Wed Dec 21 14:20:56 PST 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 Wed Dec 21 2011 at 14:20:57 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: 252 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1918 !!! WARNING: LYS 7 has a net charge of 0.0730 !!! WARNING: LYS 14 has a net charge of 0.0730 !!! WARNING: ARG 41 has a net charge of 0.0400 !!! WARNING: LYS 43 has a net charge of 0.0200 !!! WARNING: LYS 106 has a net charge of 0.0730 !!! WARNING: LYS 142 has a net charge of 0.0730 !!! WARNING: LYS 169 has a net charge of 0.0730 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6442739 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): -4.651000 35.29300 ymin,ymax (A): -3.750000 48.58200 zmin,zma (A): -24.02100 31.23500 x,y,z range (A): 39.94400 52.33200 55.25600 scale (grids/A): 0.6442739 object centre (A): 15.32100 22.41600 3.607000 number of atom coordinates read : 1918 total number of charged atoms : 1786 net assigned charge : -2.574996 assigned positive charge : 277.5331 centred at (gu) : 90.43469 92.70413 89.94199 assigned negative charge : -280.1083 centred at (gu) : 90.53419 92.87727 89.89326 start vw surface at 7.0000000E-02 fill in re-entrant regions at 7.0000000E-02 boundary points on vw surface= 5648 nv = 96 ne = 84 npr = 38915 no. pairs analyzed = 38915 no. exposed pairs = 2409 no. arc points = 16886 no. surface atoms = 818 nbur = 1100 mkacc time = 6.0000002E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 346 mr = 3235 m= 3 mr = 47 m= 0 mr = 0 time to grow re-entrant surface = 7.9999998E-02 no. cavity mid-points inaccessible to solvent = 6 time to turn everything in is 0.1600000 number of dielectric boundary points 2715 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1616 ## 145 charges are in solution ## iepsmp to db, and charging done at 0.2400000 number of grid points assigned charge 6415 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -8.3246743E-09 8.8611363E-10 midg,1,midg; midg,igrid,midg 6.8204620E-09 -3.6374935E-08 1,midg,midg; igrid,midg,midg 5.0566653E-09 -1.4323421E-08 gauss-seidel spectral radius is 0.9874610 estimated iterations to convergence 73 setup time was (sec) 0.3900000 now iterating at: 14:20:58 rms-change max change #iterations 0.1243639 19.74817 at 10iterations 1.2631466E-02 1.664379 at 20iterations 1.2451422E-03 0.1926880 at 30iterations 1.2553025E-04 2.0198822E-02 at 40iterations 1.2538886E-05 2.0332336E-03 at 50iterations finished qdiffx linear iterations at : 14:21:02 total time elapsed so far: 4.220000 # loops : 50 mean,max change (kT/e) : 1.2538886E-05 2.0332336E-03 energy calculations done at 4.220000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.350000 DelPhi exited at 14:21:03 4.354u 0.275s 0:05.47 84.4% 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 Wed Dec 21 2011 at 14:21:03 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: 252 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1918 !!! WARNING: LYS 7 has a net charge of 0.0730 !!! WARNING: LYS 14 has a net charge of 0.0730 !!! WARNING: ARG 41 has a net charge of 0.0400 !!! WARNING: LYS 43 has a net charge of 0.0200 !!! WARNING: LYS 106 has a net charge of 0.0730 !!! WARNING: LYS 142 has a net charge of 0.0730 !!! WARNING: LYS 169 has a net charge of 0.0730 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.932822 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): -4.651000 35.29300 ymin,ymax (A): -3.750000 48.58200 zmin,zma (A): -24.02100 31.23500 x,y,z range (A): 39.94400 52.33200 55.25600 scale (grids/A): 1.932822 object centre (A): 15.32100 22.41600 3.607000 number of atom coordinates read : 1918 total number of charged atoms : 1786 net assigned charge : -2.574996 assigned positive charge : 277.5331 centred at (gu) : 91.30418 98.11234 89.82613 assigned negative charge : -280.1083 centred at (gu) : 91.60283 98.63201 89.67994 start vw surface at 7.0000000E-02 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 59786 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16886 grid for indexing accessible points = 1.400000 m= 24661 mr = 41556 m= 4356 mr = 19523 m= 262 mr = 2970 m= 3 mr = 127 m= 0 mr = 0 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 1171 time to turn everything in is 0.3800000 number of dielectric boundary points 24892 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 83 iepsmp to db, and charging done at 0.5300000 number of grid points assigned charge 14085 