Sat Oct 8 11:39:18 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 Sat Oct 8 2011 at 11:39:18 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: 303 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2525 !!! WARNING: HIZ 189 has a net charge of 0.2000 !!! WARNING: HIZ 193 has a net charge of 0.2000 !!! WARNING: HIZ 199 has a net charge of 0.2000 !!! WARNING: ZN5 517 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: 0.6102892 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): -18.16800 25.27200 ymin,ymax (A): -14.54500 43.78800 zmin,zma (A): 85.68700 136.4520 x,y,z range (A): 43.44000 58.33300 50.76500 scale (grids/A): 0.6102892 object centre (A): 3.552000 14.62150 111.0695 number of atom coordinates read : 2525 total number of charged atoms : 2385 net assigned charge : -1.499991 assigned positive charge : 389.0111 centred at (gu) : 90.95538 89.09145 90.29999 assigned negative charge : -390.5115 centred at (gu) : 90.86507 89.01343 90.40845 start vw surface at 0.1700000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 6130 nv = 96 ne = 84 npr = 51958 no. pairs analyzed = 51958 no. exposed pairs = 2965 no. arc points = 21274 no. surface atoms = 995 nbur = 1530 mkacc time = 0.1400000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 307 mr = 3375 m= 2 mr = 46 m= 0 mr = 0 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 35 time to turn everything in is 0.3600000 number of dielectric boundary points 3018 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2114 ## 219 charges are in solution ## iepsmp to db, and charging done at 0.5100000 number of grid points assigned charge 7582 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 4.1985992E-09 -6.8320225E-09 midg,1,midg; midg,igrid,midg -5.9280936E-09 2.4369557E-09 1,midg,midg; igrid,midg,midg -4.3990185E-09 4.5033270E-09 gauss-seidel spectral radius is 0.9860893 estimated iterations to convergence 69 setup time was (sec) 0.6900000 now iterating at: 11:39:19 rms-change max change #iterations 0.1224749 18.84779 at 10iterations 1.0930620E-02 1.634925 at 20iterations 9.3744928E-04 0.1437817 at 30iterations 8.4431456E-05 1.5729904E-02 at 40iterations 7.4240556E-06 1.2092590E-03 at 50iterations finished qdiffx linear iterations at : 11:39:24 total time elapsed so far: 5.170000 # loops : 50 mean,max change (kT/e) : 7.4240556E-06 1.2092590E-03 energy calculations done at 5.170000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 5.370000 DelPhi exited at 11:39:24 5.372u 0.410s 0:06.17 93.6% 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 Sat Oct 8 2011 at 11:39:24 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: 303 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2525 !!! WARNING: HIZ 189 has a net charge of 0.2000 !!! WARNING: HIZ 193 has a net charge of 0.2000 !!! WARNING: HIZ 199 has a net charge of 0.2000 !!! WARNING: ZN5 517 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: 1.830868 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): -18.16800 25.27200 ymin,ymax (A): -14.54500 43.78800 zmin,zma (A): 85.68700 136.4520 x,y,z range (A): 43.44000 58.33300 50.76500 scale (grids/A): 1.830868 object centre (A): 3.552000 14.62150 111.0695 number of atom coordinates read : 2525 total number of charged atoms : 2385 net assigned charge : -1.499991 assigned positive charge : 389.0111 centred at (gu) : 92.86568 87.27390 90.89951 assigned negative charge : -390.5115 centred at (gu) : 92.59489 87.04001 91.22514 start vw surface at 0.1600000 fill in re-entrant regions at 0.2900000 boundary points on vw surface= 66824 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21274 grid for indexing accessible points = 1.400000 m= 22131 mr = 46350 m= 3131 mr = 16025 m= 199 mr = 1922 m= 1 mr = 113 m= 0 mr = 0 time to grow re-entrant surface = 0.2900000 no. cavity mid-points inaccessible to solvent = 2808 time to turn everything in is 0.6200000 number of dielectric boundary points 27876 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 176 iepsmp to db, and charging done at 0.7800000 number of grid points assigned charge 18648 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) : 0.6102892 object centre at (A) : 3.552000 14.62150 111.0695 