Sat Oct 15 15:38:37 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 Sat Oct 15 2011 at 15:38:37 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: 295 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3374 !!! WARNING: HIR 207 has a net charge of 0.5140 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: 0.5840183 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): 0.2720000 48.38500 ymin,ymax (A): -8.514000 52.44300 zmin,zma (A): 2.904000 60.63500 x,y,z range (A): 48.11300 60.95700 57.73100 scale (grids/A): 0.5840183 object centre (A): 24.32850 21.96450 31.76950 number of atom coordinates read : 3374 total number of charged atoms : 3205 net assigned charge : -1.485990 assigned positive charge : 505.4065 centred at (gu) : 89.83961 89.06190 90.12048 assigned negative charge : -506.8938 centred at (gu) : 89.77273 89.05969 90.10225 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1000000 boundary points on vw surface= 7484 nv = 96 ne = 84 npr = 70286 no. pairs analyzed = 70286 no. exposed pairs = 3816 no. arc points = 26142 no. surface atoms = 1298 nbur = 2076 mkacc time = 0.1200000 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= 318 mr = 4407 m= 0 mr = 25 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 67 time to turn everything in is 0.2400000 number of dielectric boundary points 3370 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2703 ## 295 charges are in solution ## iepsmp to db, and charging done at 0.3200000 number of grid points assigned charge 9617 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -8.6791085E-10 1.5714915E-10 midg,1,midg; midg,igrid,midg -5.3563232E-10 -2.4835725E-10 1,midg,midg; igrid,midg,midg -2.3889568E-09 1.4742363E-09 gauss-seidel spectral radius is 0.9848895 estimated iterations to convergence 67 setup time was (sec) 0.4700000 now iterating at: 15:38:38 rms-change max change #iterations 0.1079524 16.16994 at 10iterations 8.9906408E-03 1.280266 at 20iterations 7.9085608E-04 0.1174507 at 30iterations 9.3748698E-05 1.8215179E-02 at 40iterations 1.4348126E-05 2.7580261E-03 at 50iterations finished qdiffx linear iterations at : 15:38:43 total time elapsed so far: 3.620000 # loops : 50 mean,max change (kT/e) : 1.4348126E-05 2.7580261E-03 energy calculations done at 3.620000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.760000 DelPhi exited at 15:38:43 3.762u 0.239s 0:05.98 66.7% 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 15:38:43 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: 295 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3374 !!! WARNING: HIR 207 has a net charge of 0.5140 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: 1.752055 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): 0.2720000 48.38500 ymin,ymax (A): -8.514000 52.44300 zmin,zma (A): 2.904000 60.63500 x,y,z range (A): 48.11300 60.95700 57.73100 scale (grids/A): 1.752055 object centre (A): 24.32850 21.96450 31.76950 number of atom coordinates read : 3374 total number of charged atoms : 3205 net assigned charge : -1.485990 assigned positive charge : 505.4065 centred at (gu) : 89.51801 87.18465 90.36075 assigned negative charge : -506.8938 centred at (gu) : 89.31777 87.17866 90.30627 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1900000 boundary points on vw surface= 83188 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26142 grid for indexing accessible points = 1.400000 m= 28602 mr = 60291 m= 3356 mr = 21553 m= 112 mr = 2085 m= 2 mr = 32 m= 0 mr = 0 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 3985 time to turn everything in is 0.4200000 number of dielectric boundary points 31299 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 263 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.5100000 number of grid points assigned charge 24873 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) : 0.5840183 object centre at (A) : 24.32850 21.96450 31.76950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.2348103E-03 2.3902501E-03 