Mon Oct 10 14:17:17 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+sph2.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 = amb2.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 14:17:17 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: 293 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2493 !!! WARNING: ADP 667 has a net charge of -2.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 0.5889555 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): -35.30500 25.14100 ymin,ymax (A): -15.72100 34.76500 zmin,zma (A): -2.105000 52.72400 x,y,z range (A): 60.44600 50.48600 54.82900 scale (grids/A): 0.5889555 object centre (A): -5.082001 9.522001 25.30950 number of atom coordinates read : 2493 total number of charged atoms : 2371 net assigned charge : -5.999993 assigned positive charge : 386.7788 centred at (gu) : 92.82115 89.89282 89.29774 assigned negative charge : -392.7795 centred at (gu) : 92.82666 89.95754 89.42348 start vw surface at 0.1400000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 5924 nv = 96 ne = 84 npr = 47841 no. pairs analyzed = 47841 no. exposed pairs = 3522 no. arc points = 24725 no. surface atoms = 1189 nbur = 1304 mkacc time = 0.1100000 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 = 1.456000 m= 267 mr = 2915 m= 1 mr = 14 m= 0 mr = 0 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3100000 number of dielectric boundary points 3263 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2493 ## 275 charges are in solution ## iepsmp to db, and charging done at 0.4200000 number of grid points assigned charge 7310 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.6830605E-09 -4.3196891E-09 midg,1,midg; midg,igrid,midg -1.2887572E-10 -3.3834195E-09 1,midg,midg; igrid,midg,midg -8.8601965E-10 -3.6685062E-09 gauss-seidel spectral radius is 0.9850845 estimated iterations to convergence 67 setup time was (sec) 0.5300000 now iterating at: 14:17:18 rms-change max change #iterations 9.8963499E-02 17.85849 at 10iterations 8.1300698E-03 1.388220 at 20iterations 6.8748230E-04 0.1148373 at 30iterations 8.0355770E-05 1.4064789E-02 at 40iterations 1.7519580E-05 3.5076141E-03 at 50iterations finished qdiffx linear iterations at : 14:17:21 total time elapsed so far: 3.000000 # loops : 50 mean,max change (kT/e) : 1.7519580E-05 3.5076141E-03 energy calculations done at 3.000000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.180000 DelPhi exited at 14:17:21 3.187u 0.154s 0:03.71 89.7% 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 Mon Oct 10 2011 at 14:17:21 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: 293 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2493 !!! WARNING: ADP 667 has a net charge of -2.0000 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: 1.766866 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): -35.30500 25.14100 ymin,ymax (A): -15.72100 34.76500 zmin,zma (A): -2.105000 52.72400 x,y,z range (A): 60.44600 50.48600 54.82900 scale (grids/A): 1.766866 object centre (A): -5.082001 9.522001 25.30950 number of atom coordinates read : 2493 total number of charged atoms : 2371 net assigned charge : -5.999993 assigned positive charge : 386.7788 centred at (gu) : 98.46299 89.67802 87.89230 assigned negative charge : -392.7795 centred at (gu) : 98.47969 89.87243 88.27006 start vw surface at 0.2100000 fill in re-entrant regions at 0.2800000 boundary points on vw surface= 64230 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24725 grid for indexing accessible points = 1.400000 m= 21246 mr = 42328 m= 2795 mr = 14409 m= 100 mr = 1400 m= 2 mr = 21 m= 0 mr = 0 time to grow re-entrant surface = 0.2100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5200000 number of dielectric boundary points 30215 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 225 iepsmp to db, and charging done at 0.6400000 number of grid points assigned charge 18467 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) : 0.5889555 object centre at (A) : -5.082001 9.522001 25.30950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -3.8784167E-03 -2.2529501E-02 midg,1,midg; midg,igrid,midg -5.8063902E-03 -1.1304888E-02 1,midg,midg; igrid,midg,midg 1.7070677E-02 5.0626197E-03 gauss-seidel spectral radius is 0.9984204 estimated iterations to convergence 200 setup time was (sec) 0.7900000 now iterating at: 14:17:22 rms-change max change #iterations 3.713806 183.1242 at 10iterations 1.636413 75.14121 at 20iterations 0.7230958 26.84442 at 30iterations 0.3192205 11.24092 at 40iterations 0.1411901 5.521482 at 50iterations 6.2365670E-02 2.255043 at 60iterations 2.7630089E-02 1.011499 at 70iterations 1.2205802E-02 0.4124527 at 80iterations 5.3759334E-03 0.2183800 at 90iterations 2.3906825E-03 8.9141846E-02 at 100iterations 1.0529314E-03 3.5488129E-02 at 110iterations 4.6652841E-04 1.7393112E-02 at 120iterations finished qdiffx linear iterations at : 14:17:29 total time elapsed so far: 7.070000 # loops : 120 mean,max change (kT/e) : 4.6652841E-04 1.7393112E-02 energy calculations done at 7.070000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.260000 DelPhi exited at 14:17:29 7.263u 0.230s 0:08.10 92.4% 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 14:17:29 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: 293 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2493 !!! WARNING: ADP 667 has a net charge of -2.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1100000 grid size : 179 scale,in grids/A, set to be: 2.650300 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): -35.30500 25.14100 ymin,ymax (A): -15.72100 34.76500 zmin,zma (A): -2.105000 52.72400 x,y,z range (A): 60.44600 50.48600 54.82900 scale (grids/A): 2.650300 object centre (A): -5.082001 9.522001 25.30950 number of atom coordinates read : 2493 total number of charged atoms : 2371 net assigned charge : -5.999993 assigned positive charge : 386.7788 centred at (gu) : 102.6943 89.51680 86.83836 assigned negative charge : -392.7795 centred at (gu) : 102.7196 89.80857 87.40515 start vw surface at 0.2100000 fill in re-entrant regions at 0.4400000 boundary points on vw surface= 148620 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24725 grid for indexing accessible points = 1.400000 m= 70638 mr = 103798 m= 22911 mr = 54987 m= 4587 mr = 16997 m= 508 mr = 3030 m= 16 mr = 276 m= 0 mr = 2 time to grow re-entrant surface = 0.6500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.190000 number of dielectric boundary points 68190 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3 iepsmp to db, and charging done at 1.320000 number of grid points assigned charge 18965 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) : 1.766866 object centre at (A) : -5.082001 9.522001 25.30950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -7.0302278E-02 -0.2360602 midg,1,midg; midg,igrid,midg -8.0246076E-02 -8.5547097E-02 1,midg,midg; igrid,midg,midg 0.4146655 -6.4456500E-03 gauss-seidel spectral radius is 0.9992073 estimated iterations to convergence 280 setup time was (sec) 1.490000 now iterating at: 14:17:31 rms-change max change #iterations 9.258110 300.4907 at 10iterations 5.388265 159.0034 at 20iterations 3.095720 76.26699 at 30iterations 1.771933 40.80900 at 40iterations 1.009063 23.58480 at 50iterations 0.5731608 13.16768 at 60iterations 0.3251379 6.791740 at 70iterations 0.1838927 4.600903 at 80iterations 0.1038236 2.542922 at 90iterations 5.8741760E-02 1.221020 at 100iterations 3.3178948E-02 0.7157516 at 110iterations 1.8720264E-02 0.4418316 at 120iterations 1.0542765E-02 0.2319956 at 130iterations 5.9595471E-03 0.1209564 at 140iterations 3.3602107E-03 6.7956924E-02 at 150iterations 1.8912182E-03 4.1763306E-02 at 160iterations 1.0689193E-03 2.9697418E-02 at 170iterations 6.0585479E-04 1.3063431E-02 at 180iterations finished qdiffx linear iterations at : 14:17:42 total time elapsed so far: 12.05000 # loops : 180 mean,max change (kT/e) : 6.0585479E-04 1.3063431E-02 energy calculations done at 12.05000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.23000 DelPhi exited at 14:17:42 12.234u 0.249s 0:12.80 97.4% 0+0k 0+0io 0pf+0w