Sun Oct 9 00:16:17 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 00:16:17 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: 315 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3390 !!! WARNING: HIT 81 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= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 0.5543530 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): -48.10000 8.063000 ymin,ymax (A): 175.1130 239.3320 zmin,zma (A): 78.26000 141.9110 x,y,z range (A): 56.16300 64.21901 63.65101 scale (grids/A): 0.5543530 object centre (A): -20.01850 207.2225 110.0855 number of atom coordinates read : 3390 total number of charged atoms : 3246 net assigned charge : 14.51402 assigned positive charge : 506.8964 centred at (gu) : 89.56881 90.25983 90.71102 assigned negative charge : -492.3841 centred at (gu) : 89.41861 90.26956 90.81734 start vw surface at 0.1600000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 7111 nv = 96 ne = 84 npr = 64698 no. pairs analyzed = 64698 no. exposed pairs = 4615 no. arc points = 33722 no. surface atoms = 1522 nbur = 1868 mkacc time = 0.1400000 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 = 1.540000 m= 310 mr = 3500 m= 3 mr = 12 m= 0 mr = 0 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3300000 number of dielectric boundary points 3912 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3390 ## 439 charges are in solution ## iepsmp to db, and charging done at 0.4500000 number of grid points assigned charge 9139 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.9518915E-09 2.1036828E-10 midg,1,midg; midg,igrid,midg 1.2816646E-09 1.2421429E-09 1,midg,midg; igrid,midg,midg -3.0437819E-10 2.4702858E-09 gauss-seidel spectral radius is 0.9832667 estimated iterations to convergence 64 setup time was (sec) 0.5600000 now iterating at: 00:16:18 rms-change max change #iterations 8.8428959E-02 12.95312 at 10iterations 6.1054691E-03 0.9515686 at 20iterations 4.2924267E-04 6.9068909E-02 at 30iterations 3.5300931E-05 5.7487488E-03 at 40iterations 4.2947427E-06 4.7802925E-04 at 50iterations finished qdiffx linear iterations at : 00:16:20 total time elapsed so far: 3.010000 # loops : 50 mean,max change (kT/e) : 4.2947427E-06 4.7802925E-04 energy calculations done at 3.010000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.180000 DelPhi exited at 00:16:21 3.187u 0.163s 0:03.64 91.7% 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 Sun Oct 9 2011 at 00:16:21 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: 315 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3390 !!! WARNING: HIT 81 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= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 1.663059 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): -48.10000 8.063000 ymin,ymax (A): 175.1130 239.3320 zmin,zma (A): 78.26000 141.9110 x,y,z range (A): 56.16300 64.21901 63.65101 scale (grids/A): 1.663059 object centre (A): -20.01850 207.2225 110.0855 number of atom coordinates read : 3390 total number of charged atoms : 3246 net assigned charge : 14.51402 assigned positive charge : 506.8964 centred at (gu) : 88.70551 90.77845 92.13210 assigned negative charge : -492.3841 centred at (gu) : 88.25550 90.80834 92.45162 start vw surface at 0.1700000 fill in re-entrant regions at 0.2600000 boundary points on vw surface= 78560 reading accessible surface arcs data from file ARCDAT no. of arc points read = 33722 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 24956 mr = 51772 m= 2901 mr = 16982 m= 77 mr = 1391 m= 2 mr = 4 m= 0 mr = 0 time to grow re-entrant surface = 0.2400000 no. cavity mid-points inaccessible to solvent = 42 time to turn everything in is 0.5400000 number of dielectric boundary points 36347 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 393 ## 4 charges are in solution ## iepsmp to db, and charging done at 0.6600000 number of grid points assigned charge 24935 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) : 0.5543530 object centre at (A) : -20.01850 207.2225 110.0855 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 