Sun Oct 9 14:15:50 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+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 Sun Oct 9 2011 at 14:15:50 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2702 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: 0.5721265 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): 2.6999950E-02 52.11900 ymin,ymax (A): -9.943000 39.95800 zmin,zma (A): -15.37000 46.85400 x,y,z range (A): 52.09200 49.90100 62.22400 scale (grids/A): 0.5721265 object centre (A): 26.07300 15.00750 15.74200 number of atom coordinates read : 2702 total number of charged atoms : 2562 net assigned charge : 7.000018 assigned positive charge : 408.5374 centred at (gu) : 89.59760 90.51186 88.46195 assigned negative charge : -401.5385 centred at (gu) : 89.55991 90.41354 88.49140 start vw surface at 0.1600000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 5826 nv = 96 ne = 84 npr = 53129 no. pairs analyzed = 53129 no. exposed pairs = 3550 no. arc points = 24948 no. surface atoms = 1195 nbur = 1507 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 = 1.512000 m= 264 mr = 2907 m= 1 mr = 10 m= 0 mr = 0 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3000000 number of dielectric boundary points 3174 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2591 ## 308 charges are in solution ## iepsmp to db, and charging done at 0.3900000 number of grid points assigned charge 7450 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.2815250E-09 4.9391458E-10 midg,1,midg; midg,igrid,midg -3.2271116E-10 2.9597962E-09 1,midg,midg; igrid,midg,midg 6.1797345E-10 1.5606182E-09 gauss-seidel spectral radius is 0.9842163 estimated iterations to convergence 65 setup time was (sec) 0.5000000 now iterating at: 14:15:51 rms-change max change #iterations 8.7029539E-02 14.77780 at 10iterations 6.6567333E-03 1.301979 at 20iterations 4.8945274E-04 7.8393936E-02 at 30iterations 3.8670023E-05 5.8517456E-03 at 40iterations 3.3394153E-06 5.6457520E-04 at 50iterations finished qdiffx linear iterations at : 14:15:53 total time elapsed so far: 2.900000 # loops : 50 mean,max change (kT/e) : 3.3394153E-06 5.6457520E-04 energy calculations done at 2.900000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.070000 DelPhi exited at 14:15:54 3.076u 0.140s 0:03.49 91.9% 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 14:15:54 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2702 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1400000 grid size : 179 scale,in grids/A, set to be: 1.716380 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): 2.6999950E-02 52.11900 ymin,ymax (A): -9.943000 39.95800 zmin,zma (A): -15.37000 46.85400 x,y,z range (A): 52.09200 49.90100 62.22400 scale (grids/A): 1.716380 object centre (A): 26.07300 15.00750 15.74200 number of atom coordinates read : 2702 total number of charged atoms : 2562 net assigned charge : 7.000018 assigned positive charge : 408.5374 centred at (gu) : 88.79224 91.53514 85.38503 assigned negative charge : -401.5385 centred at (gu) : 88.67933 91.24058 85.47409 start vw surface at 0.2400000 fill in re-entrant regions at 0.3100000 boundary points on vw surface= 63510 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24948 grid for indexing accessible points = 1.400000 m= 20320 mr = 42208 m= 2327 mr = 13669 m= 92 mr = 1134 m= 3 mr = 14 m= 0 mr = 0 time to grow re-entrant surface = 0.2000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5400000 number of dielectric boundary points 29227 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 291 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.6600000 number of grid points assigned charge 19834 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) : 0.5721265 object centre at (A) : 26.07300 15.00750 15.74200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 6.4672805E-02 1.1526489E-02 midg,1,midg; midg,igrid,midg 