Sat Oct 15 12:09:05 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 Sat Oct 15 2011 at 12:09:05 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: 306 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2359 !!! WARNING: HIT 84 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: 0.6377300 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): -2.487000 53.33600 ymin,ymax (A): -16.26500 27.64800 zmin,zma (A): 28.57700 83.86100 x,y,z range (A): 55.82300 43.91300 55.28400 scale (grids/A): 0.6377300 object centre (A): 25.42450 5.691501 56.21900 number of atom coordinates read : 2359 total number of charged atoms : 2224 net assigned charge : 10.01402 assigned positive charge : 346.3973 centred at (gu) : 91.17346 89.83948 89.72172 assigned negative charge : -336.3840 centred at (gu) : 91.18191 89.91076 89.63930 start vw surface at 9.0000004E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 6697 nv = 96 ne = 84 npr = 47113 no. pairs analyzed = 47113 no. exposed pairs = 3130 no. arc points = 22757 no. surface atoms = 1039 nbur = 1320 mkacc time = 7.9999998E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 372 mr = 3420 m= 3 mr = 30 m= 0 mr = 0 time to grow re-entrant surface = 8.9999989E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.1900000 number of dielectric boundary points 3622 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2254 ## 206 charges are in solution ## iepsmp to db, and charging done at 0.2800000 number of grid points assigned charge 7827 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 6.0887810E-09 2.0197827E-08 midg,1,midg; midg,igrid,midg 2.1083478E-08 6.6375279E-09 1,midg,midg; igrid,midg,midg 1.1355598E-08 1.6419699E-08 gauss-seidel spectral radius is 0.9872521 estimated iterations to convergence 72 setup time was (sec) 0.4400000 now iterating at: 12:09:06 rms-change max change #iterations 0.1377459 23.95700 at 10iterations 1.3349250E-02 1.973408 at 20iterations 1.3042199E-03 0.2057800 at 30iterations 1.2951631E-04 1.8888235E-02 at 40iterations 1.3545355E-05 1.8692017E-03 at 50iterations finished qdiffx linear iterations at : 12:09:10 total time elapsed so far: 4.160000 # loops : 50 mean,max change (kT/e) : 1.3545355E-05 1.8692017E-03 energy calculations done at 4.160000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.290000 DelPhi exited at 12:09:10 4.297u 0.305s 0:05.00 91.8% 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 Sat Oct 15 2011 at 12:09:10 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: 306 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2359 !!! WARNING: HIT 84 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: 1.913190 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): -2.487000 53.33600 ymin,ymax (A): -16.26500 27.64800 zmin,zma (A): 28.57700 83.86100 x,y,z range (A): 55.82300 43.91300 55.28400 scale (grids/A): 1.913190 object centre (A): 25.42450 5.691501 56.21900 number of atom coordinates read : 2359 total number of charged atoms : 2224 net assigned charge : 10.01402 assigned positive charge : 346.3973 centred at (gu) : 93.52023 89.51814 89.16489 assigned negative charge : -336.3840 centred at (gu) : 93.54573 89.73210 88.91782 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 71157 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22757 grid for indexing accessible points = 1.400000 m= 25076 mr = 47005 m= 4159 mr = 17845 m= 248 mr = 2453 m= 3 mr = 61 m= 0 mr = 0 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 412 time to turn everything in is 0.3500000 number of dielectric boundary points 33279 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 151 iepsmp to db, and charging done at 0.4300000 number of grid points assigned charge 17515 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) : 0.6377300 object centre at (A) : 25.42450 5.691501 56.21900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.1313096E-02 6.1969675E-02 