Tue Oct 11 03:18:42 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 03:18:42 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: 269 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3316 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 0.5366942 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): -38.60000 21.15500 ymin,ymax (A): -4.799000 46.34300 zmin,zma (A): -70.00100 -3.669000 x,y,z range (A): 59.75500 51.14200 66.33200 scale (grids/A): 0.5366942 object centre (A): -8.722502 20.77200 -36.83500 number of atom coordinates read : 3316 total number of charged atoms : 3175 net assigned charge : -8.999975 assigned positive charge : 500.5835 centred at (gu) : 91.59030 91.05808 92.61453 assigned negative charge : -509.5847 centred at (gu) : 91.61946 90.99429 92.59318 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1000000 boundary points on vw surface= 6091 nv = 96 ne = 84 npr = 68457 no. pairs analyzed = 68457 no. exposed pairs = 4184 no. arc points = 29290 no. surface atoms = 1400 nbur = 1916 mkacc time = 0.1200000 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 = 1.596000 m= 241 mr = 3153 m= 0 mr = 10 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2300000 number of dielectric boundary points 3169 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2976 ## 415 charges are in solution ## iepsmp to db, and charging done at 0.2900000 number of grid points assigned charge 8139 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -2.6463909E-10 -5.1727789E-10 midg,1,midg; midg,igrid,midg -5.5839117E-10 -6.2749271E-11 1,midg,midg; igrid,midg,midg -1.6059327E-10 -8.0475737E-10 gauss-seidel spectral radius is 0.9821297 estimated iterations to convergence 62 setup time was (sec) 0.4100000 now iterating at: 03:18:43 rms-change max change #iterations 7.0665516E-02 11.64527 at 10iterations 4.6718922E-03 0.7460289 at 20iterations 4.1209348E-04 6.7718029E-02 at 30iterations 7.6436139E-05 1.5964031E-02 at 40iterations 2.0293637E-05 4.4600964E-03 at 50iterations finished qdiffx linear iterations at : 03:18:46 total time elapsed so far: 3.280000 # loops : 50 mean,max change (kT/e) : 2.0293637E-05 4.4600964E-03 energy calculations done at 3.280000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.410000 DelPhi exited at 03:18:46 3.410u 0.183s 0:03.87 92.7% 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 Tue Oct 11 2011 at 03:18:46 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: 269 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3316 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 1.610083 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): -38.60000 21.15500 ymin,ymax (A): -4.799000 46.34300 zmin,zma (A): -70.00100 -3.669000 x,y,z range (A): 59.75500 51.14200 66.33200 scale (grids/A): 1.610083 object centre (A): -8.722502 20.77200 -36.83500 number of atom coordinates read : 3316 total number of charged atoms : 3175 net assigned charge : -8.999975 assigned positive charge : 500.5835 centred at (gu) : 94.76989 93.17323 97.84232 assigned negative charge : -509.5847 centred at (gu) : 94.85784 92.98252 97.77894 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 67989 reading accessible surface arcs data from file ARCDAT no. of arc points read = 29290 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.512000 m= 19872 mr = 46066 m= 1790 mr = 13222 m= 37 mr = 733 m= 2 mr = 1 m= 0 mr = 0 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 212 time to turn everything in is 0.3200000 number of dielectric boundary points 29668 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 385 ## 2 charges are in solution ## iepsmp to db, and charging done at 0.4000000 number of grid points assigned charge 24185 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) : 0.5366942 object centre at (A) : -8.722502 20.77200 -36.83500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.4048522E-02 -1.5083835E-02 midg,1,midg; midg,igrid,midg -7.6349992E-03 -3.4509397E-03 1,midg,midg; igrid,midg,midg -2.5063981E-03 -4.8492942E-03 gauss-seidel spectral radius is 0.9981565 estimated iterations to convergence 185 setup time was (sec) 0.5300000 now iterating at: 03:18:47 rms-change max change #iterations 3.429679 179.2938 at 10iterations 1.418038 54.11659 at 20iterations 0.5872275 21.13737 at 30iterations 0.2428240 9.582500 at 40iterations 0.1006820 4.020441 at 50iterations 4.1610349E-02 1.474974 at 60iterations 1.7284112E-02 0.6217885 at 70iterations 7.1986620E-03 0.2544575 at 80iterations 3.0151678E-03 0.1236079 at 90iterations 1.2754747E-03 5.1185608E-02 at 100iterations 5.4694561E-04 2.0126343E-02 at 110iterations 2.4542364E-04 9.7303391E-03 at 120iterations finished qdiffx linear iterations at : 03:18:54 total time elapsed so far: 7.520000 # loops : 120 mean,max change (kT/e) : 2.4542364E-04 9.7303391E-03 energy calculations done at 7.520000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.650000 DelPhi exited at 03:18:54 7.653u 0.220s 0:08.27 95.1% 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 03:18:54 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: 269 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3316 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 2.415124 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): -38.60000 21.15500 ymin,ymax (A): -4.799000 46.34300 zmin,zma (A): -70.00100 -3.669000 x,y,z range (A): 59.75500 51.14200 66.33200 scale (grids/A): 2.415124 object centre (A): -8.722502 20.77200 -36.83500 number of atom coordinates read : 3316 total number of charged atoms : 3175 net assigned charge : -8.999975 assigned positive charge : 500.5835 centred at (gu) : 97.15446 94.75948 101.7634 assigned negative charge : -509.5847 centred at (gu) : 97.28667 94.47354 101.6684 start vw surface at 0.1000000 fill in re-entrant regions at 0.2900000 boundary points on vw surface= 158416 reading accessible surface arcs data from file ARCDAT no. of arc points read = 29290 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 70130 mr = 113223 m= 18342 mr = 54734 m= 2643 mr = 13237 m= 137 mr = 1520 m= 3 mr = 32 m= 0 mr = 0 time to grow re-entrant surface = 0.4400000 no. cavity mid-points inaccessible to solvent = 800 time to turn everything in is 0.8100000 number of dielectric boundary points 66925 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 43 iepsmp to db, and charging done at 0.8900000 number of grid points assigned charge 25347 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) : 1.610083 object centre at (A) : -8.722502 20.77200 -36.83500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.5010622 -0.4026615 midg,1,midg; midg,igrid,midg -0.1002373 -2.9057058E-02 1,midg,midg; igrid,midg,midg 9.5652221E-03 -1.1257605E-02 gauss-seidel spectral radius is 0.9991364 estimated iterations to convergence 269 setup time was (sec) 1.030000 now iterating at: 03:18:56 rms-change max change #iterations 9.027904 273.5489 at 10iterations 5.066376 141.4451 at 20iterations 2.829492 68.14724 at 30iterations 1.570520 33.36122 at 40iterations 0.8677480 18.13817 at 50iterations 0.4799025 9.460999 at 60iterations 0.2649581 5.669630 at 70iterations 0.1458463 3.004423 at 80iterations 8.0163680E-02 1.547791 at 90iterations 4.4136848E-02 0.9146767 at 100iterations 2.4326619E-02 0.4895828 at 110iterations 1.3358283E-02 0.3114548 at 120iterations 7.3475088E-03 0.1676788 at 130iterations 4.0307087E-03 8.3981931E-02 at 140iterations 2.2244572E-03 4.4152260E-02 at 150iterations 1.2281686E-03 2.7461052E-02 at 160iterations 6.8350200E-04 1.3710976E-02 at 170iterations 3.8308540E-04 7.7972412E-03 at 180iterations finished qdiffx linear iterations at : 03:19:07 total time elapsed so far: 12.19000 # loops : 180 mean,max change (kT/e) : 3.8308540E-04 7.7972412E-03 energy calculations done at 12.19000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.33000 DelPhi exited at 03:19:07 12.328u 0.207s 0:12.83 97.5% 0+0k 0+0io 0pf+0w