E-02 0.3760719 at 120iterations 1.0508866E-02 0.2006536 at 130iterations 5.8966558E-03 0.1253662 at 140iterations 3.3218113E-03 7.0626259E-02 at 150iterations 1.8676412E-03 3.6406994E-02 at 160iterations 1.0486030E-03 2.3548126E-02 at 170iterations 5.9179787E-04 1.1814117E-02 at 180iterations finished qdiffx linear iterations at : 23:07:35 total time elapsed so far: 12.24000 # loops : 180 mean,max change (kT/e) : 5.9179787E-04 1.1814117E-02 energy calculations done at 12.24000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.42000 DelPhi exited at 23:07:35 12.419u 0.218s 0:12.95 97.4% 0+0k 0+0io 0pf+0w