2.0808401E-04 5.1015280E-03 1,midg,midg; igrid,midg,midg -1.0295426E-02 -1.1077698E-03 gauss-seidel spectral radius is 0.9983430 estimated iterations to convergence 195 setup time was (sec) 0.8100000 now iterating at: 14:15:55 rms-change max change #iterations 3.509468 176.5192 at 10iterations 1.514592 52.50636 at 20iterations 0.6570163 24.50331 at 30iterations 0.2846967 11.35992 at 40iterations 0.1230699 4.372000 at 50iterations 5.3424660E-02 1.844719 at 60iterations 2.3112688E-02 0.8051138 at 70iterations 1.0029797E-02 0.3471655 at 80iterations 4.3696151E-03 0.1517792 at 90iterations 1.8910244E-03 6.4674377E-02 at 100iterations 8.1973785E-04 2.6727676E-02 at 110iterations 3.5760392E-04 1.2995720E-02 at 120iterations finished qdiffx linear iterations at : 14:16:00 total time elapsed so far: 6.630000 # loops : 120 mean,max change (kT/e) : 3.5760392E-04 1.2995720E-02 energy calculations done at 6.630000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 6.790000 DelPhi exited at 14:16:01 6.796u 0.164s 0:07.27 95.5% 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 14:16:01 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2702 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1200000 grid size : 179 scale,in grids/A, set to be: 2.574569 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): 2.6999950E-02 52.11900 ymin,ymax (A): -9.943000 39.95800 zmin,zma (A): -15.37000 46.85400 x,y,z range (A): 52.09200 49.90100 62.22400 scale (grids/A): 2.574569 object centre (A): 26.07300 15.00750 15.74200 number of atom coordinates read : 2702 total number of charged atoms : 2562 net assigned charge : 7.000018 assigned positive charge : 408.5374 centred at (gu) : 88.18805 92.30250 83.07738 assigned negative charge : -401.5385 centred at (gu) : 88.01891 91.86070 83.21097 start vw surface at 0.2000000 fill in re-entrant regions at 0.4300000 boundary points on vw surface= 147459 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24948 grid for indexing accessible points = 1.400000 m= 68645 mr = 103661 m= 20818 mr = 53419 m= 3753 mr = 15497 m= 363 mr = 2350 m= 11 mr = 159 m= 0 mr = 0 time to grow re-entrant surface = 0.6000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.130000 number of dielectric boundary points 65963 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 13 iepsmp to db, and charging done at 1.260000 number of grid points assigned charge 20479 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) : 1.716380 object centre at (A) : 26.07300 15.00750 15.74200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.018821 0.1707926 midg,1,midg; midg,igrid,midg -9.4745746E-03 1.4820103E-02 1,midg,midg; igrid,midg,midg -0.1200174 -2.3888953E-02 gauss-seidel spectral radius is 0.9991826 estimated iterations to convergence 276 setup time was (sec) 1.410000 now iterating at: 14:16:03 rms-change max change #iterations 8.877465 263.3877 at 10iterations 5.129467 131.3230 at 20iterations 2.939832 77.49187 at 30iterations 1.670162 37.10868 at 40iterations 0.9495014 21.31474 at 50iterations 0.5354095 13.03174 at 60iterations 0.3022228 6.185265 at 70iterations 0.1696008 3.806438 at 80iterations 9.5307402E-02 1.957409 at 90iterations 5.3477816E-02 1.240271 at 100iterations 3.0061144E-02 0.6353245 at 110iterations 1.6824473E-02 0.3570623 at 120iterations 9.4322748E-03 0.1960087 at 130iterations 5.2838577E-03 0.1100998 at 140iterations 2.9651849E-03 6.1552048E-02 at 150iterations 1.6641795E-03 3.3866882E-02 at 160iterations 9.3521219E-04 2.0153046E-02 at 170iterations 5.2692054E-04 1.0499954E-02 at 180iterations finished qdiffx linear iterations at : 14:16:12 total time elapsed so far: 10.61000 # loops : 180 mean,max change (kT/e) : 5.2692054E-04 1.0499954E-02 energy calculations done at 10.61000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.78000 DelPhi exited at 14:16:12 10.787u 0.190s 0:11.25 97.5% 0+0k 0+0io 0pf+0w