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.6020240E-02 4.8646517E-03 midg,1,midg; midg,igrid,midg -2.3170549E-02 -6.5011936E-03 1,midg,midg; igrid,midg,midg -7.8799427E-03 -2.6118960E-03 gauss-seidel spectral radius is 0.9985117 estimated iterations to convergence 206 setup time was (sec) 1.000000 now iterating at: 11:39:26 rms-change max change #iterations 3.942432 151.4690 at 10iterations 1.778444 64.05694 at 20iterations 0.8063141 29.87140 at 30iterations 0.3658416 11.81985 at 40iterations 0.1653610 5.756604 at 50iterations 7.5062908E-02 2.537206 at 60iterations 3.3963859E-02 1.266746 at 70iterations 1.5357095E-02 0.5294418 at 80iterations 6.9585466E-03 0.2325048 at 90iterations 3.1494182E-03 0.1099802 at 100iterations 1.4290434E-03 5.1139832E-02 at 110iterations 6.4874871E-04 2.1661997E-02 at 120iterations finished qdiffx linear iterations at : 11:39:37 total time elapsed so far: 11.74000 # loops : 120 mean,max change (kT/e) : 6.4874871E-04 2.1661997E-02 energy calculations done at 11.74000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.91000 DelPhi exited at 11:39:37 11.914u 0.604s 0:12.86 97.2% 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 11:39:37 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: 303 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2525 !!! WARNING: HIZ 189 has a net charge of 0.2000 !!! WARNING: HIZ 193 has a net charge of 0.2000 !!! WARNING: HIZ 199 has a net charge of 0.2000 !!! WARNING: ZN5 517 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: 2.746301 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): -18.16800 25.27200 ymin,ymax (A): -14.54500 43.78800 zmin,zma (A): 85.68700 136.4520 x,y,z range (A): 43.44000 58.33300 50.76500 scale (grids/A): 2.746301 object centre (A): 3.552000 14.62150 111.0695 number of atom coordinates read : 2525 total number of charged atoms : 2385 net assigned charge : -1.499991 assigned positive charge : 389.0111 centred at (gu) : 94.29848 85.91085 91.34927 assigned negative charge : -390.5115 centred at (gu) : 93.89236 85.55988 91.83761 start vw surface at 0.1600000 fill in re-entrant regions at 0.5400000 boundary points on vw surface= 155052 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21274 grid for indexing accessible points = 1.400000 m= 74604 mr = 112900 m= 23974 mr = 60620 m= 5489 mr = 18791 m= 916 mr = 4112 m= 60 mr = 729 m= 0 mr = 16 time to grow re-entrant surface = 0.9299999 no. cavity mid-points inaccessible to solvent = 9705 time to turn everything in is 1.600000 number of dielectric boundary points 62927 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3 iepsmp to db, and charging done at 1.820000 number of grid points assigned charge 19078 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) : 1.830868 object centre at (A) : 3.552000 14.62150 111.0695 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.4136076 8.8597707E-02 midg,1,midg; midg,igrid,midg -0.1472015 -0.1192431 1,midg,midg; igrid,midg,midg -7.2228752E-02 -6.7510217E-02 gauss-seidel spectral radius is 0.9992192 estimated iterations to convergence 283 setup time was (sec) 2.090000 now iterating at: 11:39:40 rms-change max change #iterations 9.345807 330.1581 at 10iterations 5.343413 143.6411 at 20iterations 3.035511 63.52867 at 30iterations 1.718470 33.54077 at 40iterations 0.9732577 20.33142 at 50iterations 0.5503102 11.44070 at 60iterations 0.3112676 6.032227 at 70iterations 0.1759320 3.515816 at 80iterations 9.9292815E-02 1.891448 at 90iterations 5.6222051E-02 1.037546 at 100iterations 3.1733260E-02 0.6626396 at 110iterations 1.7953034E-02 0.3717086 at 120iterations 1.0141190E-02 0.2179418 at 130iterations 5.7133911E-03 0.1092377 at 140iterations 3.2347096E-03 6.7588806E-02 at 150iterations 1.8258077E-03 3.7368774E-02 at 160iterations 1.0326771E-03 2.1577835E-02 at 170iterations 5.8296853E-04 1.0925293E-02 at 180iterations finished qdiffx linear iterations at : 11:40:01 total time elapsed so far: 23.10000 # loops : 180 mean,max change (kT/e) : 5.8296853E-04 1.0925293E-02 energy calculations done at 23.10000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 23.29000 DelPhi exited at 11:40:02 23.289u 0.537s 0:24.18 98.4% 0+0k 0+0io 0pf+0w