Mon Oct 10 17:04:05 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 17:04:05 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: 281 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2988 !!! WARNING: HIZ 83 has a net charge of 0.2000 !!! WARNING: HIZ 119 has a net charge of 0.2000 !!! WARNING: GLM 283 has a net charge of -0.0940 !!! WARNING: MG9 961 has a net charge of 1.4000 !!! WARNING: ZN9 964 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: 0.5973154 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): -1.266000 55.04200 ymin,ymax (A): 96.97900 153.6320 zmin,zma (A): -15.74400 43.85600 x,y,z range (A): 56.30800 56.65299 59.60000 scale (grids/A): 0.5973154 object centre (A): 26.88800 125.3055 14.05600 number of atom coordinates read : 2988 total number of charged atoms : 2839 net assigned charge : 3.606028 assigned positive charge : 454.1840 centred at (gu) : 88.95512 89.65916 91.00070 assigned negative charge : -450.5794 centred at (gu) : 89.09391 89.67804 91.06021 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1000000 boundary points on vw surface= 6935 nv = 96 ne = 84 npr = 60837 no. pairs analyzed = 60837 no. exposed pairs = 3854 no. arc points = 27554 no. surface atoms = 1284 nbur = 1704 mkacc time = 0.1000000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 313 mr = 3545 m= 1 mr = 24 m= 0 mr = 0 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2100000 number of dielectric boundary points 3680 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2838 ## 339 charges are in solution ## iepsmp to db, and charging done at 0.2900000 number of grid points assigned charge 8888 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.9306555E-09 -1.2275605E-09 midg,1,midg; midg,igrid,midg 2.2770310E-09 5.9717975E-10 1,midg,midg; igrid,midg,midg 8.5162126E-09 -3.2154546E-09 gauss-seidel spectral radius is 0.9855320 estimated iterations to convergence 68 setup time was (sec) 0.4200000 now iterating at: 17:04:06 rms-change max change #iterations 0.1144814 19.76171 at 10iterations 9.7251004E-03 1.710972 at 20iterations 8.2220795E-04 0.1204700 at 30iterations 8.5044318E-05 1.4778137E-02 at 40iterations 1.4384467E-05 2.1705627E-03 at 50iterations finished qdiffx linear iterations at : 17:04:09 total time elapsed so far: 3.290000 # loops : 50 mean,max change (kT/e) : 1.4384467E-05 2.1705627E-03 energy calculations done at 3.290000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.420000 DelPhi exited at 17:04:10 3.420u 0.155s 0:04.39 81.3% 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 17:04:10 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: 281 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2988 !!! WARNING: HIZ 83 has a net charge of 0.2000 !!! WARNING: HIZ 119 has a net charge of 0.2000 !!! WARNING: GLM 283 has a net charge of -0.0940 !!! WARNING: MG9 961 has a net charge of 1.4000 !!! WARNING: ZN9 964 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: 1.791946 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): -1.266000 55.04200 ymin,ymax (A): 96.97900 153.6320 zmin,zma (A): -15.74400 43.85600 x,y,z range (A): 56.30800 56.65299 59.60000 scale (grids/A): 1.791946 object centre (A): 26.88800 125.3055 14.05600 number of atom coordinates read : 2988 total number of charged atoms : 2839 net assigned charge : 3.606028 assigned positive charge : 454.1840 centred at (gu) : 86.86427 88.97652 93.00126 assigned negative charge : -450.5794 centred at (gu) : 87.28163 89.03389 93.18033 start vw surface at 0.1000000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 76252 reading accessible surface arcs data from file ARCDAT no. of arc points read = 27554 grid for indexing accessible points = 1.400000 m= 24534 mr = 51113 m= 3516 mr = 17043 m= 158 mr = 2018 m= 3 mr = 30 m= 0 mr = 0 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 266 time to turn everything in is 0.3900000 number of dielectric boundary points 34259 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 257 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.4700000 number of grid points assigned charge 22145 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) : 0.5973154 object centre at (A) : 26.88800 125.3055 14.05600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.5648464E-02 -1.0040594E-02 midg,1,midg; midg,igrid,midg 1.7316530E-02 -2.0615316E-03 1,midg,midg; igrid,midg,midg 2.1895379E-02 -2.4676593E-02 gauss-seidel spectral radius is 0.9985112 estimated iterations to convergence 206 setup time was (sec) 0.6100000 now iterating at: 17:04:11 rms-change max change #iterations 4.106101 171.9767 at 10iterations 1.860518 64.08906 at 20iterations 0.8383322 28.30134 at 30iterations 0.3805256 11.42872 at 40iterations 0.1713432 5.226448 at 50iterations 7.7778131E-02 2.603662 at 60iterations 3.5273347E-02 1.170616 at 70iterations 1.5918216E-02 0.4949317 at 80iterations 7.2061936E-03 0.2638796 at 90iterations 3.2767169E-03 0.1020718 at 100iterations 1.4819074E-03 4.8165679E-02 at 110iterations 6.7247427E-04 2.2132874E-02 at 120iterations finished qdiffx linear iterations at : 17:04:18 total time elapsed so far: 7.710000 # loops : 120 mean,max change (kT/e) : 6.7247427E-04 2.2132874E-02 energy calculations done at 7.710000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.840000 DelPhi exited at 17:04:19 7.845u 0.184s 0:09.00 89.1% 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 Mon Oct 10 2011 at 17:04:19 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: 281 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2988 !!! WARNING: HIZ 83 has a net charge of 0.2000 !!! WARNING: HIZ 119 has a net charge of 0.2000 !!! WARNING: GLM 283 has a net charge of -0.0940 !!! WARNING: MG9 961 has a net charge of 1.4000 !!! WARNING: ZN9 964 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: 2.687920 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): -1.266000 55.04200 ymin,ymax (A): 96.97900 153.6320 zmin,zma (A): -15.74400 43.85600 x,y,z range (A): 56.30800 56.65299 59.60000 scale (grids/A): 2.687920 object centre (A): 26.88800 125.3055 14.05600 number of atom coordinates read : 2988 total number of charged atoms : 2839 net assigned charge : 3.606028 assigned positive charge : 454.1840 centred at (gu) : 85.29628 88.46462 94.50179 assigned negative charge : -450.5794 centred at (gu) : 85.92231 88.55070 94.77056 start vw surface at 0.1000000 fill in re-entrant regions at 0.3300000 boundary points on vw surface= 176720 reading accessible surface arcs data from file ARCDAT no. of arc points read = 27554 grid for indexing accessible points = 1.400000 m= 81777 mr = 124902 m= 26903 mr = 64721 m= 5955 mr = 20477 m= 691 mr = 4280 m= 23 mr = 407 m= 1 mr = 4 m= 0 mr = 0 time to grow re-entrant surface = 0.5200000 no. cavity mid-points inaccessible to solvent = 834 time to turn everything in is 0.9400000 number of dielectric boundary points 77279 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3 iepsmp to db, and charging done at 1.030000 number of grid points assigned charge 22707 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) : 1.791946 object centre at (A) : 26.88800 125.3055 14.05600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.3198004 -0.1149960 midg,1,midg; midg,igrid,midg 0.2206029 -3.0677019E-02 1,midg,midg; igrid,midg,midg 0.1515372 -0.3743998 gauss-seidel spectral radius is 0.9992383 estimated iterations to convergence 286 setup time was (sec) 1.170000 now iterating at: 17:04:20 rms-change max change #iterations 9.984679 285.0008 at 10iterations 5.790698 123.4121 at 20iterations 3.328325 68.69866 at 30iterations 1.912477 40.03041 at 40iterations 1.095007 25.27620 at 50iterations 0.6254224 13.09164 at 60iterations 0.3585680 6.913700 at 70iterations 0.2042173 3.964973 at 80iterations 0.1166756 2.338665 at 90iterations 6.6615969E-02 1.512009 at 100iterations 3.7913304E-02 0.7039042 at 110iterations 2.1657268E-02 0.3955374 at 120iterations 1.2316282E-02 0.2167664 at 130iterations 7.0121656E-03 0.1336517 at 140iterations 4.0013953E-03 7.2872162E-02 at 150iterations 2.2879273E-03 4.1295052E-02 at 160iterations 1.3017688E-03 2.5394440E-02 at 170iterations 7.4496417E-04 1.3913155E-02 at 180iterations finished qdiffx linear iterations at : 17:04:32 total time elapsed so far: 12.59000 # loops : 180 mean,max change (kT/e) : 7.4496417E-04 1.3913155E-02 energy calculations done at 12.59000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.71000 DelPhi exited at 17:04:33 12.716u 0.213s 0:14.12 91.5% 0+0k 0+0io 0pf+0w