Mon Oct 10 10:19:31 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 10:19:31 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: 306 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2896 !!! WARNING: HIT 235 has a net charge of 0.5140 !!! WARNING: MG9 960 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= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.5417580 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): -22.27700 43.43500 ymin,ymax (A): -12.69900 46.30300 zmin,zma (A): -2.006000 51.26600 x,y,z range (A): 65.71200 59.00200 53.27200 scale (grids/A): 0.5417580 object centre (A): 10.57900 16.80200 24.63000 number of atom coordinates read : 2896 total number of charged atoms : 2743 net assigned charge : 7.414024 assigned positive charge : 426.4088 centred at (gu) : 91.46657 91.34775 86.95285 assigned negative charge : -418.9952 centred at (gu) : 91.57172 91.42870 86.74481 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1000000 boundary points on vw surface= 5670 nv = 96 ne = 84 npr = 55896 no. pairs analyzed = 55896 no. exposed pairs = 4285 no. arc points = 30922 no. surface atoms = 1429 nbur = 1467 mkacc time = 8.9999996E-02 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 = 1.568000 m= 211 mr = 2458 m= 0 mr = 6 time to grow re-entrant surface = 9.9999987E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2100000 number of dielectric boundary points 3417 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3108 ## 420 charges are in solution ## iepsmp to db, and charging done at 0.2800000 number of grid points assigned charge 7428 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.5256892E-09 7.0922473E-10 midg,1,midg; midg,igrid,midg 6.1589145E-10 6.4183736E-12 1,midg,midg; igrid,midg,midg 6.8391026E-10 -1.8295605E-10 gauss-seidel spectral radius is 0.9824464 estimated iterations to convergence 62 setup time was (sec) 0.4000000 now iterating at: 10:19:32 rms-change max change #iterations 7.0168488E-02 13.58349 at 10iterations 4.6322341E-03 0.7593632 at 20iterations 3.3956944E-04 5.5328369E-02 at 30iterations 4.4227909E-05 6.1128139E-03 at 40iterations 9.5478363E-06 1.3210773E-03 at 50iterations finished qdiffx linear iterations at : 10:19:35 total time elapsed so far: 3.320000 # loops : 50 mean,max change (kT/e) : 9.5478363E-06 1.3210773E-03 energy calculations done at 3.320000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.460000 DelPhi exited at 10:19:36 3.464u 0.387s 0:04.22 90.9% 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 Mon Oct 10 2011 at 10:19:36 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: 306 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2896 !!! WARNING: HIT 235 has a net charge of 0.5140 !!! WARNING: MG9 960 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= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 1.625274 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): -22.27700 43.43500 ymin,ymax (A): -12.69900 46.30300 zmin,zma (A): -2.006000 51.26600 x,y,z range (A): 65.71200 59.00200 53.27200 scale (grids/A): 1.625274 object centre (A): 10.57900 16.80200 24.63000 number of atom coordinates read : 2896 total number of charged atoms : 2743 net assigned charge : 7.414024 assigned positive charge : 426.4088 centred at (gu) : 94.39956 94.04279 80.85796 assigned negative charge : -418.9952 centred at (gu) : 94.71490 94.28571 80.23403 start vw surface at 0.1000000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 62012 reading accessible surface arcs data from file ARCDAT no. of arc points read = 30922 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 17841 mr = 38253 m= 1728 mr = 11014 m= 50 mr = 623 m= 1 mr = 1 m= 0 mr = 0 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 185 time to turn everything in is 0.3400000 number of dielectric boundary points 31741 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 308 iepsmp to db, and charging done at 0.4200000 number of grid points assigned charge 20968 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) : 0.5417580 object centre at (A) : 10.57900 16.80200 24.63000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -6.8912003E-03 