Mon Oct 10 13:55:50 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 Mon Oct 10 2011 at 13:55:50 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: 304 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3162 !!! WARNING: HIT 88 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= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.5615053 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): -47.04200 7.225000 ymin,ymax (A): 175.5460 237.0430 zmin,zma (A): 78.41500 141.8160 x,y,z range (A): 54.26700 61.49701 63.40101 scale (grids/A): 0.5615053 object centre (A): -19.90850 206.2945 110.1155 number of atom coordinates read : 3162 total number of charged atoms : 3023 net assigned charge : 15.51402 assigned positive charge : 468.4747 centred at (gu) : 90.32455 89.49386 90.27412 assigned negative charge : -452.9624 centred at (gu) : 90.25342 89.41448 90.39485 start vw surface at 0.1100000 fill in re-entrant regions at 0.1200000 boundary points on vw surface= 6855 nv = 96 ne = 84 npr = 60450 no. pairs analyzed = 60450 no. exposed pairs = 4409 no. arc points = 31636 no. surface atoms = 1455 nbur = 1707 mkacc time = 0.1000000 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 = 1.512000 m= 301 mr = 3331 m= 2 mr = 13 m= 0 mr = 0 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 15 time to turn everything in is 0.2400000 number of dielectric boundary points 3814 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3244 ## 373 charges are in solution ## iepsmp to db, and charging done at 0.3100000 number of grid points assigned charge 8730 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.9698786E-09 3.0834027E-10 midg,1,midg; midg,igrid,midg 8.9299690E-10 2.3857019E-09 1,midg,midg; igrid,midg,midg 8.3627016E-10 2.8019955E-09 gauss-seidel spectral radius is 0.9836697 estimated iterations to convergence 64 setup time was (sec) 0.4300000 now iterating at: 13:55:50 rms-change max change #iterations 8.4767036E-02 14.77424 at 10iterations 5.9007546E-03 0.9792497 at 20iterations 4.6337154E-04 6.9276333E-02 at 30iterations 4.5912850E-05 6.7787170E-03 at 40iterations 7.2165399E-06 1.0528564E-03 at 50iterations finished qdiffx linear iterations at : 13:55:53 total time elapsed so far: 3.350000 # loops : 50 mean,max change (kT/e) : 7.2165399E-06 1.0528564E-03 energy calculations done at 3.350000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.480000 DelPhi exited at 13:55:54 3.483u 0.212s 0:04.13 89.3% 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 Mon Oct 10 2011 at 13:55:54 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: 304 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3162 !!! WARNING: HIT 88 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= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.684516 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): -47.04200 7.225000 ymin,ymax (A): 175.5460 237.0430 zmin,zma (A): 78.41500 141.8160 x,y,z range (A): 54.26700 61.49701 63.40101 scale (grids/A): 1.684516 object centre (A): -19.90850 206.2945 110.1155 number of atom coordinates read : 3162 total number of charged atoms : 3023 net assigned charge : 15.51402 assigned positive charge : 468.4747 centred at (gu) : 90.97262 88.48067 90.82140 assigned negative charge : -452.9624 centred at (gu) : 90.76003 88.24297 91.18429 start vw surface at 0.1000000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 74793 reading accessible surface arcs data from file ARCDAT no. of arc points read = 31636 grid for indexing accessible points = 1.400000 m= 23698 mr = 48863 m= 2708 mr = 15777 m= 85 mr = 1245 m= 2 mr = 10 m= 0 mr = 0 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 1176 time to turn everything in is 0.3700000 number of dielectric boundary points 35391 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 338 ## 3 charges are in solution ## iepsmp to db, and charging done at 0.4400000 number of grid points assigned charge 23285 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) : 0.5615053 object centre at (A) : -19.90850 206.2945 110.1155 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 