Sat Oct 8 14:12:40 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 14:12:40 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: 284 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2947 !!! WARNING: NAP 316 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: 0.6309596 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): -11.35000 43.28300 ymin,ymax (A): 10.51400 55.06800 zmin,zma (A): 36.04800 92.47000 x,y,z range (A): 54.63300 44.55400 56.42200 scale (grids/A): 0.6309596 object centre (A): 15.96650 32.79100 64.25900 number of atom coordinates read : 2947 total number of charged atoms : 2801 net assigned charge : 8.1211329E-06 assigned positive charge : 440.7957 centred at (gu) : 89.33071 89.56449 92.07967 assigned negative charge : -440.7965 centred at (gu) : 89.31078 89.47112 92.03485 start vw surface at 0.1300000 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 7923 nv = 96 ne = 84 npr = 60998 no. pairs analyzed = 60998 no. exposed pairs = 3357 no. arc points = 23295 no. surface atoms = 1151 nbur = 1796 mkacc time = 0.1600000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 405 mr = 4708 m= 1 mr = 41 m= 0 mr = 0 time to grow re-entrant surface = 0.2000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3400000 number of dielectric boundary points 3580 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2252 ## 204 charges are in solution ## iepsmp to db, and charging done at 0.4500000 number of grid points assigned charge 9560 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -2.9618565E-09 7.2310864E-09 midg,1,midg; midg,igrid,midg -1.0711148E-08 8.5832124E-09 1,midg,midg; igrid,midg,midg -2.4246878E-09 1.7273427E-09 gauss-seidel spectral radius is 0.9870144 estimated iterations to convergence 72 setup time was (sec) 0.6500000 now iterating at: 14:12:41 rms-change max change #iterations 0.1528724 22.96852 at 10iterations 1.5239151E-02 2.064716 at 20iterations 1.5910633E-03 0.2363071 at 30iterations 2.1487710E-04 2.8885841E-02 at 40iterations 4.0319039E-05 6.5240860E-03 at 50iterations finished qdiffx linear iterations at : 14:12:46 total time elapsed so far: 5.100000 # loops : 50 mean,max change (kT/e) : 4.0319039E-05 6.5240860E-03 energy calculations done at 5.100000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 5.280000 DelPhi exited at 14:12:46 5.281u 0.462s 0:06.03 95.1% 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 14:12:46 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: 284 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2947 !!! WARNING: NAP 316 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: 1.892879 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): -11.35000 43.28300 ymin,ymax (A): 10.51400 55.06800 zmin,zma (A): 36.04800 92.47000 x,y,z range (A): 54.63300 44.55400 56.42200 scale (grids/A): 1.892879 object centre (A): 15.96650 32.79100 64.25900 number of atom coordinates read : 2947 total number of charged atoms : 2801 net assigned charge : 8.1211329E-06 assigned positive charge : 440.7957 centred at (gu) : 87.99190 88.69279 96.23856 assigned negative charge : -440.7965 centred at (gu) : 87.93227 88.41288 96.10432 start vw surface at 0.1300000 fill in re-entrant regions at 0.2800000 boundary points on vw surface= 86870 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23295 grid for indexing accessible points = 1.400000 m= 32277 mr = 63411 m= 4710 mr = 24570 m= 240 mr = 2878 m= 6 mr = 60 m= 0 mr = 0 time to grow re-entrant surface = 0.3800000 no. cavity mid-points inaccessible to solvent = 132 time to turn everything in is 0.7100000 number of dielectric boundary points 33184 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 168 ## 2 charges are in solution ## iepsmp to db, and charging done at 0.8500000 number of grid points assigned charge 22026 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) : 0.6309596 object centre at (A) : 15.96650 32.79100 64.25900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.5219601E-02 