Sat Oct 15 14:34:08 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 15 2011 at 14:34:08 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: 266 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1700 !!! WARNING: HIT 228 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= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6656694 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): -31.18000 22.30000 ymin,ymax (A): 10.57700 51.46200 zmin,zma (A): 26.51800 69.53201 x,y,z range (A): 53.48000 40.88500 43.01401 scale (grids/A): 0.6656694 object centre (A): -4.440001 31.01950 48.02500 number of atom coordinates read : 1700 total number of charged atoms : 1571 net assigned charge : 6.514028 assigned positive charge : 250.2003 centred at (gu) : 90.80927 90.07249 91.16628 assigned negative charge : -243.6865 centred at (gu) : 90.81710 90.10540 91.10680 start vw surface at 0.1100000 fill in re-entrant regions at 0.1100000 boundary points on vw surface= 5072 nv = 96 ne = 84 npr = 33614 no. pairs analyzed = 33614 no. exposed pairs = 2295 no. arc points = 16593 no. surface atoms = 769 nbur = 931 mkacc time = 8.0000006E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 301 mr = 2452 m= 1 mr = 40 m= 0 mr = 0 time to grow re-entrant surface = 0.1000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2300000 number of dielectric boundary points 2882 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1537 ## 144 charges are in solution ## iepsmp to db, and charging done at 0.3600000 number of grid points assigned charge 5793 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 8.4941583E-09 3.5036742E-08 midg,1,midg; midg,igrid,midg 2.3504942E-08 1.4625280E-08 1,midg,midg; igrid,midg,midg 1.7261788E-08 2.1180961E-08 gauss-seidel spectral radius is 0.9882286 estimated iterations to convergence 75 setup time was (sec) 0.5500000 now iterating at: 14:34:12 rms-change max change #iterations 0.1334243 25.14143 at 10iterations 1.4165171E-02 2.981548 at 20iterations 1.4892967E-03 0.2313719 at 30iterations 1.6183744E-04 2.8324127E-02 at 40iterations 1.7469440E-05 2.6817322E-03 at 50iterations finished qdiffx linear iterations at : 14:34:25 total time elapsed so far: 4.890000 # loops : 50 mean,max change (kT/e) : 1.7469440E-05 2.6817322E-03 energy calculations done at 4.890000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 5.070000 DelPhi exited at 14:34:27 5.070u 0.441s 0:19.44 28.3% 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 15 2011 at 14:34:33 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: 266 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1700 !!! WARNING: HIT 228 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= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.997008 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): -31.18000 22.30000 ymin,ymax (A): 10.57700 51.46200 zmin,zma (A): 26.51800 69.53201 x,y,z range (A): 53.48000 40.88500 43.01401 scale (grids/A): 1.997008 object centre (A): -4.440001 31.01950 48.02500 number of atom coordinates read : 1700 total number of charged atoms : 1571 net assigned charge : 6.514028 assigned positive charge : 250.2003 centred at (gu) : 92.42787 90.21751 93.49923 assigned negative charge : -243.6865 centred at (gu) : 92.45172 90.31667 93.32098 start vw surface at 0.1000000 fill in re-entrant regions at 0.1900000 boundary points on vw surface= 53457 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16593 grid for indexing accessible points = 1.400000 m= 18429 mr = 34023 m= 3361 mr = 12766 m= 241 mr = 2091 m= 0 mr = 86 time to grow re-entrant surface = 0.2200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4600000 number of dielectric boundary points 26522 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 113 iepsmp to db, and charging done at 0.5900000 number of grid points assigned charge 12417 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) : 0.6656694 object centre at (A) : -4.440001 31.01950 48.02500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 