Thu Jan 19 13:32:17 PST 2012 #!/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 Thu Jan 19 2012 at 13:32:18 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: 340 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 6758 !!! WARNING: PHE 76 has a net charge of 0.0060 !!! WARNING: ARG 148 has a net charge of 0.0400 !!! WARNING: ARG 149 has a net charge of 0.0400 !!! WARNING: LYS 155 has a net charge of 0.0200 !!! WARNING: LYS 286 has a net charge of 0.0200 !!! WARNING: ASH 331 has a net charge of -0.3190 !!! WARNING: HIZ 357 has a net charge of 0.2000 !!! WARNING: ARG 407 has a net charge of 0.0400 !!! WARNING: LYS 442 has a net charge of 0.0200 !!! WARNING: LYS 454 has a net charge of 0.0200 !!! WARNING: MET 456 has a net charge of -0.0720 !!! WARNING: LYS 542 has a net charge of 0.0200 !!! WARNING: TRP 597 has a net charge of 0.0220 !!! WARNING: HEM 1107 has a net charge of -4.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1200000 grid size : 179 scale,in grids/A, set to be: 0.4225369 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): -61.88300 3.264000 ymin,ymax (A): -96.44100 -17.36500 zmin,zma (A): -27.98300 56.27000 x,y,z range (A): 65.14700 79.07600 84.25300 scale (grids/A): 0.4225369 object centre (A): -29.30950 -56.90300 14.14350 number of atom coordinates read : 6758 total number of charged atoms : 6588 net assigned charge : -6.942936 assigned positive charge : 1021.308 centred at (gu) : 91.08169 90.13419 88.54127 assigned negative charge : -1028.261 centred at (gu) : 91.09305 90.07511 88.47942 start vw surface at 0.1700000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 7147 nv = 96 ne = 84 npr = 135885 no. pairs analyzed = 135885 no. exposed pairs = 8823 no. arc points = 60117 no. surface atoms = 2946 nbur = 3812 mkacc time = 0.2300000 writing accessible surface arcs data to file ARCDAT initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.988000 m= 171 mr = 3342 m= 0 mr = 0 time to grow re-entrant surface = 0.2400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4300000 number of dielectric boundary points 3976 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4879 ## 1066 charges are in solution ## iepsmp to db, and charging done at 0.5100000 number of grid points assigned charge 9905 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -5.2232029E-12 9.9197983E-13 midg,1,midg; midg,igrid,midg -3.0401222E-12 1.5458134E-12 1,midg,midg; igrid,midg,midg -2.7580087E-13 -1.7838251E-12 gauss-seidel spectral radius is 0.9715928 estimated iterations to convergence 50 setup time was (sec) 0.6400000 now iterating at: 13:32:22 rms-change max change #iterations 2.8629934E-02 5.154095 at 10iterations 2.7369747E-03 0.4905472 at 20iterations 1.0350582E-03 0.1896763 at 30iterations 4.0792584E-04 7.4256897E-02 at 40iterations 1.6047774E-04 2.9106140E-02 at 50iterations finished qdiffx linear iterations at : 13:32:31 total time elapsed so far: 3.730000 # loops : 50 mean,max change (kT/e) : 1.6047774E-04 2.9106140E-02 energy calculations done at 3.730000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.860000 DelPhi exited at 13:32:32 3.863u 0.168s 0:14.52 27.6% 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 Thu Jan 19 2012 at 13:32:32 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: 340 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 6758 !!! WARNING: PHE 76 has a net charge of 0.0060 !!! WARNING: ARG 148 has a net charge of 0.0400 !!! WARNING: ARG 149 has a net charge of 0.0400 !!! WARNING: LYS 155 has a net charge of 0.0200 !!! WARNING: LYS 286 has a net charge of 0.0200 !!! WARNING: ASH 331 has a net charge of -0.3190 !!! WARNING: HIZ 357 has a net charge of 0.2000 !!! WARNING: ARG 407 has a net charge of 0.0400 !!! WARNING: LYS 442 has a net charge of 0.0200 !!! WARNING: LYS 454 has a net charge of 0.0200 !!! WARNING: MET 456 has a net charge of -0.0720 !!! WARNING: LYS 542 has a net charge of 0.0200 !!! WARNING: TRP 597 has a net charge of 0.0220 !!! WARNING: HEM 1107 has a net charge of -4.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1200000 grid size : 179 scale,in grids/A, set to be: 1.267611 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): -61.88300 3.264000 ymin,ymax (A): -96.44100 -17.36500 zmin,zma (A): -27.98300 56.27000 x,y,z range (A): 65.14700 79.07600 84.25300 scale (grids/A): 1.267611 object centre (A): -29.30950 -56.90300 14.14350 number of atom coordinates read : 6758 total number of charged atoms : 6588 net assigned charge : -6.942936 assigned positive charge : 1021.308 centred at (gu) : 93.24248 90.40051 85.62135 assigned negative charge : -1028.261 centred at (gu) : 93.27895 90.22488 85.43747 start vw surface at 0.1600000 fill in re-entrant regions at 0.2300000 boundary points on vw surface= 84121 reading accessible surface arcs data from file ARCDAT no. of arc points read = 60117 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.848000 m= 19334 mr = 55279 m= 956 mr = 11328 m= 6 mr = 180 m= 0 mr = 0 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 493 time to turn everything in is 0.4500000 number of dielectric boundary points 37630 