8.0397828E-03 -1.5098011E-02 midg,1,midg; midg,igrid,midg 2.7775496E-02 2.7936986E-02 1,midg,midg; igrid,midg,midg -1.1719769E-02 2.0348245E-02 gauss-seidel spectral radius is 0.9983191 estimated iterations to convergence 194 setup time was (sec) 0.8100000 now iterating at: 00:16:22 rms-change max change #iterations 3.712350 204.2814 at 10iterations 1.585346 71.05205 at 20iterations 0.6809113 22.81110 at 30iterations 0.2923843 10.16042 at 40iterations 0.1258356 3.927801 at 50iterations 5.3920604E-02 1.768182 at 60iterations 2.3257792E-02 0.8423529 at 70iterations 1.0036723E-02 0.3231425 at 80iterations 4.2938581E-03 0.1355238 at 90iterations 1.8604690E-03 6.4882278E-02 at 100iterations 8.0287154E-04 2.5932789E-02 at 110iterations 3.4543159E-04 1.1421442E-02 at 120iterations finished qdiffx linear iterations at : 00:16:28 total time elapsed so far: 6.940000 # loops : 120 mean,max change (kT/e) : 3.4543159E-04 1.1421442E-02 energy calculations done at 6.940000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.110000 DelPhi exited at 00:16:29 7.114u 0.184s 0:07.62 95.6% 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 Sun Oct 9 2011 at 00:16:29 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: 315 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3390 !!! WARNING: HIT 81 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= 0.1000000 grid size : 179 scale,in grids/A, set to be: 2.494588 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): -48.10000 8.063000 ymin,ymax (A): 175.1130 239.3320 zmin,zma (A): 78.26000 141.9110 x,y,z range (A): 56.16300 64.21901 63.65101 scale (grids/A): 2.494588 object centre (A): -20.01850 207.2225 110.0855 number of atom coordinates read : 3390 total number of charged atoms : 3246 net assigned charge : 14.51402 assigned positive charge : 506.8964 centred at (gu) : 88.05829 91.16741 93.19792 assigned negative charge : -492.3841 centred at (gu) : 87.38327 91.21245 93.67759 start vw surface at 0.1800000 fill in re-entrant regions at 0.4500000 boundary points on vw surface= 182071 reading accessible surface arcs data from file ARCDAT no. of arc points read = 33722 grid for indexing accessible points = 1.400000 m= 84385 mr = 126918 m= 25738 mr = 65953 m= 4630 mr = 19194 m= 336 mr = 2980 m= 6 mr = 118 m= 0 mr = 0 time to grow re-entrant surface = 0.7499999 no. cavity mid-points inaccessible to solvent = 120 time to turn everything in is 1.330000 number of dielectric boundary points 82003 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 14 iepsmp to db, and charging done at 1.470000 number of grid points assigned charge 25946 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) : 1.663059 object centre at (A) : -20.01850 207.2225 110.0855 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.2176659 -0.1573654 midg,1,midg; midg,igrid,midg 0.2692073 0.5064749 1,midg,midg; igrid,midg,midg -0.2788813 0.2454848 gauss-seidel spectral radius is 0.9992024 estimated iterations to convergence 280 setup time was (sec) 1.630000 now iterating at: 00:16:30 rms-change max change #iterations 9.571786 357.2203 at 10iterations 5.565418 131.3094 at 20iterations 3.206201 73.23589 at 30iterations 1.840605 39.66837 at 40iterations 1.048298 21.94611 at 50iterations 0.5966277 12.07199 at 60iterations 0.3383984 6.870948 at 70iterations 0.1915720 3.660373 at 80iterations 0.1082535 2.090217 at 90iterations 6.1139502E-02 1.254135 at 100iterations 3.4462724E-02 0.6832008 at 110iterations 1.9465612E-02 0.3960457 at 120iterations 1.0946699E-02 0.2183776 at 130iterations 6.1589251E-03 0.1179848 at 140iterations 3.4698374E-03 6.7340851E-02 at 150iterations 1.9497180E-03 3.7865162E-02 at 160iterations 1.0995052E-03 2.0328522E-02 at 170iterations 6.1900850E-04 1.1594772E-02 at 180iterations finished qdiffx linear iterations at : 00:16:40 total time elapsed so far: 11.43000 # loops : 180 mean,max change (kT/e) : 6.1900850E-04 1.1594772E-02 energy calculations done at 11.43000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.61000 DelPhi exited at 00:16:41 11.612u 0.208s 0:12.10 97.6% 0+0k 0+0io 0pf+0w