midg,1,midg; midg,igrid,midg -1.6790517E-02 -2.1307550E-02 1,midg,midg; igrid,midg,midg -5.3197113E-03 7.6587708E-04 gauss-seidel spectral radius is 0.9984616 estimated iterations to convergence 202 setup time was (sec) 0.6700000 now iterating at: 15:38:44 rms-change max change #iterations 4.179753 159.5512 at 10iterations 1.862117 64.37050 at 20iterations 0.8352969 25.54262 at 30iterations 0.3746069 11.49104 at 40iterations 0.1682859 5.655500 at 50iterations 7.5308606E-02 2.353951 at 60iterations 3.3840615E-02 1.002723 at 70iterations 1.5114124E-02 0.4601917 at 80iterations 6.8014418E-03 0.2088928 at 90iterations 3.0496395E-03 9.8222017E-02 at 100iterations 1.3752780E-03 3.9039612E-02 at 110iterations 6.1879761E-04 2.1133423E-02 at 120iterations finished qdiffx linear iterations at : 15:38:58 total time elapsed so far: 8.440000 # loops : 120 mean,max change (kT/e) : 6.1879761E-04 2.1133423E-02 energy calculations done at 8.440000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.570000 DelPhi exited at 15:38:58 8.573u 0.275s 0:14.89 59.3% 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 Sat Oct 15 2011 at 15:38:58 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: 295 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3374 !!! WARNING: HIR 207 has a net charge of 0.5140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.628082 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): 0.2720000 48.38500 ymin,ymax (A): -8.514000 52.44300 zmin,zma (A): 2.904000 60.63500 x,y,z range (A): 48.11300 60.95700 57.73100 scale (grids/A): 2.628082 object centre (A): 24.32850 21.96450 31.76950 number of atom coordinates read : 3374 total number of charged atoms : 3205 net assigned charge : -1.485990 assigned positive charge : 505.4065 centred at (gu) : 89.27677 85.77682 90.54092 assigned negative charge : -506.8938 centred at (gu) : 88.97649 85.76783 90.45928 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.3800000 boundary points on vw surface= 193022 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26142 grid for indexing accessible points = 1.400000 m= 96692 mr = 145819 m= 30929 mr = 80766 m= 5792 mr = 25076 m= 497 mr = 4382 m= 13 mr = 297 m= 0 mr = 2 time to grow re-entrant surface = 0.6000000 no. cavity mid-points inaccessible to solvent = 13521 time to turn everything in is 1.080000 number of dielectric boundary points 70603 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 8 iepsmp to db, and charging done at 1.190000 number of grid points assigned charge 25627 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) : 1.752055 object centre at (A) : 24.32850 21.96450 31.76950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.2430054E-02 -0.1091584 midg,1,midg; midg,igrid,midg -0.2248534 -0.3253614 1,midg,midg; igrid,midg,midg -5.2738104E-02 -8.2590645E-03 gauss-seidel spectral radius is 0.9992202 estimated iterations to convergence 283 setup time was (sec) 1.350000 now iterating at: 15:39:01 rms-change max change #iterations 10.12826 261.1286 at 10iterations 5.788612 126.1790 at 20iterations 3.297613 69.77814 at 30iterations 1.872086 38.82346 at 40iterations 1.060869 19.20323 at 50iterations 0.6027068 11.38044 at 60iterations 0.3419727 6.212518 at 70iterations 0.1934037 3.535489 at 80iterations 0.1096706 2.029419 at 90iterations 6.2123328E-02 1.327850 at 100iterations 3.5133731E-02 0.6209550 at 110iterations 1.9928757E-02 0.3538218 at 120iterations 1.1264369E-02 0.2337859 at 130iterations 6.3775489E-03 0.1156921 at 140iterations 3.6126394E-03 6.0954094E-02 at 150iterations 2.0424521E-03 3.8753510E-02 at 160iterations 1.1611129E-03 2.0335197E-02 at 170iterations 6.5748172E-04 1.1039734E-02 at 180iterations finished qdiffx linear iterations at : 15:39:19 total time elapsed so far: 14.26000 # loops : 180 mean,max change (kT/e) : 6.5748172E-04 1.1039734E-02 energy calculations done at 14.26000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 14.41000 DelPhi exited at 15:39:20 14.409u 0.320s 0:21.65 67.9% 0+0k 0+0io 0pf+0w