Sat Oct 8 19:58:49 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 Sat Oct 8 2011 at 19:58:49 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: 262 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2586 !!! WARNING: HIZ 94 has a net charge of 0.2000 !!! WARNING: HIZ 96 has a net charge of 0.2000 !!! WARNING: HIY 119 has a net charge of 0.2000 !!! WARNING: ZN5 531 has a net charge of 1.4000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 0.6192597 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): -31.28600 17.45100 ymin,ymax (A): -23.50300 22.69600 zmin,zma (A): -12.39100 45.09700 x,y,z range (A): 48.73700 46.19900 57.48800 scale (grids/A): 0.6192597 object centre (A): -6.917500 -0.4035006 16.35300 number of atom coordinates read : 2586 total number of charged atoms : 2466 net assigned charge : 4.500007 assigned positive charge : 393.3950 centred at (gu) : 88.51092 89.21652 89.53118 assigned negative charge : -388.8955 centred at (gu) : 88.39148 89.27831 89.41115 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 6361 nv = 96 ne = 84 npr = 53832 no. pairs analyzed = 53832 no. exposed pairs = 3051 no. arc points = 21669 no. surface atoms = 1021 nbur = 1565 mkacc time = 0.1200000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 312 mr = 3494 m= 2 mr = 37 m= 0 mr = 0 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 34 time to turn everything in is 0.3000000 number of dielectric boundary points 3144 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2184 ## 250 charges are in solution ## iepsmp to db, and charging done at 0.4100000 number of grid points assigned charge 8038 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -4.7194582E-09 1.0254848E-08 midg,1,midg; midg,igrid,midg 9.1085601E-09 -2.7810954E-10 1,midg,midg; igrid,midg,midg -5.9598562E-09 8.1792786E-09 gauss-seidel spectral radius is 0.9864901 estimated iterations to convergence 70 setup time was (sec) 0.5200000 now iterating at: 19:58:50 rms-change max change #iterations 0.1249584 18.93471 at 10iterations 1.1377081E-02 1.549023 at 20iterations 1.0464595E-03 0.1559601 at 30iterations 1.0101881E-04 1.4087677E-02 at 40iterations 9.2539158E-06 1.5792847E-03 at 50iterations finished qdiffx linear iterations at : 19:58:52 total time elapsed so far: 2.950000 # loops : 50 mean,max change (kT/e) : 9.2539158E-06 1.5792847E-03 energy calculations done at 2.950000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.120000 DelPhi exited at 19:58:52 3.128u 0.133s 0:03.59 90.5% 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 Sat Oct 8 2011 at 19:58:53 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: 262 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2586 !!! WARNING: HIZ 94 has a net charge of 0.2000 !!! WARNING: HIZ 96 has a net charge of 0.2000 !!! WARNING: HIY 119 has a net charge of 0.2000 !!! WARNING: ZN5 531 has a net charge of 1.4000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 1.857779 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): -31.28600 17.45100 ymin,ymax (A): -23.50300 22.69600 zmin,zma (A): -12.39100 45.09700 x,y,z range (A): 48.73700 46.19900 57.48800 scale (grids/A): 1.857779 object centre (A): -6.917500 -0.4035006 16.35300 number of atom coordinates read : 2586 total number of charged atoms : 2466 net assigned charge : 4.500007 assigned positive charge : 393.3950 centred at (gu) : 85.53216 87.64919 88.59258 assigned negative charge : -388.8955 centred at (gu) : 85.17442 87.83472 88.23343 start vw surface at 0.1600000 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 69715 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21669 grid for indexing accessible points = 1.400000 m= 23582 mr = 48380 m= 3290 mr = 17289 m= 141 mr = 1957 m= 1 mr = 42 m= 0 mr = 0 time to grow re-entrant surface = 0.2100000 no. cavity mid-points inaccessible to solvent = 4097 time to turn everything in is 0.5000000 number of dielectric boundary points 29061 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 175 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.6100000 number of grid points assigned charge 19333 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) : 0.6192597 object centre at (A) : -6.917500 -0.4035006 