Sat Oct 15 13:16:13 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 Sat Oct 15 2011 at 13:16:13 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: 311 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3387 !!! WARNING: LLP 1 has a net charge of 1.7400 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.5734536 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): -10.97500 51.10500 ymin,ymax (A): -12.95700 42.65900 zmin,zma (A): 19.88900 76.33700 x,y,z range (A): 62.08000 55.61600 56.44800 scale (grids/A): 0.5734536 object centre (A): 20.06500 14.85100 48.11300 number of atom coordinates read : 3387 total number of charged atoms : 3230 net assigned charge : 5.240015 assigned positive charge : 524.9060 centred at (gu) : 90.85963 89.88957 87.71857 assigned negative charge : -519.6671 centred at (gu) : 90.75889 89.98434 87.70394 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1000000 boundary points on vw surface= 7516 nv = 96 ne = 84 npr = 65178 no. pairs analyzed = 65178 no. exposed pairs = 4598 no. arc points = 32784 no. surface atoms = 1540 nbur = 1847 mkacc time = 0.1100000 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 = 1.484000 m= 383 mr = 3731 m= 1 mr = 21 m= 0 mr = 0 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2300000 number of dielectric boundary points 4148 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3222 ## 343 charges are in solution ## iepsmp to db, and charging done at 0.2900000 number of grid points assigned charge 9385 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 9.8679132E-10 7.0628969E-10 midg,1,midg; midg,igrid,midg 2.8881928E-09 -1.0473304E-09 1,midg,midg; igrid,midg,midg -9.7085040E-10 3.6004335E-09 gauss-seidel spectral radius is 0.9843494 estimated iterations to convergence 66 setup time was (sec) 0.4200000 now iterating at: 13:16:14 rms-change max change #iterations 9.8158710E-02 19.81655 at 10iterations 7.5788000E-03 1.079000 at 20iterations 6.1591394E-04 9.7005844E-02 at 30iterations 1.2504001E-04 1.6565323E-02 at 40iterations 6.4093590E-05 8.8114738E-03 at 50iterations finished qdiffx linear iterations at : 13:16:17 total time elapsed so far: 3.410000 # loops : 50 mean,max change (kT/e) : 6.4093590E-05 8.8114738E-03 energy calculations done at 3.410000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.540000 DelPhi exited at 13:16:18 3.541u 0.211s 0:04.10 91.4% 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 15 2011 at 13:16:18 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: 311 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3387 !!! WARNING: LLP 1 has a net charge of 1.7400 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.720361 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): -10.97500 51.10500 ymin,ymax (A): -12.95700 42.65900 zmin,zma (A): 19.88900 76.33700 x,y,z range (A): 62.08000 55.61600 56.44800 scale (grids/A): 1.720361 object centre (A): 20.06500 14.85100 48.11300 number of atom coordinates read : 3387 total number of charged atoms : 3230 net assigned charge : 5.240015 assigned positive charge : 524.9060 centred at (gu) : 92.57781 89.66815 83.15509 assigned negative charge : -519.6671 centred at (gu) : 92.27640 89.95265 83.11137 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 81843 reading accessible surface arcs data from file ARCDAT no. of arc points read = 32784 grid for indexing accessible points = 1.400000 m= 27484 mr = 54284 m= 3603 mr = 18588 m= 188 mr = 1840 m= 0 mr = 44 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4000000 number of dielectric boundary points 38362 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 281 ## 2 charges are in solution ## iepsmp to db, and charging done at 0.4800000 number of grid points assigned charge 24992 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) : 0.5734536 object centre at (A) : 20.06500 14.85100 48.11300 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.8309794E-02 6.2820930E-03 