Tue Oct 11 08:33:17 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 Tue Oct 11 2011 at 08:33:17 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: 247 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2449 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: 0.5902737 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): -6.950000 53.36100 ymin,ymax (A): -3.134000 46.83900 zmin,zma (A): -23.31100 27.25400 x,y,z range (A): 60.31100 49.97300 50.56500 scale (grids/A): 0.5902737 object centre (A): 23.20550 21.85250 1.971500 number of atom coordinates read : 2449 total number of charged atoms : 2315 net assigned charge : 4.000000 assigned positive charge : 373.7753 centred at (gu) : 87.89510 90.27133 89.86323 assigned negative charge : -369.7757 centred at (gu) : 87.98173 90.04420 90.02909 start vw surface at 0.1900000 fill in re-entrant regions at 0.1900000 boundary points on vw surface= 5631 nv = 96 ne = 84 npr = 48004 no. pairs analyzed = 48004 no. exposed pairs = 3181 no. arc points = 22352 no. surface atoms = 1078 nbur = 1371 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= 257 mr = 2865 m= 2 mr = 10 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 0.3500000 number of dielectric boundary points 3015 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2334 ## 286 charges are in solution ## iepsmp to db, and charging done at 0.4600000 number of grid points assigned charge 7088 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 5.4883187E-09 -3.0366512E-09 midg,1,midg; midg,igrid,midg -4.4743400E-09 7.2513053E-09 1,midg,midg; igrid,midg,midg 5.4854179E-09 -6.3061184E-10 gauss-seidel spectral radius is 0.9851391 estimated iterations to convergence 67 setup time was (sec) 0.5800000 now iterating at: 08:33:18 rms-change max change #iterations 9.5599145E-02 15.45225 at 10iterations 8.1486152E-03 1.331432 at 20iterations 8.7155355E-04 0.1408424 at 30iterations 1.5006612E-04 2.7889252E-02 at 40iterations 3.2762033E-05 6.1798096E-03 at 50iterations finished qdiffx linear iterations at : 08:33:20 total time elapsed so far: 3.220000 # loops : 50 mean,max change (kT/e) : 3.2762033E-05 6.1798096E-03 energy calculations done at 3.220000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.410000 DelPhi exited at 08:33:21 3.415u 0.144s 0:03.91 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 Tue Oct 11 2011 at 08:33:21 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: 247 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2449 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: 1.770821 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): -6.950000 53.36100 ymin,ymax (A): -3.134000 46.83900 zmin,zma (A): -23.31100 27.25400 x,y,z range (A): 60.31100 49.97300 50.56500 scale (grids/A): 1.770821 object centre (A): 23.20550 21.85250 1.971500 number of atom coordinates read : 2449 total number of charged atoms : 2315 net assigned charge : 4.000000 assigned positive charge : 373.7753 centred at (gu) : 83.68493 90.81353 89.58943 assigned negative charge : -369.7757 centred at (gu) : 83.94498 90.13245 90.08708 start vw surface at 0.1300000 fill in re-entrant regions at 0.2100000 boundary points on vw surface= 61351 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22352 grid for indexing accessible points = 1.400000 m= 20027 mr = 41090 m= 2380 mr = 13595 m= 126 mr = 1194 m= 1 mr = 24 m= 0 mr = 0 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4300000 number of dielectric boundary points 27982 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 237 iepsmp to db, and charging done at 0.5400000 number of grid points assigned charge 18012 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) : 0.5902737 object centre at (A) : 23.20550 21.85250 1.971500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.1265035E-02 1.6027192E-03 midg,1,midg; midg,igrid,midg -2.7180126E-02 5.6218188E-03 