Tue Oct 11 08:26:15 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 Tue Oct 11 2011 at 08:26:15 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: 311 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2876 !!! WARNING: HIR 79 has a net charge of 0.5140 !!! WARNING: SEP 241 has a net charge of -0.4750 !!! WARNING: TYS 1 has a net charge of -0.3380 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 0.6601517 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): -15.30200 34.34100 ymin,ymax (A): 6.935000 55.45000 zmin,zma (A): 25.98100 79.90800 x,y,z range (A): 49.64301 48.51500 53.92700 scale (grids/A): 0.6601517 object centre (A): 9.519502 31.19250 52.94450 number of atom coordinates read : 2876 total number of charged atoms : 2720 net assigned charge : 1.701019 assigned positive charge : 437.8867 centred at (gu) : 90.00934 90.27319 89.00006 assigned negative charge : -436.1862 centred at (gu) : 90.25092 90.17126 89.00899 start vw surface at 0.1700000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 8333 nv = 96 ne = 84 npr = 59173 no. pairs analyzed = 59173 no. exposed pairs = 3515 no. arc points = 24296 no. surface atoms = 1180 nbur = 1696 mkacc time = 0.1900000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 483 mr = 4781 m= 5 mr = 66 m= 0 mr = 0 time to grow re-entrant surface = 0.2300000 no. cavity mid-points inaccessible to solvent = 13 time to turn everything in is 0.4400000 number of dielectric boundary points 3974 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2337 ## 215 charges are in solution ## iepsmp to db, and charging done at 0.5500000 number of grid points assigned charge 9935 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 7.7707965E-09 1.9391084E-09 midg,1,midg; midg,igrid,midg -1.7586220E-08 2.8422649E-08 1,midg,midg; igrid,midg,midg 5.6765774E-08 -5.1070668E-08 gauss-seidel spectral radius is 0.9881285 estimated iterations to convergence 75 setup time was (sec) 0.7300000 now iterating at: 08:26:17 rms-change max change #iterations 0.1765050 24.44826 at 10iterations 1.9855024E-02 2.503934 at 20iterations 2.2795424E-03 0.2739220 at 30iterations 3.6717541E-04 4.2030334E-02 at 40iterations 9.5754884E-05 1.1472240E-02 at 50iterations finished qdiffx linear iterations at : 08:26:20 total time elapsed so far: 4.410000 # loops : 50 mean,max change (kT/e) : 9.5754884E-05 1.1472240E-02 energy calculations done at 4.410000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.750000 DelPhi exited at 08:26:21 4.757u 0.405s 0:05.44 94.6% 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 08:26:21 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: 311 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2876 !!! WARNING: HIR 79 has a net charge of 0.5140 !!! WARNING: SEP 241 has a net charge of -0.4750 !!! WARNING: TYS 1 has a net charge of -0.3380 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 1.980455 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): -15.30200 34.34100 ymin,ymax (A): 6.935000 55.45000 zmin,zma (A): 25.98100 79.90800 x,y,z range (A): 49.64301 48.51500 53.92700 scale (grids/A): 1.980455 object centre (A): 9.519502 31.19250 52.94450 number of atom coordinates read : 2876 total number of charged atoms : 2720 net assigned charge : 1.701019 assigned positive charge : 437.8867 centred at (gu) : 90.02745 90.81894 86.99961 assigned negative charge : -436.1862 centred at (gu) : 90.75235 90.51353 87.02666 start vw surface at 0.1700000 fill in re-entrant regions at 0.3700000 boundary points on vw surface= 89862 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24296 grid for indexing accessible points = 1.400000 m= 34080 mr = 63859 m= 5761 mr = 25656 m= 444 mr = 3705 m= 9 mr = 194 m= 0 mr = 0 time to grow re-entrant surface = 0.4900000 no. cavity mid-points inaccessible to solvent = 557 time to turn everything in is 0.9300000 number of dielectric boundary points 36742 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 136 iepsmp to db, and charging done at 1.100000 number of grid points assigned charge 21466 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) : 0.6601517 object centre at (A) : 9.519502 