16.35300 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.7373774E-02 3.1998269E-02 midg,1,midg; midg,igrid,midg 1.1946008E-02 3.9731950E-04 1,midg,midg; igrid,midg,midg -5.1053767E-03 3.6806863E-02 gauss-seidel spectral radius is 0.9985615 estimated iterations to convergence 209 setup time was (sec) 0.7600000 now iterating at: 19:58:53 rms-change max change #iterations 4.017978 163.7132 at 10iterations 1.847349 64.10827 at 20iterations 0.8439064 33.30656 at 30iterations 0.3879836 14.54853 at 40iterations 0.1779711 5.441793 at 50iterations 8.1889115E-02 2.740691 at 60iterations 3.7494514E-02 1.237033 at 70iterations 1.7213775E-02 0.5669689 at 80iterations 7.9032350E-03 0.2908185 at 90iterations 3.6377308E-03 0.1175003 at 100iterations 1.6687028E-03 5.6640625E-02 at 110iterations 7.6750957E-04 2.5029182E-02 at 120iterations finished qdiffx linear iterations at : 19:58:59 total time elapsed so far: 6.710000 # loops : 120 mean,max change (kT/e) : 7.6750957E-04 2.5029182E-02 energy calculations done at 6.710000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 6.890000 DelPhi exited at 19:59:00 6.892u 0.167s 0:07.41 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 Sat Oct 8 2011 at 19:59:00 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: 262 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2586 !!! WARNING: HIZ 94 has a net charge of 0.2000 !!! WARNING: HIZ 96 has a net charge of 0.2000 !!! WARNING: HIY 119 has a net charge of 0.2000 !!! WARNING: ZN5 531 has a net charge of 1.4000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 2.786669 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): -31.28600 17.45100 ymin,ymax (A): -23.50300 22.69600 zmin,zma (A): -12.39100 45.09700 x,y,z range (A): 48.73700 46.19900 57.48800 scale (grids/A): 2.786669 object centre (A): -6.917500 -0.4035006 16.35300 number of atom coordinates read : 2586 total number of charged atoms : 2466 net assigned charge : 4.500007 assigned positive charge : 393.3950 centred at (gu) : 83.29822 86.47364 87.88898 assigned negative charge : -388.8955 centred at (gu) : 82.76147 86.75199 87.35005 start vw surface at 0.1400000 fill in re-entrant regions at 0.4200000 boundary points on vw surface= 161611 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21669 grid for indexing accessible points = 1.400000 m= 78558 mr = 117493 m= 25954 mr = 64085 m= 5645 mr = 20741 m= 694 mr = 4186 m= 32 mr = 426 m= 0 mr = 8 time to grow re-entrant surface = 0.6500000 no. cavity mid-points inaccessible to solvent = 13735 time to turn everything in is 1.170000 number of dielectric boundary points 65555 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.290000 number of grid points assigned charge 19726 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) : 1.857779 object centre at (A) : -6.917500 -0.4035006 16.35300 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -9.4792143E-02 0.3978458 midg,1,midg; midg,igrid,midg 0.1500994 -9.0676714E-03 1,midg,midg; igrid,midg,midg -4.9071230E-02 0.4845864 gauss-seidel spectral radius is 0.9992335 estimated iterations to convergence 285 setup time was (sec) 1.440000 now iterating at: 19:59:02 rms-change max change #iterations 9.440380 334.0422 at 10iterations 5.429192 117.3807 at 20iterations 3.099007 79.36049 at 30iterations 1.766762 46.73927 at 40iterations 1.008070 19.43820 at 50iterations 0.5742502 11.28894 at 60iterations 0.3272145 7.293526 at 70iterations 0.1856696 3.435968 at 80iterations 0.1056226 2.017076 at 90iterations 6.0221344E-02 1.272867 at 100iterations 3.4244835E-02 0.6313438 at 110iterations 1.9503070E-02 0.3789291 at 120iterations 1.1096677E-02 0.2524064 at 130iterations 6.2978682E-03 0.1282740 at 140iterations 3.5843118E-03 6.8451405E-02 at 150iterations 2.0384812E-03 3.8122177E-02 at 160iterations 1.1648231E-03 2.1800995E-02 at 170iterations 6.6382566E-04 1.2435913E-02 at 180iterations finished qdiffx linear iterations at : 19:59:11 total time elapsed so far: 10.92000 # loops : 180 mean,max change (kT/e) : 6.6382566E-04 1.2435913E-02 energy calculations done at 10.92000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.09000 DelPhi exited at 19:59:12 11.097u 0.157s 0:11.55 97.3% 0+0k 0+0io 0pf+0w