1,midg,midg; igrid,midg,midg 3.8463894E-02 1.1625469E-02 gauss-seidel spectral radius is 0.9984086 estimated iterations to convergence 199 setup time was (sec) 0.7000000 now iterating at: 08:33:22 rms-change max change #iterations 3.546515 165.1850 at 10iterations 1.564141 68.25546 at 20iterations 0.6892462 24.44934 at 30iterations 0.3046746 10.97890 at 40iterations 0.1341967 5.152024 at 50iterations 5.9368994E-02 2.062901 at 60iterations 2.6242068E-02 1.022085 at 70iterations 1.1692147E-02 0.4075413 at 80iterations 5.1871324E-03 0.2031898 at 90iterations 2.3585611E-03 8.5682869E-02 at 100iterations 1.0982682E-03 4.2943954E-02 at 110iterations 5.2087527E-04 2.2998810E-02 at 120iterations finished qdiffx linear iterations at : 08:33:28 total time elapsed so far: 7.170000 # loops : 120 mean,max change (kT/e) : 5.2087527E-04 2.2998810E-02 energy calculations done at 7.170000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.350000 DelPhi exited at 08:33:29 7.351u 0.186s 0:07.90 95.3% 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 Tue Oct 11 2011 at 08:33:29 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: 247 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2449 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: 2.656232 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): -6.950000 53.36100 ymin,ymax (A): -3.134000 46.83900 zmin,zma (A): -23.31100 27.25400 x,y,z range (A): 60.31100 49.97300 50.56500 scale (grids/A): 2.656232 object centre (A): 23.20550 21.85250 1.971500 number of atom coordinates read : 2449 total number of charged atoms : 2315 net assigned charge : 4.000000 assigned positive charge : 373.7753 centred at (gu) : 80.52738 91.22014 89.38424 assigned negative charge : -369.7757 centred at (gu) : 80.91745 90.19865 90.13063 start vw surface at 0.1500000 fill in re-entrant regions at 0.3800000 boundary points on vw surface= 142232 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22352 grid for indexing accessible points = 1.400000 m= 67618 mr = 100422 m= 20761 mr = 53363 m= 3890 mr = 15322 m= 472 mr = 2492 m= 17 mr = 260 m= 0 mr = 0 time to grow re-entrant surface = 0.5900000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.050000 number of dielectric boundary points 63131 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 8 iepsmp to db, and charging done at 1.170000 number of grid points assigned charge 18513 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) : 1.770821 object centre at (A) : 23.20550 21.85250 1.971500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.3501720 2.7001474E-02 midg,1,midg; midg,igrid,midg -0.4007016 2.3662673E-02 1,midg,midg; igrid,midg,midg 0.6752560 0.1601825 gauss-seidel spectral radius is 0.9991953 estimated iterations to convergence 278 setup time was (sec) 1.340000 now iterating at: 08:33:30 rms-change max change #iterations 8.819231 292.9832 at 10iterations 5.135500 143.2383 at 20iterations 2.954572 86.10562 at 30iterations 1.690333 38.00345 at 40iterations 0.9615012 22.39624 at 50iterations 0.5461231 13.49386 at 60iterations 0.3091550 7.422050 at 70iterations 0.1751522 3.625518 at 80iterations 9.8969616E-02 2.206165 at 90iterations 5.5607829E-02 1.393464 at 100iterations 3.1412356E-02 0.6548691 at 110iterations 1.7755356E-02 0.3478627 at 120iterations 1.0044151E-02 0.2023945 at 130iterations 5.6945416E-03 0.1163492 at 140iterations 3.2762587E-03 7.2860718E-02 at 150iterations 1.9043427E-03 3.8505554E-02 at 160iterations 1.1341181E-03 2.4551392E-02 at 170iterations 6.9585221E-04 1.5380859E-02 at 180iterations finished qdiffx linear iterations at : 08:33:41 total time elapsed so far: 11.37000 # loops : 180 mean,max change (kT/e) : 6.9585221E-04 1.5380859E-02 energy calculations done at 11.37000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.55000 DelPhi exited at 08:33:41 11.550u 0.222s 0:12.34 95.3% 0+0k 0+0io 0pf+0w