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1145 ## 54 charges are in solution ## iepsmp to db, and charging done at 0.5400000 number of grid points assigned charge 45362 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) : 0.4225369 object centre at (A) : -29.30950 -56.90300 14.14350 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.7050982E-02 1.0606226E-04 midg,1,midg; midg,igrid,midg -1.2874175E-03 5.1968504E-04 1,midg,midg; igrid,midg,midg 1.3017332E-03 -1.3848090E-03 gauss-seidel spectral radius is 0.9972978 estimated iterations to convergence 153 setup time was (sec) 0.6800000 now iterating at: 13:32:33 rms-change max change #iterations 2.907739 119.5002 at 10iterations 1.002450 43.94268 at 20iterations 0.3454815 13.40284 at 30iterations 0.1189836 4.028912 at 40iterations 4.1640460E-02 1.665592 at 50iterations 1.4710790E-02 0.5112972 at 60iterations 5.5394885E-03 0.2154064 at 70iterations 2.4920651E-03 9.7499847E-02 at 80iterations 1.4344323E-03 5.6835175E-02 at 90iterations 9.5771800E-04 3.5066605E-02 at 100iterations 6.7389011E-04 2.5077820E-02 at 110iterations 4.8041740E-04 1.7679214E-02 at 120iterations finished qdiffx linear iterations at : 13:32:47 total time elapsed so far: 7.970000 # loops : 120 mean,max change (kT/e) : 4.8041740E-04 1.7679214E-02 energy calculations done at 7.970000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.100000 DelPhi exited at 13:32:48 8.100u 0.224s 0:15.68 53.0% 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 Thu Jan 19 2012 at 13:32:48 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: 340 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 6758 !!! WARNING: PHE 76 has a net charge of 0.0060 !!! WARNING: ARG 148 has a net charge of 0.0400 !!! WARNING: ARG 149 has a net charge of 0.0400 !!! WARNING: LYS 155 has a net charge of 0.0200 !!! WARNING: LYS 286 has a net charge of 0.0200 !!! WARNING: ASH 331 has a net charge of -0.3190 !!! WARNING: HIZ 357 has a net charge of 0.2000 !!! WARNING: ARG 407 has a net charge of 0.0400 !!! WARNING: LYS 442 has a net charge of 0.0200 !!! WARNING: LYS 454 has a net charge of 0.0200 !!! WARNING: MET 456 has a net charge of -0.0720 !!! WARNING: LYS 542 has a net charge of 0.0200 !!! WARNING: TRP 597 has a net charge of 0.0220 !!! WARNING: HEM 1107 has a net charge of -4.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1200000 grid size : 179 scale,in grids/A, set to be: 1.901416 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): -61.88300 3.264000 ymin,ymax (A): -96.44100 -17.36500 zmin,zma (A): -27.98300 56.27000 x,y,z range (A): 65.14700 79.07600 84.25300 scale (grids/A): 1.901416 object centre (A): -29.30950 -56.90300 14.14350 number of atom coordinates read : 6758 total number of charged atoms : 6588 net assigned charge : -6.942936 assigned positive charge : 1021.308 centred at (gu) : 94.86337 90.59994 83.43136 assigned negative charge : -1028.261 centred at (gu) : 94.91840 90.33716 83.15606 start vw surface at 0.1600000 fill in re-entrant regions at 0.3700000 boundary points on vw surface= 197366 reading accessible surface arcs data from file ARCDAT no. of arc points read = 60117 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.820000 m= 75689 mr = 138092 m= 13322 mr = 55512 m= 888 mr = 8237 m= 11 mr = 310 m= 0 mr = 0 time to grow re-entrant surface = 0.5600000 no. cavity mid-points inaccessible to solvent = 1805 time to turn everything in is 1.010000 number of dielectric boundary points 85125 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 351 iepsmp to db, and charging done at 1.110000 number of grid points assigned charge 51845 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) : 1.267611 object centre at (A) : -29.30950 -56.90300 14.14350 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.5271366 2.7830230E-02 midg,1,midg; midg,igrid,midg -2.5171725E-02 2.0904142E-02 1,midg,midg; igrid,midg,midg 3.1979620E-02 -1.7323461E-03 gauss-seidel spectral radius is 0.9989443 estimated iterations to convergence 243 setup time was (sec) 1.270000 now iterating at: 13:32:50 rms-change max change #iterations 9.053345 282.9177 at 10iterations 4.848114 119.6895 at 20iterations 2.568584 64.27140 at 30iterations 1.354592 32.30274 at 40iterations 0.7118157 16.51514 at 50iterations 0.3721188 8.542480 at 60iterations 0.1943705 4.499240 at 70iterations 0.1009909 2.523979 at 80iterations 5.2586623E-02 1.281734 at 90iterations 2.7274070E-02 0.6133347 at 100iterations 1.4151883E-02 0.2931223 at 110iterations 7.3416797E-03 0.1736107 at 120iterations 3.8143960E-03 8.4274292E-02 at 130iterations 1.9864039E-03 4.0707588E-02 at 140iterations 1.0442060E-03 2.4116516E-02 at 150iterations 5.5902667E-04 1.1245728E-02 at 160iterations 3.1017387E-04 6.8855286E-03 at 170iterations 1.8316196E-04 4.8751831E-03 at 180iterations finished qdiffx linear iterations at : 13:33:15 total time elapsed so far: 13.48000 # loops : 180 mean,max change (kT/e) : 1.8316196E-04 4.8751831E-03 energy calculations done at 13.48000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.62000 DelPhi exited at 13:33:16 13.623u 0.246s 0:27.74 49.9% 0+0k 0+0io 0pf+0w