1.1456860E-02 midg,1,midg; midg,igrid,midg 1.4554220E-02 3.3214882E-03 1,midg,midg; igrid,midg,midg -1.1068465E-02 -1.5506696E-02 gauss-seidel spectral radius is 0.9981694 estimated iterations to convergence 186 setup time was (sec) 0.5700000 now iterating at: 10:19:37 rms-change max change #iterations 3.209101 174.1430 at 10iterations 1.328780 54.13430 at 20iterations 0.5502640 21.92906 at 30iterations 0.2267440 8.396433 at 40iterations 9.4176173E-02 3.778048 at 50iterations 3.9033465E-02 1.516216 at 60iterations 1.6228832E-02 0.6284943 at 70iterations 6.7231893E-03 0.2479610 at 80iterations 2.7954618E-03 0.1192322 at 90iterations 1.1642149E-03 4.8767090E-02 at 100iterations 4.8500800E-04 1.8615723E-02 at 110iterations 2.0553677E-04 7.4310303E-03 at 120iterations finished qdiffx linear iterations at : 10:19:44 total time elapsed so far: 8.370000 # loops : 120 mean,max change (kT/e) : 2.0553677E-04 7.4310303E-03 energy calculations done at 8.370000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.500000 DelPhi exited at 10:19:45 8.507u 0.230s 0:09.13 95.6% 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 10:19:45 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: 306 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2896 !!! WARNING: HIT 235 has a net charge of 0.5140 !!! WARNING: MG9 960 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= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 2.437911 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): -22.27700 43.43500 ymin,ymax (A): -12.69900 46.30300 zmin,zma (A): -2.006000 51.26600 x,y,z range (A): 65.71200 59.00200 53.27200 scale (grids/A): 2.437911 object centre (A): 10.57900 16.80200 24.63000 number of atom coordinates read : 2896 total number of charged atoms : 2743 net assigned charge : 7.414024 assigned positive charge : 426.4088 centred at (gu) : 96.59909 96.06400 76.28688 assigned negative charge : -418.9952 centred at (gu) : 97.07230 96.42850 75.35099 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.2600000 boundary points on vw surface= 143897 reading accessible surface arcs data from file ARCDAT no. of arc points read = 30922 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 62088 mr = 95050 m= 16843 mr = 45940 m= 2381 mr = 11356 m= 127 mr = 1264 m= 3 mr = 24 m= 0 mr = 0 time to grow re-entrant surface = 0.4400000 no. cavity mid-points inaccessible to solvent = 560 time to turn everything in is 0.7800000 number of dielectric boundary points 71705 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 28 iepsmp to db, and charging done at 0.8800000 number of grid points assigned charge 21907 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) : 1.625274 object centre at (A) : 10.57900 16.80200 24.63000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -8.1123710E-02 0.1646097 midg,1,midg; midg,igrid,midg 0.3376241 1.1165824E-02 1,midg,midg; igrid,midg,midg -0.6210392 -0.5496731 gauss-seidel spectral radius is 0.9991374 estimated iterations to convergence 269 setup time was (sec) 1.030000 now iterating at: 10:19:46 rms-change max change #iterations 8.601090 369.5240 at 10iterations 4.929099 134.4175 at 20iterations 2.784534 82.05256 at 30iterations 1.560500 44.31182 at 40iterations 0.8707067 25.05055 at 50iterations 0.4836762 11.64002 at 60iterations 0.2685112 7.541919 at 70iterations 0.1487202 3.500800 at 80iterations 8.2154915E-02 2.153711 at 90iterations 4.5339473E-02 1.088379 at 100iterations 2.5035646E-02 0.5715046 at 110iterations 1.3762710E-02 0.3432159 at 120iterations 7.6007475E-03 0.1668510 at 130iterations 4.1739442E-03 9.4036102E-02 at 140iterations 2.2986964E-03 4.8557758E-02 at 150iterations 1.2617515E-03 3.2321930E-02 at 160iterations 6.9510413E-04 1.5876770E-02 at 170iterations 3.8261933E-04 8.9187622E-03 at 180iterations finished qdiffx linear iterations at : 10:19:58 total time elapsed so far: 12.45000 # loops : 180 mean,max change (kT/e) : 3.8261933E-04 8.9187622E-03 energy calculations done at 12.45000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.58000 DelPhi exited at 10:19:58 12.585u 0.302s 0:13.56 94.9% 0+0k 0+0io 0pf+0w