midg,1,midg; midg,igrid,midg 2.7059224E-02 -1.6254170E-03 1,midg,midg; igrid,midg,midg 1.6099544E-02 4.4233818E-02 gauss-seidel spectral radius is 0.9986395 estimated iterations to convergence 215 setup time was (sec) 0.5800000 now iterating at: 12:09:11 rms-change max change #iterations 4.007898 204.4718 at 10iterations 1.875805 69.18484 at 20iterations 0.8772371 32.41289 at 30iterations 0.4076118 14.27623 at 40iterations 0.1909534 6.187528 at 50iterations 8.9430891E-02 2.913788 at 60iterations 4.1970033E-02 1.376990 at 70iterations 1.9505199E-02 0.6367536 at 80iterations 9.1766398E-03 0.2921066 at 90iterations 4.2981422E-03 0.1380463 at 100iterations 2.0072465E-03 7.1540833E-02 at 110iterations 9.4066490E-04 3.3018112E-02 at 120iterations finished qdiffx linear iterations at : 12:09:18 total time elapsed so far: 8.010000 # loops : 120 mean,max change (kT/e) : 9.4066490E-04 3.3018112E-02 energy calculations done at 8.010000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.150000 DelPhi exited at 12:09:19 8.154u 0.230s 0:08.78 95.4% 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 12:09:19 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: 306 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2359 !!! WARNING: HIT 84 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: 2.869785 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): -2.487000 53.33600 ymin,ymax (A): -16.26500 27.64800 zmin,zma (A): 28.57700 83.86100 x,y,z range (A): 55.82300 43.91300 55.28400 scale (grids/A): 2.869785 object centre (A): 25.42450 5.691501 56.21900 number of atom coordinates read : 2359 total number of charged atoms : 2224 net assigned charge : 10.01402 assigned positive charge : 346.3973 centred at (gu) : 95.28014 89.27692 88.74731 assigned negative charge : -336.3840 centred at (gu) : 95.31860 89.59820 88.37679 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.3300000 boundary points on vw surface= 164126 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22757 grid for indexing accessible points = 1.400000 m= 80842 mr = 114594 m= 29686 mr = 64433 m= 7281 mr = 23156 m= 1090 mr = 5279 m= 74 mr = 665 m= 2 mr = 31 m= 0 mr = 0 time to grow re-entrant surface = 0.5400000 no. cavity mid-points inaccessible to solvent = 1315 time to turn everything in is 0.9700000 number of dielectric boundary points 74943 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.080000 number of grid points assigned charge 17791 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) : 1.913190 object centre at (A) : 25.42450 5.691501 56.21900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1414422 0.8533714 midg,1,midg; midg,igrid,midg 0.2552003 -2.6130421E-02 1,midg,midg; igrid,midg,midg 0.2097216 0.3668588 gauss-seidel spectral radius is 0.9992703 estimated iterations to convergence 292 setup time was (sec) 1.260000 now iterating at: 12:09:20 rms-change max change #iterations 9.609854 467.1074 at 10iterations 5.694141 169.3895 at 20iterations 3.336052 81.29041 at 30iterations 1.952745 44.12652 at 40iterations 1.136422 26.47489 at 50iterations 0.6602337 14.47086 at 60iterations 0.3832324 7.945313 at 70iterations 0.2219701 4.387865 at 80iterations 0.1286065 2.451730 at 90iterations 7.4379943E-02 1.332605 at 100iterations 4.2989302E-02 0.8210897 at 110iterations 2.4812339E-02 0.5127754 at 120iterations 1.4319922E-02 0.2675018 at 130iterations 8.2738996E-03 0.1551781 at 140iterations 4.7724075E-03 9.4455719E-02 at 150iterations 2.7538857E-03 5.6964636E-02 at 160iterations 1.5877485E-03 3.2998085E-02 at 170iterations 9.1510831E-04 1.7313957E-02 at 180iterations finished qdiffx linear iterations at : 12:09:33 total time elapsed so far: 13.32000 # loops : 180 mean,max change (kT/e) : 9.1510831E-04 1.7313957E-02 energy calculations done at 13.32000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.45000 DelPhi exited at 12:09:33 13.454u 0.291s 0:14.24 96.4% 0+0k 0+0io 0pf+0w