31.19250 52.94450 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.6992487E-02 -2.3785448E-02 midg,1,midg; midg,igrid,midg -1.1254327E-02 1.6556798E-02 1,midg,midg; igrid,midg,midg 7.6548487E-02 -9.7575877E-03 gauss-seidel spectral radius is 0.9987602 estimated iterations to convergence 225 setup time was (sec) 1.300000 now iterating at: 08:26:23 rms-change max change #iterations 4.916485 234.5670 at 10iterations 2.390768 83.43193 at 20iterations 1.161139 33.45855 at 30iterations 0.5636637 15.93132 at 40iterations 0.2756387 7.762840 at 50iterations 0.1337930 3.944515 at 60iterations 6.5145902E-02 2.007755 at 70iterations 3.1699695E-02 0.8664112 at 80iterations 1.5414323E-02 0.4454613 at 90iterations 7.5492128E-03 0.2040062 at 100iterations 3.7126031E-03 0.1087036 at 110iterations 1.8581507E-03 5.5452347E-02 at 120iterations finished qdiffx linear iterations at : 08:26:32 total time elapsed so far: 10.89000 # loops : 120 mean,max change (kT/e) : 1.8581507E-03 5.5452347E-02 energy calculations done at 10.89000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.11000 DelPhi exited at 08:26:33 11.117u 0.419s 0:12.00 96.0% 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 08:26:33 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: 311 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2876 !!! WARNING: HIR 79 has a net charge of 0.5140 !!! WARNING: SEP 241 has a net charge of -0.4750 !!! WARNING: TYS 1 has a net charge of -0.3380 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 2.970682 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): -15.30200 34.34100 ymin,ymax (A): 6.935000 55.45000 zmin,zma (A): 25.98100 79.90800 x,y,z range (A): 49.64301 48.51500 53.92700 scale (grids/A): 2.970682 object centre (A): 9.519502 31.19250 52.94450 number of atom coordinates read : 2876 total number of charged atoms : 2720 net assigned charge : 1.701019 assigned positive charge : 437.8867 centred at (gu) : 90.04110 91.22820 85.49940 assigned negative charge : -436.1862 centred at (gu) : 91.12850 90.77003 85.53992 start vw surface at 0.1600000 fill in re-entrant regions at 0.7800000 boundary points on vw surface= 207388 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24296 grid for indexing accessible points = 1.400000 m= 109285 mr = 153925 m= 40712 mr = 90462 m= 10425 mr = 33237 m= 1830 mr = 7898 m= 141 mr = 1312 m= 3 mr = 78 m= 0 mr = 2 time to grow re-entrant surface = 1.530000 no. cavity mid-points inaccessible to solvent = 1838 time to turn everything in is 2.470000 number of dielectric boundary points 82870 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.630000 number of grid points assigned charge 21760 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) : 1.980455 object centre at (A) : 9.519502 31.19250 52.94450 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -4.0959031E-03 -0.3856727 midg,1,midg; midg,igrid,midg -0.1411143 0.2180187 1,midg,midg; igrid,midg,midg 0.6577815 -5.7550289E-02 gauss-seidel spectral radius is 0.9992898 estimated iterations to convergence 296 setup time was (sec) 2.870000 now iterating at: 08:26:36 rms-change max change #iterations 11.24142 408.4318 at 10iterations 6.617311 153.4839 at 20iterations 3.896615 77.21147 at 30iterations 2.284623 42.68900 at 40iterations 1.340328 23.88315 at 50iterations 0.7841702 13.78511 at 60iterations 0.4582716 8.400005 at 70iterations 0.2679726 4.524195 at 80iterations 0.1562433 2.685844 at 90iterations 9.1283396E-02 1.496031 at 100iterations 5.3290095E-02 0.8672703 at 110iterations 3.1100107E-02 0.5292549 at 120iterations 1.8163618E-02 0.3084440 at 130iterations 1.0640816E-02 0.1855798 at 140iterations 6.2624188E-03 0.1136494 at 150iterations 3.7279639E-03 6.3465595E-02 at 160iterations 2.2477561E-03 3.6163330E-02 at 170iterations 1.3830783E-03 2.4070740E-02 at 180iterations finished qdiffx linear iterations at : 08:26:56 total time elapsed so far: 22.69000 # loops : 180 mean,max change (kT/e) : 1.3830783E-03 2.4070740E-02 energy calculations done at 22.69000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 22.91000 DelPhi exited at 08:26:57 22.917u 0.458s 0:23.68 98.6% 0+0k 0+0io 0pf+0w