midg,1,midg; midg,igrid,midg 2.4162656E-02 -8.5368678E-03 1,midg,midg; igrid,midg,midg -8.2212593E-03 4.0382185E-04 gauss-seidel spectral radius is 0.9984210 estimated iterations to convergence 200 setup time was (sec) 0.6300000 now iterating at: 13:16:18 rms-change max change #iterations 4.113605 177.0931 at 10iterations 1.817524 63.94834 at 20iterations 0.8047038 29.73750 at 30iterations 0.3561073 11.40467 at 40iterations 0.1583163 5.379015 at 50iterations 7.0428967E-02 2.328202 at 60iterations 3.1127056E-02 0.9708118 at 70iterations 1.3825140E-02 0.5540466 at 80iterations 6.1401301E-03 0.2045212 at 90iterations 2.7223439E-03 8.5613251E-02 at 100iterations 1.2102338E-03 3.9993286E-02 at 110iterations 5.3686439E-04 1.7860413E-02 at 120iterations finished qdiffx linear iterations at : 13:16:26 total time elapsed so far: 8.030000 # loops : 120 mean,max change (kT/e) : 5.3686439E-04 1.7860413E-02 energy calculations done at 8.030000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.160000 DelPhi exited at 13:16:26 8.162u 0.247s 0:08.96 93.7% 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 Sat Oct 15 2011 at 13:16:27 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 = 3387 !!! WARNING: LLP 1 has a net charge of 1.7400 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.580541 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): -10.97500 51.10500 ymin,ymax (A): -12.95700 42.65900 zmin,zma (A): 19.88900 76.33700 x,y,z range (A): 62.08000 55.61600 56.44800 scale (grids/A): 2.580541 object centre (A): 20.06500 14.85100 48.11300 number of atom coordinates read : 3387 total number of charged atoms : 3230 net assigned charge : 5.240015 assigned positive charge : 524.9060 centred at (gu) : 93.86659 89.50215 79.73241 assigned negative charge : -519.6671 centred at (gu) : 93.41460 89.92905 79.66702 start vw surface at 0.1000000 fill in re-entrant regions at 0.3400000 boundary points on vw surface= 189519 reading accessible surface arcs data from file ARCDAT no. of arc points read = 32784 grid for indexing accessible points = 1.400000 m= 91512 mr = 133128 m= 29643 mr = 71329 m= 5894 mr = 21877 m= 688 mr = 3860 m= 31 mr = 357 m= 1 mr = 6 m= 0 mr = 0 time to grow re-entrant surface = 0.5900000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.030000 number of dielectric boundary points 86731 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 13 iepsmp to db, and charging done at 1.120000 number of grid points assigned charge 25804 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) : 1.720361 object centre at (A) : 20.06500 14.85100 48.11300 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.3292440 7.7047803E-02 midg,1,midg; midg,igrid,midg 0.3899301 -0.1114166 1,midg,midg; igrid,midg,midg 8.4834747E-02 -0.4920298 gauss-seidel spectral radius is 0.9992280 estimated iterations to convergence 284 setup time was (sec) 1.280000 now iterating at: 13:16:28 rms-change max change #iterations 10.53126 365.6761 at 10iterations 6.230132 149.5673 at 20iterations 3.638402 82.02264 at 30iterations 2.113708 48.71747 at 40iterations 1.221476 32.25894 at 50iterations 0.7016333 15.17735 at 60iterations 0.4037217 7.928957 at 70iterations 0.2309060 4.725769 at 80iterations 0.1322521 2.762783 at 90iterations 7.5618975E-02 1.606924 at 100iterations 4.3131880E-02 0.8870754 at 110iterations 2.4648814E-02 0.4384460 at 120iterations 1.4024514E-02 0.2776639 at 130iterations 7.9923337E-03 0.1539841 at 140iterations 4.5494530E-03 9.1648102E-02 at 150iterations 2.5962081E-03 4.7840118E-02 at 160iterations 1.4804004E-03 3.0515194E-02 at 170iterations 8.5016398E-04 1.7175674E-02 at 180iterations finished qdiffx linear iterations at : 13:16:40 total time elapsed so far: 13.30000 # loops : 180 mean,max change (kT/e) : 8.5016398E-04 1.7175674E-02 energy calculations done at 13.30000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.43000 DelPhi exited at 13:16:41 13.434u 0.231s 0:14.08 97.0% 0+0k 0+0io 0pf+0w