3.7369772E-04 midg,1,midg; midg,igrid,midg -3.6916151E-03 1.2405980E-02 1,midg,midg; igrid,midg,midg 5.5842316E-03 1.9509451E-02 gauss-seidel spectral radius is 0.9986469 estimated iterations to convergence 215 setup time was (sec) 1.070000 now iterating at: 14:12:48 rms-change max change #iterations 4.554435 169.4409 at 10iterations 2.145036 69.35820 at 20iterations 1.009972 30.02316 at 30iterations 0.4756871 16.66975 at 40iterations 0.2240672 6.782452 at 50iterations 0.1051879 3.182950 at 60iterations 4.9521573E-02 1.550297 at 70iterations 2.3308828E-02 0.6620598 at 80iterations 1.1051833E-02 0.3277292 at 90iterations 5.1951683E-03 0.1671581 at 100iterations 2.4595209E-03 7.8330040E-02 at 110iterations 1.1657845E-03 3.3460617E-02 at 120iterations finished qdiffx linear iterations at : 14:12:59 total time elapsed so far: 12.56000 # loops : 120 mean,max change (kT/e) : 1.1657845E-03 3.3460617E-02 energy calculations done at 12.56000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.72000 DelPhi exited at 14:13:00 12.724u 0.526s 0:13.54 97.7% 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 8 2011 at 14:13:00 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: 284 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2947 !!! WARNING: NAP 316 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: 2.839318 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): -11.35000 43.28300 ymin,ymax (A): 10.51400 55.06800 zmin,zma (A): 36.04800 92.47000 x,y,z range (A): 54.63300 44.55400 56.42200 scale (grids/A): 2.839318 object centre (A): 15.96650 32.79100 64.25900 number of atom coordinates read : 2947 total number of charged atoms : 2801 net assigned charge : 8.1211329E-06 assigned positive charge : 440.7957 centred at (gu) : 86.98761 88.03906 99.35753 assigned negative charge : -440.7965 centred at (gu) : 86.89845 87.61929 99.15639 start vw surface at 0.1300000 fill in re-entrant regions at 0.5900000 boundary points on vw surface= 201378 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23295 grid for indexing accessible points = 1.400000 m= 105587 mr = 152986 m= 37593 mr = 88859 m= 8274 mr = 30539 m= 1066 mr = 6044 m= 51 mr = 701 m= 0 mr = 9 time to grow re-entrant surface = 1.170000 no. cavity mid-points inaccessible to solvent = 479 time to turn everything in is 1.880000 number of dielectric boundary points 74811 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2 iepsmp to db, and charging done at 2.110000 number of grid points assigned charge 22403 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) : 1.892879 object centre at (A) : 15.96650 32.79100 64.25900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.1936830E-02 8.9771502E-02 midg,1,midg; midg,igrid,midg -2.9961940E-02 0.1434209 1,midg,midg; igrid,midg,midg 0.2316515 0.3591767 gauss-seidel spectral radius is 0.9992654 estimated iterations to convergence 291 setup time was (sec) 2.360000 now iterating at: 14:13:03 rms-change max change #iterations 10.66448 338.9941 at 10iterations 6.262286 135.0110 at 20iterations 3.646208 71.41180 at 30iterations 2.127626 44.94023 at 40iterations 1.235849 23.59724 at 50iterations 0.7152991 12.47502 at 60iterations 0.4146248 7.619314 at 70iterations 0.2392889 4.331266 at 80iterations 0.1383466 2.325552 at 90iterations 7.9976715E-02 1.413879 at 100iterations 4.6218529E-02 0.7171345 at 110iterations 2.6670808E-02 0.4428101 at 120iterations 1.5367769E-02 0.2609177 at 130iterations 8.8836337E-03 0.1566696 at 140iterations 5.1397458E-03 8.3715439E-02 at 150iterations 2.9763523E-03 4.7316551E-02 at 160iterations 1.7315361E-03 2.9211998E-02 at 170iterations 1.0144244E-03 1.6986847E-02 at 180iterations finished qdiffx linear iterations at : 14:13:22 total time elapsed so far: 21.86000 # loops : 180 mean,max change (kT/e) : 1.0144244E-03 1.6986847E-02 energy calculations done at 21.86000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 22.02000 DelPhi exited at 14:13:23 22.023u 0.554s 0:22.89 98.6% 0+0k 0+0io 0pf+0w