Sat Oct 8 21:07:02 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 Sat Oct 8 2011 at 21:07:02 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: 262 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2591 !!! WARNING: HIZ 94 has a net charge of 0.2000 !!! WARNING: HIZ 96 has a net charge of 0.2000 !!! WARNING: HIY 119 has a net charge of 0.2000 !!! WARNING: ZN5 551 has a net charge of 1.4000 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: 0.6238062 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): -31.23500 17.69000 ymin,ymax (A): -23.86000 21.78300 zmin,zma (A): -12.29600 44.77300 x,y,z range (A): 48.92500 45.64300 57.06900 scale (grids/A): 0.6238062 object centre (A): -6.772500 -1.038499 16.23850 number of atom coordinates read : 2591 total number of charged atoms : 2466 net assigned charge : 4.500007 assigned positive charge : 393.3950 centred at (gu) : 88.43429 89.58633 89.61595 assigned negative charge : -388.8955 centred at (gu) : 88.32134 89.64677 89.50675 start vw surface at 0.1400000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 6586 nv = 96 ne = 84 npr = 54014 no. pairs analyzed = 54014 no. exposed pairs = 2992 no. arc points = 21357 no. surface atoms = 1007 nbur = 1584 mkacc time = 0.1200000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 326 mr = 3682 m= 0 mr = 36 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 63 time to turn everything in is 0.2800000 number of dielectric boundary points 3194 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2173 ## 252 charges are in solution ## iepsmp to db, and charging done at 0.3900000 number of grid points assigned charge 8222 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -4.3396833E-09 1.1237171E-08 midg,1,midg; midg,igrid,midg 9.4977946E-09 -2.3847474E-10 1,midg,midg; igrid,midg,midg -6.1578085E-09 8.8897787E-09 gauss-seidel spectral radius is 0.9866863 estimated iterations to convergence 71 setup time was (sec) 0.5000000 now iterating at: 21:07:03 rms-change max change #iterations 0.1341212 19.76594 at 10iterations 1.2339326E-02 1.751877 at 20iterations 1.1607572E-03 0.1976299 at 30iterations 1.0823795E-04 1.6311646E-02 at 40iterations 1.0483370E-05 1.6851425E-03 at 50iterations finished qdiffx linear iterations at : 21:07:05 total time elapsed so far: 2.920000 # loops : 50 mean,max change (kT/e) : 1.0483370E-05 1.6851425E-03 energy calculations done at 2.920000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.090000 DelPhi exited at 21:07:06 3.094u 0.144s 0:03.51 92.0% 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 Sat Oct 8 2011 at 21:07:06 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: 262 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2591 !!! WARNING: HIZ 94 has a net charge of 0.2000 !!! WARNING: HIZ 96 has a net charge of 0.2000 !!! WARNING: HIY 119 has a net charge of 0.2000 !!! WARNING: ZN5 551 has a net charge of 1.4000 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: 1.871419 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): -31.23500 17.69000 ymin,ymax (A): -23.86000 21.78300 zmin,zma (A): -12.29600 44.77300 x,y,z range (A): 48.92500 45.64300 57.06900 scale (grids/A): 1.871419 object centre (A): -6.772500 -1.038499 16.23850 number of atom coordinates read : 2591 total number of charged atoms : 2466 net assigned charge : 4.500007 assigned positive charge : 393.3950 centred at (gu) : 85.30221 88.75858 88.84755 assigned negative charge : -388.8955 centred at (gu) : 84.96380 88.93993 88.51999 start vw surface at 0.1500000 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 71652 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21357 grid for indexing accessible points = 1.400000 m= 24742 mr = 50105 m= 3452 mr = 18377 m= 164 mr = 2056 m= 3 mr = 43 m= 0 mr = 0 time to grow re-entrant surface = 0.2200000 no. cavity mid-points inaccessible to solvent = 3867 time to turn everything in is 0.5000000 number of dielectric boundary points 29432 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 157 iepsmp to db, and charging done at 0.6100000 number of grid points assigned charge 19353 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) : 0.6238062 object centre at (A) : -6.772500 -1.038499 