Mon Oct 10 11:03:15 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 11:03:15 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: 326 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5316 !!! WARNING: HIR 283 has a net charge of 0.5140 !!! WARNING: HIT 392 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= 0.1200000 grid size : 179 scale,in grids/A, set to be: 0.4807303 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): -28.75000 29.73100 ymin,ymax (A): -42.38000 19.82200 zmin,zma (A): -31.45300 42.60100 x,y,z range (A): 58.48100 62.20200 74.05400 scale (grids/A): 0.4807303 object centre (A): 0.4904995 -11.27900 5.574001 number of atom coordinates read : 5316 total number of charged atoms : 5162 net assigned charge : 13.02803 assigned positive charge : 848.1725 centred at (gu) : 90.72979 89.85310 91.91113 assigned negative charge : -835.1531 centred at (gu) : 90.70870 89.92005 91.97099 start vw surface at 0.1800000 fill in re-entrant regions at 0.1900000 boundary points on vw surface= 7699 nv = 96 ne = 84 npr = 104189 no. pairs analyzed = 104189 no. exposed pairs = 6468 no. arc points = 44550 no. surface atoms = 2166 nbur = 3150 mkacc time = 0.2800000 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 = 1.764000 m= 238 mr = 4091 m= 1 mr = 0 m= 0 mr = 0 time to grow re-entrant surface = 0.3200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5200000 number of dielectric boundary points 3847 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4160 ## 695 charges are in solution ## iepsmp to db, and charging done at 0.6500000 number of grid points assigned charge 10395 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 5.4288532E-11 -4.1732533E-12 midg,1,midg; midg,igrid,midg 1.0110176E-10 -6.6556565E-12 1,midg,midg; igrid,midg,midg 2.3987215E-11 7.5633583E-11 gauss-seidel spectral radius is 0.9779205 estimated iterations to convergence 56 setup time was (sec) 0.8200000 now iterating at: 11:03:16 rms-change max change #iterations 5.4201163E-02 9.187315 at 10iterations 2.8200664E-03 0.4259453 at 20iterations 5.3818960E-04 8.9025497E-02 at 30iterations 2.5938172E-04 4.3585777E-02 at 40iterations 1.3009057E-04 2.1984100E-02 at 50iterations finished qdiffx linear iterations at : 11:03:20 total time elapsed so far: 4.630000 # loops : 50 mean,max change (kT/e) : 1.3009057E-04 2.1984100E-02 energy calculations done at 4.630000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.780000 DelPhi exited at 11:03:20 4.789u 0.406s 0:05.46 94.8% 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 11:03:21 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: 326 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5316 !!! WARNING: HIR 283 has a net charge of 0.5140 !!! WARNING: HIT 392 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= 0.1700000 grid size : 179 scale,in grids/A, set to be: 1.442191 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): -28.75000 29.73100 ymin,ymax (A): -42.38000 19.82200 zmin,zma (A): -31.45300 42.60100 x,y,z range (A): 58.48100 62.20200 74.05400 scale (grids/A): 1.442191 object centre (A): 0.4904995 -11.27900 5.574001 number of atom coordinates read : 5316 total number of charged atoms : 5162 net assigned charge : 13.02803 assigned positive charge : 848.1725 centred at (gu) : 92.18765 89.55775 95.73141 assigned negative charge : -835.1531 centred at (gu) : 92.12605 89.76025 95.91300 start vw surface at 0.2300000 fill in re-entrant regions at 0.3500000 boundary points on vw surface= 89161 reading accessible surface arcs data from file ARCDAT no. of arc points read = 44550 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.652000 m= 24487 mr = 62592 m= 1755 mr = 16258 m= 18 mr = 607 m= 0 mr = 0 time to grow re-entrant surface = 0.3600000 no. cavity mid-points inaccessible to solvent = 859 time to turn everything in is 0.7800000 number of dielectric boundary points 35964 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 714 ## 17 charges are in solution ## iepsmp to db, and charging done at 0.9600000 number of grid points assigned charge 37874 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) : 0.4807303 object centre at (A) : 0.4904995 -11.27900 5.574001 