Sun Oct 9 00:31:03 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 00:31:03 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: 247 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3235 !!! WARNING: TPO 1 has a net charge of -1.2740 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1100000 grid size : 179 scale,in grids/A, set to be: 0.5395166 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): 87.70600 149.7650 ymin,ymax (A): 73.00000 138.9850 zmin,zma (A): -3.230000 45.92000 x,y,z range (A): 62.05900 65.98500 49.15000 scale (grids/A): 0.5395166 object centre (A): 118.7355 105.9925 21.34500 number of atom coordinates read : 3235 total number of charged atoms : 3093 net assigned charge : 10.72604 assigned positive charge : 475.6998 centred at (gu) : 91.23894 90.80669 90.73354 assigned negative charge : -464.9754 centred at (gu) : 91.10941 91.01579 90.65535 start vw surface at 0.1900000 fill in re-entrant regions at 0.2000000 boundary points on vw surface= 6497 nv = 96 ne = 84 npr = 61882 no. pairs analyzed = 61882 no. exposed pairs = 4389 no. arc points = 31542 no. surface atoms = 1437 nbur = 1798 mkacc time = 0.1900000 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= 262 mr = 3291 m= 1 mr = 6 m= 0 mr = 0 time to grow re-entrant surface = 0.2100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4200000 number of dielectric boundary points 3463 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3079 ## 390 charges are in solution ## iepsmp to db, and charging done at 0.5600000 number of grid points assigned charge 8275 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 7.5007424E-11 1.1221487E-09 midg,1,midg; midg,igrid,midg 1.3245659E-09 -8.0684270E-10 1,midg,midg; igrid,midg,midg -1.4082709E-10 1.6466998E-09 gauss-seidel spectral radius is 0.9823276 estimated iterations to convergence 62 setup time was (sec) 0.7100000 now iterating at: 00:31:03 rms-change max change #iterations 7.2647959E-02 12.23232 at 10iterations 4.5992634E-03 0.7340698 at 20iterations 3.2578505E-04 5.8706284E-02 at 30iterations 2.8440947E-05 4.7760010E-03 at 40iterations 3.8446842E-06 7.1144104E-04 at 50iterations finished qdiffx linear iterations at : 00:31:07 total time elapsed so far: 3.840000 # loops : 50 mean,max change (kT/e) : 3.8446842E-06 7.1144104E-04 energy calculations done at 3.840000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.080000 DelPhi exited at 00:31:07 4.080u 0.168s 0:04.55 93.1% 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 Sun Oct 9 2011 at 00:31:07 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: 247 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3235 !!! WARNING: TPO 1 has a net charge of -1.2740 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1100000 grid size : 179 scale,in grids/A, set to be: 1.618550 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): 87.70600 149.7650 ymin,ymax (A): 73.00000 138.9850 zmin,zma (A): -3.230000 45.92000 x,y,z range (A): 62.05900 65.98500 49.15000 scale (grids/A): 1.618550 object centre (A): 118.7355 105.9925 21.34500 number of atom coordinates read : 3235 total number of charged atoms : 3093 net assigned charge : 10.72604 assigned positive charge : 475.6998 centred at (gu) : 93.71591 92.41949 92.19923 assigned negative charge : -464.9754 centred at (gu) : 93.32811 93.04713 91.96600 start vw surface at 0.2000000 fill in re-entrant regions at 0.3100000 boundary points on vw surface= 71437 reading accessible surface arcs data from file ARCDAT no. of arc points read = 31542 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 22490 mr = 47379 m= 2375 mr = 15429 m= 71 mr = 1062 m= 0 mr = 0 time to grow re-entrant surface = 0.2900000 no. cavity mid-points inaccessible to solvent = 368 time to turn everything in is 0.6400000 number of dielectric boundary points 32503 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 408 ## 4 charges are in solution ## iepsmp to db, and charging done at 0.7900000 number of grid points assigned charge 23615 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) : 0.5395166 object centre at (A) : 118.7355 105.9925 21.34500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.7343632E-04 