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+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 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: 263 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2513 !!! WARNING: ADP 670 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: 0.5840470 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): -35.02500 25.92900 ymin,ymax (A): -15.76100 34.92300 zmin,zma (A): -1.4000058E-02 52.64900 x,y,z range (A): 60.95400 50.68400 52.66300 scale (grids/A): 0.5840470 object centre (A): -4.548000 9.581000 26.31750 number of atom coordinates read : 2513 total number of charged atoms : 2373 net assigned charge : -5.999994 assigned positive charge : 385.7148 centred at (gu) : 92.60911 89.85846 88.70029 assigned negative charge : -391.7155 centred at (gu) : 92.59922 89.92778 88.82722 start vw surface at 0.1600000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 5791 nv = 96 ne = 84 npr = 48884 no. pairs analyzed = 48884 no. exposed pairs = 3514 no. arc points = 24463 no. surface atoms = 1176 nbur = 1337 mkacc time = 0.1400000 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 = 1.484000 m= 266 mr = 2872 m= 1 mr = 19 m= 0 mr = 0 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3400000 number of dielectric boundary points 3167 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2566 ## 321 charges are in solution ## iepsmp to db, and charging done at 0.4700000 number of grid points assigned charge 7285 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.6734291E-09 -3.2345657E-09 midg,1,midg; midg,igrid,midg -2.9337414E-11 -2.9749647E-09 1,midg,midg; igrid,midg,midg -9.8091124E-10 -2.3926565E-09 gauss-seidel spectral radius is 0.9848368 estimated iterations to convergence 67 setup time was (sec) 0.6700000 now iterating at: 14:17:18 rms-change max change #iterations 9.5691778E-02 15.13899 at 10iterations 7.5236754E-03 1.166100 at 20iterations 5.8798492E-04 9.6036911E-02 at 30iterations 4.7074329E-05 8.5868835E-03 at 40iterations 3.9341780E-06 6.4086914E-04 at 50iterations finished qdiffx linear iterations at : 14:17:22 total time elapsed so far: 5.020000 # loops : 50 mean,max change (kT/e) : 3.9341780E-06 6.4086914E-04 energy calculations done at 5.020000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 5.200000 DelPhi exited at 14:17:23 5.199u 0.423s 0:06.18 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 Mon Oct 10 2011 at 14:17:23 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: 263 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2513 !!! WARNING: ADP 670 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: 1.752141 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): -35.02500 25.92900 ymin,ymax (A): -15.76100 34.92300 zmin,zma (A): -1.4000058E-02 52.64900 x,y,z range (A): 60.95400 50.68400 52.66300 scale (grids/A): 1.752141 object centre (A): -4.548000 9.581000 26.31750 number of atom coordinates read : 2513 total number of charged atoms : 2373 net assigned charge : -5.999994 assigned positive charge : 385.7148 centred at (gu) : 97.82674 89.57478 86.10040 assigned negative charge : -391.7155 centred at (gu) : 97.79742 89.78288 86.48150 start vw surface at 0.1600000 fill in re-entrant regions at 0.2700000 boundary points on vw surface= 63143 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24463 grid for indexing accessible points = 1.400000 m= 20960 mr = 41543 m= 2759 mr = 14505 m= 125 mr = 1510 m= 2 mr = 41 m= 0 mr = 0 time to grow re-entrant surface = 0.3000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.6200000 number of dielectric boundary points 29390 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 222 iepsmp to db, and charging done at 0.7700000 number of grid points assigned charge 18413 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) : 0.5840470 object centre at (A) : -4.548000 9.581000 26.31750 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.8719622E-03 -1.9070722E-02 