Sun Oct 9 09:01:17 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+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 Sun Oct 9 2011 at 09:01:18 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: 271 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5837 !!! WARNING: HIR 701 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= 0.1500000 grid size : 179 scale,in grids/A, set to be: 0.4968112 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): -19.18900 52.46800 ymin,ymax (A): -66.60400 -3.063000 zmin,zma (A): -14.49200 50.55700 x,y,z range (A): 71.65700 63.54100 65.04900 scale (grids/A): 0.4968112 object centre (A): 16.63950 -34.83350 18.03250 number of atom coordinates read : 5837 total number of charged atoms : 5669 net assigned charge : 0.5140426 assigned positive charge : 882.6666 centred at (gu) : 90.33193 90.20135 89.00954 assigned negative charge : -882.1598 centred at (gu) : 90.47958 90.18495 89.00839 start vw surface at 0.2100000 fill in re-entrant regions at 0.2200000 boundary points on vw surface= 8859 nv = 96 ne = 84 npr = 118879 no. pairs analyzed = 118879 no. exposed pairs = 7173 no. arc points = 49753 no. surface atoms = 2407 nbur = 3430 mkacc time = 0.2500000 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 = 1.708000 m= 295 mr = 4504 m= 1 mr = 5 m= 0 mr = 0 time to grow re-entrant surface = 0.2700000 no. cavity mid-points inaccessible to solvent = 5 time to turn everything in is 0.5100000 number of dielectric boundary points 4646 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4863 ## 760 charges are in solution ## iepsmp to db, and charging done at 0.6000000 number of grid points assigned charge 12168 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 3.8257045E-12 5.3393449E-12 midg,1,midg; midg,igrid,midg -2.2469880E-11 3.5436907E-11 1,midg,midg; igrid,midg,midg 2.3540314E-10 -2.8305011E-10 gauss-seidel spectral radius is 0.9793563 estimated iterations to convergence 58 setup time was (sec) 0.7200000 now iterating at: 09:01:18 rms-change max change #iterations 6.7057572E-02 10.40284 at 10iterations 3.6608458E-03 0.4832230 at 20iterations 3.6806485E-04 8.0375671E-02 at 30iterations 8.8457251E-05 1.9767761E-02 at 40iterations 2.6131287E-05 5.3291321E-03 at 50iterations finished qdiffx linear iterations at : 09:01:21 total time elapsed so far: 3.270000 # loops : 50 mean,max change (kT/e) : 2.6131287E-05 5.3291321E-03 energy calculations done at 3.270000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.450000 DelPhi exited at 09:01:21 3.457u 0.151s 0:03.89 92.5% 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 Sun Oct 9 2011 at 09:01:21 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: 271 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5837 !!! WARNING: HIR 701 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= 0.1800000 grid size : 179 scale,in grids/A, set to be: 1.490434 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): -19.18900 52.46800 ymin,ymax (A): -66.60400 -3.063000 zmin,zma (A): -14.49200 50.55700 x,y,z range (A): 71.65700 63.54100 65.04900 scale (grids/A): 1.490434 object centre (A): 16.63950 -34.83350 18.03250 number of atom coordinates read : 5837 total number of charged atoms : 5669 net assigned charge : 0.5140426 assigned positive charge : 882.6666 centred at (gu) : 90.99397 90.60214 87.02660 assigned negative charge : -882.1598 centred at (gu) : 91.43835 90.55470 87.02457 start vw surface at 0.2400000 fill in re-entrant regions at 0.3500000 boundary points on vw surface= 101232 reading accessible surface arcs data from file ARCDAT no. of arc points read = 49753 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.596000 m= 27328 mr = 69087 m= 2017 mr = 17536 m= 34 mr = 764 m= 0 mr = 2 time to grow re-entrant surface = 0.3000000 no. cavity mid-points inaccessible to solvent = 1527 time to turn everything in is 0.7000000 number of dielectric boundary points 43222 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 731 ## 7 charges are in solution ## iepsmp to db, and charging done at 0.8000000 number of grid points assigned charge 42158 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) : 0.4968112 object centre at (A) : 