1.2286856E-02 midg,1,midg; midg,igrid,midg 2.1789314E-02 -1.5930304E-02 1,midg,midg; igrid,midg,midg -1.6530462E-02 2.5939384E-02 gauss-seidel spectral radius is 0.9981990 estimated iterations to convergence 187 setup time was (sec) 0.9900000 now iterating at: 00:31:08 rms-change max change #iterations 3.362756 170.1734 at 10iterations 1.396710 62.79590 at 20iterations 0.5843982 21.92984 at 30iterations 0.2427005 8.326462 at 40iterations 0.1015937 3.309334 at 50iterations 4.2523205E-02 1.373631 at 60iterations 1.7774070E-02 0.5967455 at 70iterations 7.4261567E-03 0.2455978 at 80iterations 3.1142689E-03 0.1189206 at 90iterations 1.3018582E-03 4.4544220E-02 at 100iterations 5.4304412E-04 1.9203186E-02 at 110iterations 2.2793809E-04 8.4314346E-03 at 120iterations finished qdiffx linear iterations at : 00:31:16 total time elapsed so far: 8.750000 # loops : 120 mean,max change (kT/e) : 2.2793809E-04 8.4314346E-03 energy calculations done at 8.750000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.980000 DelPhi exited at 00:31:17 8.983u 0.187s 0:09.53 96.1% 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 Sun Oct 9 2011 at 00:31:17 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: 247 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3235 !!! WARNING: TPO 1 has a net charge of -1.2740 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1000000 grid size : 179 scale,in grids/A, set to be: 2.427824 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): 87.70600 149.7650 ymin,ymax (A): 73.00000 138.9850 zmin,zma (A): -3.230000 45.92000 x,y,z range (A): 62.05900 65.98500 49.15000 scale (grids/A): 2.427824 object centre (A): 118.7355 105.9925 21.34500 number of atom coordinates read : 3235 total number of charged atoms : 3093 net assigned charge : 10.72604 assigned positive charge : 475.6998 centred at (gu) : 95.57361 93.62887 93.29861 assigned negative charge : -464.9754 centred at (gu) : 94.99227 94.57050 92.94913 start vw surface at 0.2200000 fill in re-entrant regions at 0.5300000 boundary points on vw surface= 165695 reading accessible surface arcs data from file ARCDAT no. of arc points read = 31542 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 77252 mr = 116333 m= 22531 mr = 60518 m= 3524 mr = 16765 m= 198 mr = 2161 m= 1 mr = 50 m= 0 mr = 0 time to grow re-entrant surface = 0.9000000 no. cavity mid-points inaccessible to solvent = 1197 time to turn everything in is 1.550000 number of dielectric boundary points 73374 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 27 iepsmp to db, and charging done at 1.720000 number of grid points assigned charge 24697 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) : 1.618550 object centre at (A) : 118.7355 105.9925 21.34500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 7.3666470E-03 0.1525058 midg,1,midg; midg,igrid,midg 0.4035494 -0.2089706 1,midg,midg; igrid,midg,midg -0.3892197 0.3946134 gauss-seidel spectral radius is 0.9991590 estimated iterations to convergence 272 setup time was (sec) 1.920000 now iterating at: 00:31:19 rms-change max change #iterations 8.904182 266.7203 at 10iterations 5.083638 147.6467 at 20iterations 2.888277 69.30942 at 30iterations 1.627902 42.13018 at 40iterations 0.9113674 21.20749 at 50iterations 0.5092108 10.13787 at 60iterations 0.2845795 6.144412 at 70iterations 0.1584895 3.000659 at 80iterations 8.8221960E-02 1.783602 at 90iterations 4.8976567E-02 0.9601593 at 100iterations 2.7139002E-02 0.5334740 at 110iterations 1.5040657E-02 0.3225596 at 120iterations 8.3310809E-03 0.1881142 at 130iterations 4.6194536E-03 9.3424916E-02 at 140iterations 2.5554823E-03 5.3997278E-02 at 150iterations 1.4154996E-03 2.9708862E-02 at 160iterations 7.8303338E-04 1.6543865E-02 at 170iterations 4.3231482E-04 9.1476440E-03 at 180iterations finished qdiffx linear iterations at : 00:31:31 total time elapsed so far: 14.30000 # loops : 180 mean,max change (kT/e) : 4.3231482E-04 9.1476440E-03 energy calculations done at 14.30000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 14.53000 DelPhi exited at 00:31:32 14.530u 0.179s 0:14.96 98.2% 0+0k 0+0io 0pf+0w