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.3791163E-02 2.4510536E-02 midg,1,midg; midg,igrid,midg 3.3485813E-03 5.0236057E-03 1,midg,midg; igrid,midg,midg -1.9443374E-03 2.4444850E-03 gauss-seidel spectral radius is 0.9978784 estimated iterations to convergence 173 setup time was (sec) 1.140000 now iterating at: 11:03:22 rms-change max change #iterations 3.600979 147.7914 at 10iterations 1.393878 44.02838 at 20iterations 0.5433588 20.22176 at 30iterations 0.2110821 6.928505 at 40iterations 8.2535125E-02 2.618488 at 50iterations 3.2094505E-02 1.106623 at 60iterations 1.2544129E-02 0.4561689 at 70iterations 4.9994518E-03 0.1669769 at 80iterations 2.0926970E-03 6.9796562E-02 at 90iterations 1.0069436E-03 3.8103104E-02 at 100iterations 6.1287690E-04 2.4475098E-02 at 110iterations 4.3715598E-04 1.5367508E-02 at 120iterations finished qdiffx linear iterations at : 11:03:32 total time elapsed so far: 10.72000 # loops : 120 mean,max change (kT/e) : 4.3715598E-04 1.5367508E-02 energy calculations done at 10.72000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.88000 DelPhi exited at 11:03:32 10.887u 0.444s 0:11.69 96.8% 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 11:03:32 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: 326 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5316 !!! WARNING: HIR 283 has a net charge of 0.5140 !!! WARNING: HIT 392 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= 0.1200000 grid size : 179 scale,in grids/A, set to be: 2.163286 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): -28.75000 29.73100 ymin,ymax (A): -42.38000 19.82200 zmin,zma (A): -31.45300 42.60100 x,y,z range (A): 58.48100 62.20200 74.05400 scale (grids/A): 2.163286 object centre (A): 0.4904995 -11.27900 5.574001 number of atom coordinates read : 5316 total number of charged atoms : 5162 net assigned charge : 13.02803 assigned positive charge : 848.1725 centred at (gu) : 93.28100 89.33604 98.59675 assigned negative charge : -835.1531 centred at (gu) : 93.18914 89.64034 98.86959 start vw surface at 0.1600000 fill in re-entrant regions at 0.5300000 boundary points on vw surface= 208907 reading accessible surface arcs data from file ARCDAT no. of arc points read = 44550 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.652000 m= 91070 mr = 154247 m= 20253 mr = 71345 m= 2076 mr = 14202 m= 55 mr = 1126 m= 0 mr = 8 time to grow re-entrant surface = 1.100000 no. cavity mid-points inaccessible to solvent = 2836 time to turn everything in is 1.740000 number of dielectric boundary points 81433 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 144 iepsmp to db, and charging done at 1.890000 number of grid points assigned charge 41077 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) : 1.442191 object centre at (A) : 0.4904995 -11.27900 5.574001 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2156560 0.6732807 midg,1,midg; midg,igrid,midg 6.6545993E-02 0.1138331 1,midg,midg; igrid,midg,midg -2.4358165E-02 1.9509645E-02 gauss-seidel spectral radius is 0.9990902 estimated iterations to convergence 262 setup time was (sec) 2.080000 now iterating at: 11:03:35 rms-change max change #iterations 10.06902 320.1155 at 10iterations 5.580561 143.6964 at 20iterations 3.078175 67.37267 at 30iterations 1.692129 38.65112 at 40iterations 0.9274789 17.65656 at 50iterations 0.5058157 11.02455 at 60iterations 0.2755516 5.413929 at 70iterations 0.1503753 2.751090 at 80iterations 8.1686541E-02 1.534048 at 90iterations 4.4388473E-02 0.9530411 at 100iterations 2.4051784E-02 0.4575195 at 110iterations 1.3074634E-02 0.3011875 at 120iterations 7.0847585E-03 0.1344872 at 130iterations 3.8400942E-03 7.3292255E-02 at 140iterations 2.0810433E-03 3.8839817E-02 at 150iterations 1.1308650E-03 2.2327423E-02 at 160iterations 6.1429094E-04 1.3492584E-02 at 170iterations 3.3683184E-04 6.7424774E-03 at 180iterations finished qdiffx linear iterations at : 11:03:51 total time elapsed so far: 18.42000 # loops : 180 mean,max change (kT/e) : 3.3683184E-04 6.7424774E-03 energy calculations done at 18.42000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 18.58000 DelPhi exited at 11:03:52 18.588u 0.506s 0:19.57 97.4% 0+0k 0+0io 0pf+0w