7.6662218E-03 1.2768590E-02 midg,1,midg; midg,igrid,midg 2.2412391E-02 6.0780868E-03 1,midg,midg; igrid,midg,midg 1.2943113E-02 6.4100213E-03 gauss-seidel spectral radius is 0.9986718 estimated iterations to convergence 217 setup time was (sec) 0.8200000 now iterating at: 14:34:38 rms-change max change #iterations 3.592350 170.0764 at 10iterations 1.692342 68.96570 at 20iterations 0.7960995 28.92323 at 30iterations 0.3769144 13.33395 at 40iterations 0.1779312 7.138515 at 50iterations 8.4063038E-02 3.076880 at 60iterations 3.9537020E-02 1.424406 at 70iterations 1.8632637E-02 0.6994934 at 80iterations 8.7965326E-03 0.3431997 at 90iterations 4.1589001E-03 0.1449852 at 100iterations 1.9665528E-03 7.2212219E-02 at 110iterations 9.2610548E-04 4.2812347E-02 at 120iterations finished qdiffx linear iterations at : 14:35:03 total time elapsed so far: 12.09000 # loops : 120 mean,max change (kT/e) : 9.2610548E-04 4.2812347E-02 energy calculations done at 12.09000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.27000 DelPhi exited at 14:35:04 12.273u 0.533s 0:31.04 41.2% 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 15 2011 at 14:35:06 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: 266 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1700 !!! WARNING: HIT 228 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= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.995512 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): -31.18000 22.30000 ymin,ymax (A): 10.57700 51.46200 zmin,zma (A): 26.51800 69.53201 x,y,z range (A): 53.48000 40.88500 43.01401 scale (grids/A): 2.995512 object centre (A): -4.440001 31.01950 48.02500 number of atom coordinates read : 1700 total number of charged atoms : 1571 net assigned charge : 6.514028 assigned positive charge : 250.2003 centred at (gu) : 93.64191 90.32629 95.24892 assigned negative charge : -243.6865 centred at (gu) : 93.67767 90.47514 94.98154 start vw surface at 0.1000000 fill in re-entrant regions at 0.4100000 boundary points on vw surface= 123462 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16593 grid for indexing accessible points = 1.400000 m= 57677 mr = 83196 m= 22258 mr = 44942 m= 6157 mr = 17468 m= 978 mr = 4604 m= 64 mr = 617 m= 1 mr = 31 m= 0 mr = 0 time to grow re-entrant surface = 0.6999999 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.210000 number of dielectric boundary points 59739 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.360000 number of grid points assigned charge 12564 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) : 1.997008 object centre at (A) : -4.440001 31.01950 48.02500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.2377427E-02 7.0160828E-03 midg,1,midg; midg,igrid,midg 0.2086280 -1.2824605E-02 1,midg,midg; igrid,midg,midg 0.1129675 1.8724516E-02 gauss-seidel spectral radius is 0.9992579 estimated iterations to convergence 290 setup time was (sec) 1.600000 now iterating at: 14:35:12 rms-change max change #iterations 8.368176 402.6643 at 10iterations 4.853704 160.5480 at 20iterations 2.816897 82.77463 at 30iterations 1.626052 44.68352 at 40iterations 0.9377142 19.65776 at 50iterations 0.5415397 11.75040 at 60iterations 0.3115920 7.158226 at 70iterations 0.1786125 3.891335 at 80iterations 0.1026818 2.094939 at 90iterations 5.8946561E-02 1.502075 at 100iterations 3.3848297E-02 0.7078753 at 110iterations 1.9432751E-02 0.4293051 at 120iterations 1.1146222E-02 0.2289734 at 130iterations 6.3919062E-03 0.1295208 at 140iterations 3.6633622E-03 7.8132629E-02 at 150iterations 2.0992185E-03 4.5909405E-02 at 160iterations 1.2061056E-03 2.5683403E-02 at 170iterations 6.9086271E-04 1.3150215E-02 at 180iterations finished qdiffx linear iterations at : 14:35:52 total time elapsed so far: 19.88000 # loops : 180 mean,max change (kT/e) : 6.9086271E-04 1.3150215E-02 energy calculations done at 19.88000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 20.05000 DelPhi exited at 14:35:53 20.057u 0.586s 0:47.21 43.6% 0+0k 0+0io 0pf+0w