16.63950 -34.83350 18.03250 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -5.1453449E-03 -9.7172195E-03 midg,1,midg; midg,igrid,midg 1.6408075E-03 9.2446171E-03 1,midg,midg; igrid,midg,midg 2.7490154E-02 -1.6011594E-02 gauss-seidel spectral radius is 0.9980887 estimated iterations to convergence 182 setup time was (sec) 0.9600000 now iterating at: 09:01:23 rms-change max change #iterations 3.993711 157.6726 at 10iterations 1.633049 53.26247 at 20iterations 0.6648849 19.72951 at 30iterations 0.2712454 8.816080 at 40iterations 0.1110368 3.561413 at 50iterations 4.5336954E-02 1.311135 at 60iterations 1.8519336E-02 0.6008377 at 70iterations 7.5935386E-03 0.2310181 at 80iterations 3.1143525E-03 9.6695900E-02 at 90iterations 1.2898899E-03 4.0088654E-02 at 100iterations 5.4032262E-04 1.7706871E-02 at 110iterations 2.3238789E-04 7.0800781E-03 at 120iterations finished qdiffx linear iterations at : 09:01:30 total time elapsed so far: 7.970000 # loops : 120 mean,max change (kT/e) : 2.3238789E-04 7.0800781E-03 energy calculations done at 7.970000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.170000 DelPhi exited at 09:01:30 8.170u 0.194s 0:08.68 96.3% 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 Sun Oct 9 2011 at 09:01:30 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: 271 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5837 !!! WARNING: HIR 701 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= 0.1500000 grid size : 179 scale,in grids/A, set to be: 2.235651 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): -19.18900 52.46800 ymin,ymax (A): -66.60400 -3.063000 zmin,zma (A): -14.49200 50.55700 x,y,z range (A): 71.65700 63.54100 65.04900 scale (grids/A): 2.235651 object centre (A): 16.63950 -34.83350 18.03250 number of atom coordinates read : 5837 total number of charged atoms : 5669 net assigned charge : 0.5140426 assigned positive charge : 882.6666 centred at (gu) : 91.49043 90.90300 85.53934 assigned negative charge : -882.1598 centred at (gu) : 92.15739 90.83199 85.53674 start vw surface at 0.2200000 fill in re-entrant regions at 0.5500000 boundary points on vw surface= 236524 reading accessible surface arcs data from file ARCDAT no. of arc points read = 49753 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.596000 m= 100504 mr = 170710 m= 23141 mr = 77037 m= 2757 mr = 16101 m= 114 mr = 1580 m= 1 mr = 31 m= 0 mr = 0 time to grow re-entrant surface = 0.9400001 no. cavity mid-points inaccessible to solvent = 4954 time to turn everything in is 1.600000 number of dielectric boundary points 97582 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 107 iepsmp to db, and charging done at 1.730000 number of grid points assigned charge 45160 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) : 1.490434 object centre at (A) : 16.63950 -34.83350 18.03250 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.2382977 -0.2805034 midg,1,midg; midg,igrid,midg 3.6290016E-02 0.2182264 1,midg,midg; igrid,midg,midg 0.7907357 -0.4447219 gauss-seidel spectral radius is 0.9991828 estimated iterations to convergence 276 setup time was (sec) 1.880000 now iterating at: 09:01:32 rms-change max change #iterations 11.11443 299.0341 at 10iterations 6.447965 138.2294 at 20iterations 3.709694 93.30348 at 30iterations 2.129766 46.46967 at 40iterations 1.215926 26.96761 at 50iterations 0.6907715 13.20034 at 60iterations 0.3924099 8.778134 at 70iterations 0.2225907 4.340439 at 80iterations 0.1257260 2.615754 at 90iterations 7.1051478E-02 1.384542 at 100iterations 4.0069737E-02 0.7321892 at 110iterations 2.2573883E-02 0.4252205 at 120iterations 1.2742749E-02 0.2650499 at 130iterations 7.1617700E-03 0.1265526 at 140iterations 4.0468914E-03 7.3062897E-02 at 150iterations 2.2770891E-03 4.0756226E-02 at 160iterations 1.2851554E-03 2.2935867E-02 at 170iterations 7.2818151E-04 1.2664795E-02 at 180iterations finished qdiffx linear iterations at : 09:01:43 total time elapsed so far: 12.53000 # loops : 180 mean,max change (kT/e) : 7.2818151E-04 1.2664795E-02 energy calculations done at 12.53000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.70000 DelPhi exited at 09:01:43 12.705u 0.168s 0:13.18 97.5% 0+0k 0+0io 0pf+0w