16.23850 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.9910060E-02 1.6868725E-02 midg,1,midg; midg,igrid,midg 1.3769711E-02 -3.0398855E-04 1,midg,midg; igrid,midg,midg -4.2376556E-03 4.1509021E-02 gauss-seidel spectral radius is 0.9985837 estimated iterations to convergence 211 setup time was (sec) 0.7600000 now iterating at: 21:07:07 rms-change max change #iterations 4.103226 209.1834 at 10iterations 1.886151 71.53914 at 20iterations 0.8705510 29.70607 at 30iterations 0.4028389 13.15105 at 40iterations 0.1863185 5.923124 at 50iterations 8.5587405E-02 3.207727 at 60iterations 3.9747730E-02 1.330013 at 70iterations 1.8367399E-02 0.6293297 at 80iterations 8.4675606E-03 0.2935982 at 90iterations 3.9101611E-03 0.1275253 at 100iterations 1.8069975E-03 5.8205605E-02 at 110iterations 8.3284057E-04 2.5897980E-02 at 120iterations finished qdiffx linear iterations at : 21:07:13 total time elapsed so far: 6.730000 # loops : 120 mean,max change (kT/e) : 8.3284057E-04 2.5897980E-02 energy calculations done at 6.730000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 6.900000 DelPhi exited at 21:07:13 6.906u 0.162s 0:07.35 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 Sat Oct 8 2011 at 21:07:13 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: 262 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2591 !!! WARNING: HIZ 94 has a net charge of 0.2000 !!! WARNING: HIZ 96 has a net charge of 0.2000 !!! WARNING: HIY 119 has a net charge of 0.2000 !!! WARNING: ZN5 551 has a net charge of 1.4000 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: 2.807128 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): -31.23500 17.69000 ymin,ymax (A): -23.86000 21.78300 zmin,zma (A): -12.29600 44.77300 x,y,z range (A): 48.92500 45.64300 57.06900 scale (grids/A): 2.807128 object centre (A): -6.772500 -1.038499 16.23850 number of atom coordinates read : 2591 total number of charged atoms : 2466 net assigned charge : 4.500007 assigned positive charge : 393.3950 centred at (gu) : 82.95329 88.13772 88.27117 assigned negative charge : -388.8955 centred at (gu) : 82.44565 88.40979 87.78000 start vw surface at 0.1500000 fill in re-entrant regions at 0.4300000 boundary points on vw surface= 165780 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21357 grid for indexing accessible points = 1.400000 m= 82105 mr = 121329 m= 27689 mr = 67627 m= 6082 mr = 22244 m= 733 mr = 4432 m= 29 mr = 436 m= 1 mr = 6 m= 0 mr = 0 time to grow re-entrant surface = 0.6799999 no. cavity mid-points inaccessible to solvent = 12373 time to turn everything in is 1.190000 number of dielectric boundary points 66345 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.310000 number of grid points assigned charge 19727 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) : 1.871419 object centre at (A) : -6.772500 -1.038499 16.23850 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1919908 0.1522026 midg,1,midg; midg,igrid,midg 0.1558750 -5.9263529E-03 1,midg,midg; igrid,midg,midg -4.0471680E-02 0.5419189 gauss-seidel spectral radius is 0.9992396 estimated iterations to convergence 286 setup time was (sec) 1.460000 now iterating at: 21:07:15 rms-change max change #iterations 9.566999 318.3383 at 10iterations 5.513193 137.4926 at 20iterations 3.157019 66.77974 at 30iterations 1.800986 39.28176 at 40iterations 1.027679 22.88440 at 50iterations 0.5865602 12.54026 at 60iterations 0.3350922 7.016500 at 70iterations 0.1911643 3.412065 at 80iterations 0.1088589 2.100060 at 90iterations 6.2099539E-02 1.236583 at 100iterations 3.5347693E-02 0.7217731 at 110iterations 2.0127621E-02 0.3555613 at 120iterations 1.1478341E-02 0.2254081 at 130iterations 6.5364116E-03 0.1202936 at 140iterations 3.7288228E-03 6.6436768E-02 at 150iterations 2.1224604E-03 4.0465355E-02 at 160iterations 1.2077314E-03 2.3353577E-02 at 170iterations 6.8882696E-04 1.3237953E-02 at 180iterations finished qdiffx linear iterations at : 21:07:24 total time elapsed so far: 10.81000 # loops : 180 mean,max change (kT/e) : 6.8882696E-04 1.3237953E-02 energy calculations done at 10.81000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.97000 DelPhi exited at 21:07:25 10.972u 0.186s 0:11.44 97.4% 0+0k 0+0io 0pf+0w