Sat Oct 8 11:48:18 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 8 2011 at 11:48:18 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 = 4455 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1000000 grid size : 179 scale,in grids/A, set to be: 0.5645238 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): -27.06900 35.12600 ymin,ymax (A): 35.04000 98.10201 zmin,zma (A): 30.76900 89.91600 x,y,z range (A): 62.19500 63.06201 59.14700 scale (grids/A): 0.5645238 object centre (A): 4.028500 66.57100 60.34250 number of atom coordinates read : 4455 total number of charged atoms : 4294 net assigned charge : -7.499953 assigned positive charge : 671.2148 centred at (gu) : 90.52673 88.25279 88.85553 assigned negative charge : -678.7183 centred at (gu) : 90.39076 88.30035 89.03322 start vw surface at 0.1600000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 8972 nv = 96 ne = 84 npr = 94030 no. pairs analyzed = 94030 no. exposed pairs = 5028 no. arc points = 33946 no. surface atoms = 1712 nbur = 2743 mkacc time = 0.3000000 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 = 1.540000 m= 383 mr = 5184 m= 0 mr = 31 time to grow re-entrant surface = 0.3300000 no. cavity mid-points inaccessible to solvent = 106 time to turn everything in is 0.5200000 number of dielectric boundary points 4140 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3551 ## 406 charges are in solution ## iepsmp to db, and charging done at 0.6800000 number of grid points assigned charge 11946 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 3.2269638E-09 -3.4931369E-09 midg,1,midg; midg,igrid,midg -8.9945051E-11 -1.2952973E-09 1,midg,midg; igrid,midg,midg -3.2975043E-09 1.8610474E-09 gauss-seidel spectral radius is 0.9839125 estimated iterations to convergence 65 setup time was (sec) 0.8600000 now iterating at: 11:48:19 rms-change max change #iterations 0.1086968 16.94351 at 10iterations 8.5041095E-03 1.151909 at 20iterations 1.0568926E-03 0.1462631 at 30iterations 2.6000643E-04 3.4801483E-02 at 40iterations 8.2311555E-05 9.9115372E-03 at 50iterations finished qdiffx linear iterations at : 11:48:23 total time elapsed so far: 5.050000 # loops : 50 mean,max change (kT/e) : 8.2311555E-05 9.9115372E-03 energy calculations done at 5.050000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 5.210000 DelPhi exited at 11:48:24 5.219u 0.438s 0:05.94 94.9% 0+0k 0+0io 6pf+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 8 2011 at 11:48:24 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 = 4455 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1000000 grid size : 179 scale,in grids/A, set to be: 1.693571 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): -27.06900 35.12600 ymin,ymax (A): 35.04000 98.10201 zmin,zma (A): 30.76900 89.91600 x,y,z range (A): 62.19500 63.06201 59.14700 scale (grids/A): 1.693571 object centre (A): 4.028500 66.57100 60.34250 number of atom coordinates read : 4455 total number of charged atoms : 4294 net assigned charge : -7.499953 assigned positive charge : 671.2148 centred at (gu) : 91.57905 84.75707 86.56530 assigned negative charge : -678.7183 centred at (gu) : 91.17192 84.90051 87.09932 start vw surface at 0.1600000 fill in re-entrant regions at 0.3300000 boundary points on vw surface= 100802 reading accessible surface arcs data from file ARCDAT no. of arc points read = 33946 grid for indexing accessible points = 1.400000 m= 33330 mr = 73177 m= 3968 mr = 24434 m= 123 mr = 2316 m= 1 mr = 16 m= 0 mr = 0 time to grow re-entrant surface = 0.4300000 no. cavity mid-points inaccessible to solvent = 6770 time to turn everything in is 0.8200000 number of dielectric boundary points 38281 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 326 ## 3 charges are in solution ## iepsmp to db, and charging done at 0.9900000 number of grid points assigned charge 33128 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) : 0.5645238 object centre at (A) : 4.028500 66.57100 60.34250 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.8818374E-02 -2.6074702E-02 midg,1,midg; midg,igrid,midg 1.8013569E-02 -5.4190303E-03 1,midg,midg; igrid,midg,midg -2.9382976E-02 2.4909319E-02 gauss-seidel spectral radius is 0.9984383 estimated iterations to convergence 201 setup time was (sec) 1.190000 now iterating at: 11:48:25 rms-change max change #iterations 4.578265 171.3567 at 10iterations 2.029734 63.78545 at 20iterations 0.9066288 25.96621 at 30iterations 0.4029424 14.14787 at 40iterations 0.1793291 5.655544 at 50iterations 8.0065444E-02 2.575113 at 60iterations 3.5767082E-02 0.9607887 at 70iterations 1.6005538E-02 0.4450035 at 80iterations 7.2056581E-03 0.2072277 at 90iterations 3.2799845E-03 0.1053352 at 100iterations 1.5242969E-03 4.2839050E-02 at 110iterations 7.4026728E-04 2.2705078E-02 at 120iterations finished qdiffx linear iterations at : 11:48:36 total time elapsed so far: 12.10000 # loops : 120 mean,max change (kT/e) : 7.4026728E-04 2.2705078E-02 energy calculations done at 12.11000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.26000 DelPhi exited at 11:48:37 12.269u 0.517s 0:13.04 97.9% 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 8 2011 at 11:48:37 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 = 4455 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1000000 grid size : 179 scale,in grids/A, set to be: 2.540357 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): -27.06900 35.12600 ymin,ymax (A): 35.04000 98.10201 zmin,zma (A): 30.76900 89.91600 x,y,z range (A): 62.19500 63.06201 59.14700 scale (grids/A): 2.540357 object centre (A): 4.028500 66.57100 60.34250 number of atom coordinates read : 4455 total number of charged atoms : 4294 net assigned charge : -7.499953 assigned positive charge : 671.2148 centred at (gu) : 92.36825 82.13510 84.84744 assigned negative charge : -678.7183 centred at (gu) : 91.75761 82.35067 85.64880 start vw surface at 0.1600000 fill in re-entrant regions at 0.6500000 boundary points on vw surface= 234616 reading accessible surface arcs data from file ARCDAT no. of arc points read = 33946 grid for indexing accessible points = 1.400000 m= 114636 mr = 177894 m= 35043 mr = 94259 m= 6629 mr = 27770 m= 594 mr = 4928 m= 11 mr = 357 m= 1 mr = 1 m= 0 mr = 0 time to grow re-entrant surface = 1.220000 no. cavity mid-points inaccessible to solvent = 23166 time to turn everything in is 2.030000 number of dielectric boundary points 86321 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 15 iepsmp to db, and charging done at 2.190000 number of grid points assigned charge 34328 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) : 1.693571 object centre at (A) : 4.028500 66.57100 60.34250 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.6917642 -0.3024640 midg,1,midg; midg,igrid,midg 0.3583416 -8.0981858E-02 1,midg,midg; igrid,midg,midg -0.3796822 0.2495786 gauss-seidel spectral radius is 0.9992305 estimated iterations to convergence 285 setup time was (sec) 2.420000 now iterating at: 11:48:40 rms-change max change #iterations 11.34285 377.0226 at 10iterations 6.569330 120.0141 at 20iterations 3.787795 72.64906 at 30iterations 2.176732 40.10818 at 40iterations 1.248080 22.56874 at 50iterations 0.7148112 12.38206 at 60iterations 0.4084411 7.453361 at 70iterations 0.2334144 3.609104 at 80iterations 0.1330041 2.446108 at 90iterations 7.6109059E-02 1.286213 at 100iterations 4.3382540E-02 0.7825381 at 110iterations 2.4764935E-02 0.4038602 at 120iterations 1.4165101E-02 0.2344055 at 130iterations 8.1184553E-03 0.1324387 at 140iterations 4.6649482E-03 8.3751678E-02 at 150iterations 2.7154007E-03 4.8381805E-02 at 160iterations 1.6025878E-03 2.5411606E-02 at 170iterations 9.7051176E-04 1.7360687E-02 at 180iterations finished qdiffx linear iterations at : 11:48:59 total time elapsed so far: 21.34000 # loops : 180 mean,max change (kT/e) : 9.7051176E-04 1.7360687E-02 energy calculations done at 21.34000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 21.51000 DelPhi exited at 11:48:59 21.512u 0.543s 0:22.34 98.7% 0+0k 0+0io 0pf+0w