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) : 0.6442739 object centre at (A) : 15.32100 22.41600 3.607000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.1676361E-03 -1.4313074E-03 midg,1,midg; midg,igrid,midg 2.5204087E-02 -2.5593981E-02 1,midg,midg; igrid,midg,midg 1.8083906E-03 -6.4569209E-03 gauss-seidel spectral radius is 0.9985964 estimated iterations to convergence 212 setup time was (sec) 0.7500000 now iterating at: 14:21:04 rms-change max change #iterations 3.613663 161.8689 at 10iterations 1.669497 62.87342 at 20iterations 0.7765331 27.27481 at 30iterations 0.3615172 12.57338 at 40iterations 0.1671334 5.895554 at 50iterations 7.7078864E-02 2.458126 at 60iterations 3.5822354E-02 1.206285 at 70iterations 1.6583337E-02 0.5898952 at 80iterations 7.6874504E-03 0.2574410 at 90iterations 3.5548948E-03 0.1199551 at 100iterations 1.6505163E-03 5.8198929E-02 at 110iterations 7.6740608E-04 3.0294418E-02 at 120iterations finished qdiffx linear iterations at : 14:21:15 total time elapsed so far: 11.36000 # loops : 120 mean,max change (kT/e) : 7.6740608E-04 3.0294418E-02 energy calculations done at 11.36000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.49000 DelPhi exited at 14:21:16 11.492u 0.544s 0:13.05 92.1% 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 Wed Dec 21 2011 at 14:21:16 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: 252 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1918 !!! WARNING: LYS 7 has a net charge of 0.0730 !!! WARNING: LYS 14 has a net charge of 0.0730 !!! WARNING: ARG 41 has a net charge of 0.0400 !!! WARNING: LYS 43 has a net charge of 0.0200 !!! WARNING: LYS 106 has a net charge of 0.0730 !!! WARNING: LYS 142 has a net charge of 0.0730 !!! WARNING: LYS 169 has a net charge of 0.0730 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.899233 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): -4.651000 35.29300 ymin,ymax (A): -3.750000 48.58200 zmin,zma (A): -24.02100 31.23500 x,y,z range (A): 39.94400 52.33200 55.25600 scale (grids/A): 2.899233 object centre (A): 15.32100 22.41600 3.607000 number of atom coordinates read : 1918 total number of charged atoms : 1786 net assigned charge : -2.574996 assigned positive charge : 277.5331 centred at (gu) : 91.95624 102.1685 89.73930 assigned negative charge : -280.1083 centred at (gu) : 92.40430 102.9481 89.51994 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.3600000 boundary points on vw surface= 137684 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16886 grid for indexing accessible points = 1.400000 m= 75978 mr = 99879 m= 31646 mr = 64281 m= 8075 mr = 27029 m= 1154 mr = 6363 m= 96 mr = 877 m= 1 mr = 45 m= 0 mr = 0 time to grow re-entrant surface = 0.5300000 no. cavity mid-points inaccessible to solvent = 3921 time to turn everything in is 1.020000 number of dielectric boundary points 56160 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.220000 number of grid points assigned charge 14288 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) : 1.932822 object centre at (A) : 15.32100 22.41600 3.607000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.4560019 -8.4925860E-02 midg,1,midg; midg,igrid,midg 0.2501784 -0.2732357 1,midg,midg; igrid,midg,midg 8.5683791E-03 -3.4249973E-02 gauss-seidel spectral radius is 0.9992344 estimated iterations to convergence 285 setup time was (sec) 1.460000 now iterating at: 14:21:18 rms-change max change #iterations 8.457376 468.0079 at 10iterations 4.836669 118.4313 at 20iterations 2.760158 77.85376 at 30iterations 1.566715 32.96935 at 40iterations 0.8948246 20.54891 at 50iterations 0.5092763 13.18921 at 60iterations 0.2899354 7.915051 at 70iterations 0.1647904 3.673171 at 80iterations 9.3538553E-02 1.926489 at 90iterations 5.3170666E-02 1.227194 at 100iterations 3.0136118E-02 0.6392970 at 110iterations 1.7153053E-02 0.3949242 at 120iterations 9.7569888E-03 0.1979666 at 130iterations 5.5354973E-03 0.1091118 at 140iterations 3.1545879E-03 6.2885284E-02 at 150iterations 1.7874300E-03 3.7689209E-02 at 160iterations 1.0151655E-03 1.9334793E-02 at 170iterations 5.7620427E-04 1.1177063E-02 at 180iterations finished qdiffx linear iterations at : 14:21:32 total time elapsed so far: 14.65000 # loops : 180 mean,max change (kT/e) : 5.7620427E-04 1.1177063E-02 energy calculations done at 14.65000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 14.79000 DelPhi exited at 14:21:42 14.793u 0.535s 0:26.30 58.2% 0+0k 0+0io 0pf+0w