Sat Oct 8 19:49:04 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 Sat Oct 8 2011 at 19:49:05 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: 262 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2436 !!! WARNING: HIZ 94 has a net charge of 0.2000 !!! WARNING: HIZ 96 has a net charge of 0.2000 !!! WARNING: HIY 119 has a net charge of 0.2000 !!! WARNING: ZN4 461 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: 0.6604334 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): -30.77300 17.06100 ymin,ymax (A): -23.51600 23.19000 zmin,zma (A): -12.10500 41.79900 x,y,z range (A): 47.83400 46.70600 53.90400 scale (grids/A): 0.6604334 object centre (A): -6.856000 -0.1629992 14.84700 number of atom coordinates read : 2436 total number of charged atoms : 2296 net assigned charge : 4.500006 assigned positive charge : 366.1383 centred at (gu) : 88.72534 89.26907 89.73406 assigned negative charge : -361.6388 centred at (gu) : 88.60214 89.35930 89.58656 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 6878 nv = 96 ne = 84 npr = 51973 no. pairs analyzed = 51973 no. exposed pairs = 2720 no. arc points = 19196 no. surface atoms = 917 nbur = 1519 mkacc time = 0.1700000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 350 mr = 3990 m= 1 mr = 45 m= 0 mr = 0 time to grow re-entrant surface = 0.2000000 no. cavity mid-points inaccessible to solvent = 192 time to turn everything in is 0.3700000 number of dielectric boundary points 3194 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1777 ## 173 charges are in solution ## iepsmp to db, and charging done at 0.5300000 number of grid points assigned charge 8200 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.6971503E-08 3.6784549E-08 midg,1,midg; midg,igrid,midg 3.3178040E-08 -4.2605990E-09 1,midg,midg; igrid,midg,midg -1.5143300E-08 2.6502484E-08 gauss-seidel spectral radius is 0.9880937 estimated iterations to convergence 75 setup time was (sec) 0.7100000 now iterating at: 19:49:06 rms-change max change #iterations 0.1627077 21.62824 at 10iterations 1.7345939E-02 2.303736 at 20iterations 1.8451705E-03 0.3247223 at 30iterations 1.9590255E-04 2.6611328E-02 at 40iterations 2.1682226E-05 2.7465820E-03 at 50iterations finished qdiffx linear iterations at : 19:49:09 total time elapsed so far: 4.260000 # loops : 50 mean,max change (kT/e) : 2.1682226E-05 2.7465820E-03 energy calculations done at 4.260000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.480000 DelPhi exited at 19:49:10 4.484u 0.441s 0:05.18 94.9% 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 Sat Oct 8 2011 at 19:49:10 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: 262 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2436 !!! WARNING: HIZ 94 has a net charge of 0.2000 !!! WARNING: HIZ 96 has a net charge of 0.2000 !!! WARNING: HIY 119 has a net charge of 0.2000 !!! WARNING: ZN4 461 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= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 1.981300 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): -30.77300 17.06100 ymin,ymax (A): -23.51600 23.19000 zmin,zma (A): -12.10500 41.79900 x,y,z range (A): 47.83400 46.70600 53.90400 scale (grids/A): 1.981300 object centre (A): -6.856000 -0.1629992 14.84700 number of atom coordinates read : 2436 total number of charged atoms : 2296 net assigned charge : 4.500006 assigned positive charge : 366.1383 centred at (gu) : 86.17572 87.80663 89.20193 assigned negative charge : -361.6388 centred at (gu) : 85.80627 88.07769 88.75966 start vw surface at 0.1500000 fill in re-entrant regions at 0.3200000 boundary points on vw surface= 74194 reading accessible surface arcs data from file ARCDAT no. of arc points read = 19196 grid for indexing accessible points = 1.400000 m= 26887 mr = 52869 m= 4546 mr = 20373 m= 286 mr = 3100 m= 5 mr = 125 m= 0 mr = 0 time to grow re-entrant surface = 0.3700000 no. cavity mid-points inaccessible to solvent = 5098 time to turn everything in is 0.7600000 number of dielectric boundary points 29451 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 116 iepsmp to db, and charging done at 0.8900000 number of grid points assigned charge 18131 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) : 0.6604334 object