Sat Oct 15 12:23:53 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 12:23:53 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 = 2777 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 0.5529152 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): -67.30000 -9.790000 ymin,ymax (A): -24.68100 39.70500 zmin,zma (A): -0.7140000 55.15500 x,y,z range (A): 57.50999 64.38600 55.86900 scale (grids/A): 0.5529152 object centre (A): -38.54500 7.512001 27.22050 number of atom coordinates read : 2777 total number of charged atoms : 2639 net assigned charge : -4.999992 assigned positive charge : 367.8647 centred at (gu) : 92.00133 87.72101 89.05993 assigned negative charge : -372.8654 centred at (gu) : 91.93582 87.71403 88.84457 start vw surface at 0.1000000 fill in re-entrant regions at 0.1100000 boundary points on vw surface= 6010 nv = 96 ne = 84 npr = 55096 no. pairs analyzed = 55096 no. exposed pairs = 4264 no. arc points = 31605 no. surface atoms = 1420 nbur = 1357 mkacc time = 9.0000004E-02 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 = 1.568000 m= 271 mr = 2519 m= 2 mr = 6 m= 0 mr = 0 time to grow re-entrant surface = 0.1000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2200000 number of dielectric boundary points 3758 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2887 ## 243 charges are in solution ## iepsmp to db, and charging done at 0.3100000 number of grid points assigned charge 7368 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -2.4813320E-09 8.6613589E-10 midg,1,midg; midg,igrid,midg -7.6753781E-10 -2.0239775E-10 1,midg,midg; igrid,midg,midg -5.3284444E-10 1.2929643E-10 gauss-seidel spectral radius is 0.9831492 estimated iterations to convergence 63 setup time was (sec) 0.4400000 now iterating at: 12:23:54 rms-change max change #iterations 7.0109852E-02 11.97343 at 10iterations 4.8318198E-03 0.7088776 at 20iterations 5.7773490E-04 0.1069736 at 30iterations 1.4298758E-04 2.8097153E-02 at 40iterations 4.2590844E-05 8.4829330E-03 at 50iterations finished qdiffx linear iterations at : 12:23:57 total time elapsed so far: 3.470000 # loops : 50 mean,max change (kT/e) : 4.2590844E-05 8.4829330E-03 energy calculations done at 3.470000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.610000 DelPhi exited at 12:23:58 3.612u 0.216s 0:04.21 90.7% 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 Sat Oct 15 2011 at 12:23:58 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 = 2777 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 1.658746 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): -67.30000 -9.790000 ymin,ymax (A): -24.68100 39.70500 zmin,zma (A): -0.7140000 55.15500 x,y,z range (A): 57.50999 64.38600 55.86900 scale (grids/A): 1.658746 object centre (A): -38.54500 7.512001 27.22050 number of atom coordinates read : 2777 total number of charged atoms : 2639 net assigned charge : -4.999992 assigned positive charge : 367.8647 centred at (gu) : 96.00341 83.16224 87.17905 assigned negative charge : -372.8654 centred at (gu) : 95.80725 83.14188 86.53335 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 64763 reading accessible surface arcs data from file ARCDAT no. of arc points read = 31605 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 18926 mr = 38405 m= 2231 mr = 11672 m= 69 mr = 923 m= 1 mr = 5 m= 0 mr = 0 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3300000 number of dielectric boundary points 34985 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 149 ## 3 charges are in solution ## iepsmp to db, and charging done at 0.4100000 number of grid points assigned charge 20336 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) : 0.5529152 object centre at (A) : -38.54500 7.512001 27.22050 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.4837021E-02 1.1460889E-02 midg,1,midg; midg,igrid,midg 9.7850039E-05 -1.0210203E-02 1,midg,midg; igrid,midg,midg -1.5223257E-02 1.5674744E-03 gauss-seidel spectral radius is 0.9982665 estimated iterations to convergence 191 setup time was (sec) 0.5600000 now iterating at: 12:23:58 rms-change max change #iterations 3.116618 186.4774 at 10iterations 1.312485 47.94067 at 20iterations 0.5544366 20.09648 at 30iterations 0.2351076 8.231598 at 40iterations 9.9569641E-02 4.058690 at 50iterations 4.2123951E-02 1.495338 at 60iterations 1.7879874E-02 0.6365089 at 70iterations 7.6148128E-03 0.2945461 at 80iterations 3.2772659E-03 0.1291971 at 90iterations 1.4262104E-03 5.6247711E-02 at 100iterations 6.4751128E-04 2.7767181E-02 at 110iterations 3.1137792E-04 1.3115883E-02 at 120iterations finished qdiffx linear iterations at : 12:24:06 total time elapsed so far: 7.810000 # loops : 120 mean,max change (kT/e) : 3.1137792E-04 1.3115883E-02 energy calculations done at 7.810000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.960000 DelPhi exited at 12:24:06 7.958u 0.206s 0:08.44 96.5% 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 Sat Oct 15 2011 at 12:24:06 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 = 2777 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 2.488118 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): -67.30000 -9.790000 ymin,ymax (A): -24.68100 39.70500 zmin,zma (A): -0.7140000 55.15500 x,y,z range (A): 57.50999 64.38600 55.86900 scale (grids/A): 2.488118 object centre (A): -38.54500 7.512001 27.22050 number of atom coordinates read : 2777 total number of charged atoms : 2639 net assigned charge : -4.999992 assigned positive charge : 367.8647 centred at (gu) : 99.00505 79.74310 85.76844 assigned negative charge : -372.8654 centred at (gu) : 98.71070 79.71274 84.80001 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.2700000 boundary points on vw surface= 149901 reading accessible surface arcs data from file ARCDAT no. of arc points read = 31605 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 63198 mr = 95523 m= 19574 mr = 46069 m= 3361 mr = 13649 m= 230 mr = 1931 m= 3 mr = 54 m= 0 mr = 0 time to grow re-entrant surface = 0.4400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.8100000 number of dielectric boundary points 79041 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 10 iepsmp to db, and charging done at 0.9000000 number of grid points assigned charge 21099 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) : 1.658746 object centre at (A) : -38.54500 7.512001 27.22050 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.3710553 0.1277495 midg,1,midg; midg,igrid,midg 3.2426114E-03 -0.2834846 1,midg,midg; igrid,midg,midg -0.2998334 6.0114372E-03 gauss-seidel spectral radius is 0.9991822 estimated iterations to convergence 276 setup time was (sec) 1.070000 now iterating at: 12:24:07 rms-change max change #iterations 8.166210 340.0049 at 10iterations 4.747555 118.9567 at 20iterations 2.718367 64.50830 at 30iterations 1.553854 37.42510 at 40iterations 0.8809519 18.86226 at 50iterations 0.4985066 11.46803 at 60iterations 0.2808380 6.335732 at 70iterations 0.1581975 3.312267 at 80iterations 8.8906147E-02 1.813714 at 90iterations 4.9973946E-02 1.060602 at 100iterations 2.8008211E-02 0.6090012 at 110iterations 1.5681244E-02 0.3273525 at 120iterations 8.8241296E-03 0.1787567 at 130iterations 4.9464167E-03 0.1055794 at 140iterations 2.7962136E-03 5.8044434E-02 at 150iterations 1.5935183E-03 3.9710999E-02 at 160iterations 9.1953261E-04 2.0532608E-02 at 170iterations 5.4373505E-04 1.4599442E-02 at 180iterations finished qdiffx linear iterations at : 12:24:19 total time elapsed so far: 12.88000 # loops : 180 mean,max change (kT/e) : 5.4373505E-04 1.4599442E-02 energy calculations done at 12.88000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.01000 DelPhi exited at 12:24:20 13.010u 0.249s 0:13.52 98.0% 0+0k 0+0io 0pf+0w