Sun Oct 9 08:17:26 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 Sun Oct 9 2011 at 08:17:26 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: 261 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5066 !!! WARNING: HIR 702 has a net charge of 0.5140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1500000 grid size : 179 scale,in grids/A, set to be: 0.5283624 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): -32.57600 25.26300 ymin,ymax (A): -12.72400 54.65400 zmin,zma (A): -29.01100 35.97700 x,y,z range (A): 57.83900 67.37800 64.98800 scale (grids/A): 0.5283624 object centre (A): -3.656500 20.96500 3.483001 number of atom coordinates read : 5066 total number of charged atoms : 4903 net assigned charge : -4.985997 assigned positive charge : 758.1955 centred at (gu) : 88.13603 89.70108 89.69324 assigned negative charge : -763.1874 centred at (gu) : 88.10457 89.55735 89.78291 start vw surface at 0.2300000 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 9169 nv = 96 ne = 84 npr = 100945 no. pairs analyzed = 100945 no. exposed pairs = 6634 no. arc points = 45688 no. surface atoms = 2215 nbur = 2851 mkacc time = 0.2400000 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 = 1.624000 m= 365 mr = 4702 m= 1 mr = 14 m= 0 mr = 0 time to grow re-entrant surface = 0.2700000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5300000 number of dielectric boundary points 4819 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4530 ## 606 charges are in solution ## iepsmp to db, and charging done at 0.6500000 number of grid points assigned charge 12141 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 3.9420450E-10 -6.1716210E-10 midg,1,midg; midg,igrid,midg -1.0673603E-09 6.1504724E-10 1,midg,midg; igrid,midg,midg -5.2909260E-10 1.9078373E-11 gauss-seidel spectral radius is 0.9817032 estimated iterations to convergence 61 setup time was (sec) 0.7900000 now iterating at: 08:17:27 rms-change max change #iterations 8.3621673E-02 12.35389 at 10iterations 5.3638928E-03 0.7272987 at 20iterations 5.8741518E-04 0.1120911 at 30iterations 1.5863529E-04 3.3271790E-02 at 40iterations 5.2835523E-05 1.0589600E-02 at 50iterations finished qdiffx linear iterations at : 08:17:30 total time elapsed so far: 3.640000 # loops : 50 mean,max change (kT/e) : 5.2835523E-05 1.0589600E-02 energy calculations done at 3.640000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.830000 DelPhi exited at 08:17:30 3.832u 0.177s 0:04.31 92.8% 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 08:17:30 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: 261 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5066 !!! WARNING: HIR 702 has a net charge of 0.5140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1300000 grid size : 179 scale,in grids/A, set to be: 1.585087 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): -32.57600 25.26300 ymin,ymax (A): -12.72400 54.65400 zmin,zma (A): -29.01100 35.97700 x,y,z range (A): 57.83900 67.37800 64.98800 scale (grids/A): 1.585087 object centre (A): -3.656500 20.96500 3.483001 number of atom coordinates read : 5066 total number of charged atoms : 4903 net assigned charge : -4.985997 assigned positive charge : 758.1955 centred at (gu) : 84.40654 89.10160 89.07756 assigned negative charge : -763.1874 centred at (gu) : 84.31319 88.67145 89.34832 start vw surface at 0.2000000 fill in re-entrant regions at 0.3400000 boundary points on vw surface= 102835 reading accessible surface arcs data from file ARCDAT no. of arc points read = 45688 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.512000 m= 31106 mr = 70255 m= 2870 mr = 20549 m= 66 mr = 1151 m= 0 mr = 0 time to grow re-entrant surface = 0.3600000 no. cavity mid-points inaccessible to solvent = 254 time to turn everything in is 0.7500000 number of dielectric boundary points 44922 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 544 ## 4 charges are in solution ## iepsmp to db, and charging done at 0.8900000 number of grid points assigned charge 37209 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) : 0.5283624 object centre at (A) : -3.656500 20.96500 