centre at (A) : -6.856000 -0.1629992 14.84700 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.3893362E-02 3.4178473E-02 midg,1,midg; midg,igrid,midg 2.8347448E-02 -1.8264824E-03 1,midg,midg; igrid,midg,midg -4.9704104E-03 4.7382601E-02 gauss-seidel spectral radius is 0.9987083 estimated iterations to convergence 220 setup time was (sec) 1.090000 now iterating at: 19:49:11 rms-change max change #iterations 4.405066 182.8441 at 10iterations 2.108801 69.78956 at 20iterations 1.009168 30.39190 at 30iterations 0.4833854 15.55365 at 40iterations 0.2318400 7.180926 at 50iterations 0.1111761 3.381027 at 60iterations 5.3133670E-02 1.492886 at 70iterations 2.5507523E-02 0.8627310 at 80iterations 1.2169038E-02 0.3858795 at 90iterations 5.8342242E-03 0.1867409 at 100iterations 2.7933156E-03 9.4779968E-02 at 110iterations 1.3376934E-03 3.9431572E-02 at 120iterations finished qdiffx linear iterations at : 19:49:20 total time elapsed so far: 10.06000 # loops : 120 mean,max change (kT/e) : 1.3376934E-03 3.9431572E-02 energy calculations done at 10.06000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.28000 DelPhi exited at 19:49:21 10.285u 0.464s 0:11.03 97.3% 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 Sat Oct 8 2011 at 19:49:21 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: 262 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2436 !!! WARNING: HIZ 94 has a net charge of 0.2000 !!! WARNING: HIZ 96 has a net charge of 0.2000 !!! WARNING: HIY 119 has a net charge of 0.2000 !!! WARNING: ZN4 461 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: 2.971950 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): -30.77300 17.06100 ymin,ymax (A): -23.51600 23.19000 zmin,zma (A): -12.10500 41.79900 x,y,z range (A): 47.83400 46.70600 53.90400 scale (grids/A): 2.971950 object centre (A): -6.856000 -0.1629992 14.84700 number of atom coordinates read : 2436 total number of charged atoms : 2296 net assigned charge : 4.500006 assigned positive charge : 366.1383 centred at (gu) : 84.26355 86.70990 88.80283 assigned negative charge : -361.6388 centred at (gu) : 83.70947 87.11658 88.13942 start vw surface at 0.1400000 fill in re-entrant regions at 0.6700000 boundary points on vw surface= 171919 reading accessible surface arcs data from file ARCDAT no. of arc points read = 19196 grid for indexing accessible points = 1.400000 m= 87106 mr = 127895 m= 32141 mr = 72494 m= 8527 mr = 26543 m= 1281 mr = 6750 m= 80 mr = 900 m= 3 mr = 39 m= 0 mr = 0 time to grow re-entrant surface = 1.210000 no. cavity mid-points inaccessible to solvent = 17155 time to turn everything in is 2.020000 number of dielectric boundary points 66436 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.160000 number of grid points assigned charge 18368 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) : 1.981300 object centre at (A) : -6.856000 -0.1629992 14.84700 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1067080 0.3432541 midg,1,midg; midg,igrid,midg 0.2716508 -5.5552788E-02 1,midg,midg; igrid,midg,midg 9.9871801E-03 0.5128915 gauss-seidel spectral radius is 0.9992650 estimated iterations to convergence 291 setup time was (sec) 2.380000 now iterating at: 19:49:24 rms-change max change #iterations 10.02076 480.6867 at 10iterations 5.802590 115.7713 at 20iterations 3.351919 68.79665 at 30iterations 1.935486 33.20560 at 40iterations 1.120457 21.14212 at 50iterations 0.6446598 11.74848 at 60iterations 0.3727317 6.524233 at 70iterations 0.2144758 3.926804 at 80iterations 0.1236826 2.227707 at 90iterations 7.1144268E-02 1.456602 at 100iterations 4.1122582E-02 0.8219566 at 110iterations 2.3680724E-02 0.4573879 at 120iterations 1.3632296E-02 0.2586937 at 130iterations 7.8722369E-03 0.1415367 at 140iterations 4.5451550E-03 8.8054657E-02 at 150iterations 2.6326026E-03 4.9240112E-02 at 160iterations 1.5243997E-03 2.7547836E-02 at 170iterations 8.8525505E-04 1.5826225E-02 at 180iterations finished qdiffx linear iterations at : 19:49:42 total time elapsed so far: 21.17000 # loops : 180 mean,max change (kT/e) : 8.8525505E-04 1.5826225E-02 energy calculations done at 21.17000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 21.39000 DelPhi exited at 19:49:43 21.392u 0.503s 0:22.17 98.7% 0+0k 0+0io 0pf+0w