9.5334155E-03 5.6255027E-03 midg,1,midg; midg,igrid,midg 5.0496473E-03 2.7730368E-02 1,midg,midg; igrid,midg,midg 9.0506002E-03 1.7413909E-02 gauss-seidel spectral radius is 0.9983443 estimated iterations to convergence 195 setup time was (sec) 0.5800000 now iterating at: 13:55:55 rms-change max change #iterations 3.639864 167.4261 at 10iterations 1.566520 54.91713 at 20iterations 0.6750300 23.85916 at 30iterations 0.2923357 10.25490 at 40iterations 0.1260550 5.153217 at 50iterations 5.4440238E-02 1.838466 at 60iterations 2.3594946E-02 0.8051248 at 70iterations 1.0222430E-02 0.3420043 at 80iterations 4.4327853E-03 0.1561470 at 90iterations 1.9177945E-03 7.7562332E-02 at 100iterations 8.3394180E-04 3.0246735E-02 at 110iterations 3.6288178E-04 1.1947513E-02 at 120iterations finished qdiffx linear iterations at : 13:56:02 total time elapsed so far: 7.790000 # loops : 120 mean,max change (kT/e) : 3.6288178E-04 1.1947513E-02 energy calculations done at 7.790000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.940000 DelPhi exited at 13:56:03 7.939u 0.216s 0:08.79 92.6% 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 Mon Oct 10 2011 at 13:56:03 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: 304 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3162 !!! WARNING: HIT 88 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= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 2.526774 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): -47.04200 7.225000 ymin,ymax (A): 175.5460 237.0430 zmin,zma (A): 78.41500 141.8160 x,y,z range (A): 54.26700 61.49701 63.40101 scale (grids/A): 2.526774 object centre (A): -19.90850 206.2945 110.1155 number of atom coordinates read : 3162 total number of charged atoms : 3023 net assigned charge : 15.51402 assigned positive charge : 468.4747 centred at (gu) : 91.45872 87.72079 91.23172 assigned negative charge : -452.9624 centred at (gu) : 91.14012 87.36459 91.77637 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.3100000 boundary points on vw surface= 173322 reading accessible surface arcs data from file ARCDAT no. of arc points read = 31636 grid for indexing accessible points = 1.400000 m= 80295 mr = 120122 m= 24072 mr = 61988 m= 4244 mr = 17571 m= 316 mr = 2650 m= 4 mr = 130 m= 0 mr = 0 time to grow re-entrant surface = 0.5200000 no. cavity mid-points inaccessible to solvent = 4307 time to turn everything in is 0.9300000 number of dielectric boundary points 79792 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 18 iepsmp to db, and charging done at 1.050000 number of grid points assigned charge 24174 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) : 1.684516 object centre at (A) : -19.90850 206.2945 110.1155 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1935001 9.9625699E-02 midg,1,midg; midg,igrid,midg -0.2621264 0.4238290 1,midg,midg; igrid,midg,midg 0.1347876 0.1836060 gauss-seidel spectral radius is 0.9992059 estimated iterations to convergence 280 setup time was (sec) 1.210000 now iterating at: 13:56:04 rms-change max change #iterations 9.277055 303.8578 at 10iterations 5.378221 142.5738 at 20iterations 3.089142 70.23415 at 30iterations 1.768331 39.00545 at 40iterations 1.009851 21.48610 at 50iterations 0.5748886 12.37978 at 60iterations 0.3255851 6.838021 at 70iterations 0.1844838 3.756335 at 80iterations 0.1042608 2.306887 at 90iterations 5.8985781E-02 1.148113 at 100iterations 3.3288173E-02 0.6619301 at 110iterations 1.8766530E-02 0.3905258 at 120iterations 1.0556769E-02 0.1915741 at 130iterations 5.9586917E-03 0.1182747 at 140iterations 3.3603208E-03 6.0554504E-02 at 150iterations 1.8899044E-03 3.9739609E-02 at 160iterations 1.0646239E-03 2.0294189E-02 at 170iterations 6.0000643E-04 1.1551380E-02 at 180iterations finished qdiffx linear iterations at : 13:56:16 total time elapsed so far: 13.15000 # loops : 180 mean,max change (kT/e) : 6.0000643E-04 1.1551380E-02 energy calculations done at 13.15000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.30000 DelPhi exited at 13:56:17 13.297u 0.281s 0:13.93 97.4% 0+0k 0+0io 0pf+0w