3.483001 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -7.2178766E-03 -6.6924547E-03 midg,1,midg; midg,igrid,midg -1.6742278E-02 1.1700161E-02 1,midg,midg; igrid,midg,midg -1.8598880E-03 -3.3880470E-03 gauss-seidel spectral radius is 0.9982886 estimated iterations to convergence 192 setup time was (sec) 1.070000 now iterating at: 08:17:32 rms-change max change #iterations 4.258255 180.4271 at 10iterations 1.815465 56.98267 at 20iterations 0.7761996 24.80347 at 30iterations 0.3321977 9.595026 at 40iterations 0.1419610 4.051483 at 50iterations 6.0899358E-02 1.759009 at 60iterations 2.6119456E-02 0.8178768 at 70iterations 1.1232400E-02 0.3191452 at 80iterations 4.8528174E-03 0.1627750 at 90iterations 2.1182999E-03 6.2210083E-02 at 100iterations 9.5331168E-04 3.0487537E-02 at 110iterations 4.5037881E-04 1.5172005E-02 at 120iterations finished qdiffx linear iterations at : 08:17:39 total time elapsed so far: 8.280000 # loops : 120 mean,max change (kT/e) : 4.5037881E-04 1.5172005E-02 energy calculations done at 8.280000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.470000 DelPhi exited at 08:17:39 8.469u 0.227s 0:09.06 95.8% 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 08:17:39 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: 261 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5066 !!! WARNING: HIR 702 has a net charge of 0.5140 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: 2.377631 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): -32.57600 25.26300 ymin,ymax (A): -12.72400 54.65400 zmin,zma (A): -29.01100 35.97700 x,y,z range (A): 57.83900 67.37800 64.98800 scale (grids/A): 2.377631 object centre (A): -3.656500 20.96500 3.483001 number of atom coordinates read : 5066 total number of charged atoms : 4903 net assigned charge : -4.985997 assigned positive charge : 758.1955 centred at (gu) : 81.60950 88.65167 88.61575 assigned negative charge : -763.1874 centred at (gu) : 81.46982 88.00719 89.02252 start vw surface at 0.2100000 fill in re-entrant regions at 0.6100000 boundary points on vw surface= 238989 reading accessible surface arcs data from file ARCDAT no. of arc points read = 45688 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.512000 m= 109988 mr = 172574 m= 29081 mr = 85352 m= 4092 mr = 20753 m= 232 mr = 2378 m= 1 mr = 71 m= 0 mr = 0 time to grow re-entrant surface = 1.120000 no. cavity mid-points inaccessible to solvent = 881 time to turn everything in is 1.880000 number of dielectric boundary points 101255 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 54 iepsmp to db, and charging done at 2.050000 number of grid points assigned charge 39147 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) : 1.585087 object centre at (A) : -3.656500 20.96500 3.483001 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1748554 3.6175039E-02 midg,1,midg; midg,igrid,midg -0.2289591 0.1464251 1,midg,midg; igrid,midg,midg 5.5969276E-02 -7.5854674E-02 gauss-seidel spectral radius is 0.9992325 estimated iterations to convergence 285 setup time was (sec) 2.240000 now iterating at: 08:17:42 rms-change max change #iterations 11.37268 255.0784 at 10iterations 6.748606 139.2752 at 20iterations 3.960989 96.86787 at 30iterations 2.319648 47.29976 at 40iterations 1.350145 27.86789 at 50iterations 0.7815026 14.75376 at 60iterations 0.4519241 8.157773 at 70iterations 0.2604178 4.475742 at 80iterations 0.1497018 2.603689 at 90iterations 8.6008511E-02 1.438702 at 100iterations 4.9270466E-02 0.8029861 at 110iterations 2.8277313E-02 0.5254841 at 120iterations 1.6245103E-02 0.2963524 at 130iterations 9.3058478E-03 0.1623669 at 140iterations 5.3428393E-03 8.9752197E-02 at 150iterations 3.0822654E-03 5.5221915E-02 at 160iterations 1.7894550E-03 3.0590057E-02 at 170iterations 1.0507531E-03 1.8335342E-02 at 180iterations finished qdiffx linear iterations at : 08:17:54 total time elapsed so far: 14.17000 # loops : 180 mean,max change (kT/e) : 1.0507531E-03 1.8335342E-02 energy calculations done at 14.17000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 14.36000 DelPhi exited at 08:17:54 14.363u 0.236s 0:14.88 98.0% 0+0k 0+0io 0pf+0w