midg,1,midg; midg,igrid,midg -7.2963885E-03 -1.3733599E-02 1,midg,midg; igrid,midg,midg 1.8475063E-02 1.0546693E-02 gauss-seidel spectral radius is 0.9983947 estimated iterations to convergence 198 setup time was (sec) 0.9700000 now iterating at: 14:17:24 rms-change max change #iterations 3.640707 174.5675 at 10iterations 1.587523 60.23625 at 20iterations 0.6936087 25.61304 at 30iterations 0.3039089 10.80969 at 40iterations 0.1332791 4.697821 at 50iterations 5.8598656E-02 2.340403 at 60iterations 2.5698368E-02 0.9087582 at 70iterations 1.1254374E-02 0.3824010 at 80iterations 4.9413713E-03 0.1806951 at 90iterations 2.1716519E-03 7.6575756E-02 at 100iterations 9.5406070E-04 3.1558990E-02 at 110iterations 4.1831675E-04 1.5411377E-02 at 120iterations finished qdiffx linear iterations at : 14:17:36 total time elapsed so far: 12.52000 # loops : 120 mean,max change (kT/e) : 4.1831675E-04 1.5411377E-02 energy calculations done at 12.52000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.71000 DelPhi exited at 14:17:36 12.713u 0.479s 0:13.53 97.4% 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 14:17:37 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: 263 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2513 !!! WARNING: ADP 670 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: 2.628211 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): -35.02500 25.92900 ymin,ymax (A): -15.76100 34.92300 zmin,zma (A): -1.4000058E-02 52.64900 x,y,z range (A): 60.95400 50.68400 52.66300 scale (grids/A): 2.628211 object centre (A): -4.548000 9.581000 26.31750 number of atom coordinates read : 2513 total number of charged atoms : 2373 net assigned charge : -5.999994 assigned positive charge : 385.7148 centred at (gu) : 101.7400 89.36201 84.15054 assigned negative charge : -391.7155 centred at (gu) : 101.6962 89.67435 84.72218 start vw surface at 0.1600000 fill in re-entrant regions at 0.4900000 boundary points on vw surface= 146265 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24463 grid for indexing accessible points = 1.400000 m= 70015 mr = 101983 m= 22477 mr = 55010 m= 4581 mr = 17134 m= 505 mr = 3214 m= 19 mr = 317 m= 0 mr = 3 time to grow re-entrant surface = 0.9100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.540000 number of dielectric boundary points 66201 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 6 iepsmp to db, and charging done at 1.750000 number of grid points assigned charge 18979 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) : 1.752141 object centre at (A) : -4.548000 9.581000 26.31750 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.4727246E-02 -0.2023803 midg,1,midg; midg,igrid,midg -9.1543771E-02 -0.1057776 1,midg,midg; igrid,midg,midg 0.4642166 5.1173113E-02 gauss-seidel spectral radius is 0.9991964 estimated iterations to convergence 279 setup time was (sec) 2.020000 now iterating at: 14:17:39 rms-change max change #iterations 8.963394 326.2834 at 10iterations 5.158183 129.8913 at 20iterations 2.934364 67.12835 at 30iterations 1.661535 35.52737 at 40iterations 0.9395133 20.77084 at 50iterations 0.5307566 11.61310 at 60iterations 0.2986070 6.422863 at 70iterations 0.1681898 3.624992 at 80iterations 9.4444603E-02 2.235084 at 90iterations 5.3020988E-02 1.200073 at 100iterations 2.9792255E-02 0.6634254 at 110iterations 1.6701208E-02 0.3476660 at 120iterations 9.3897544E-03 0.1943359 at 130iterations 5.2572181E-03 0.1086082 at 140iterations 2.9479696E-03 5.8097839E-02 at 150iterations 1.6572094E-03 3.3222198E-02 at 160iterations 9.2691771E-04 1.9329786E-02 at 170iterations 5.2039238E-04 1.0875702E-02 at 180iterations finished qdiffx linear iterations at : 14:17:59 total time elapsed so far: 21.56000 # loops : 180 mean,max change (kT/e) : 5.2039238E-04 1.0875702E-02 energy calculations done at 21.56000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 21.75000 DelPhi exited at 14:17:59 21.747u 0.556s 0:22.68 98.2% 0+0k 0+0io 0pf+0w