Wed Dec 21 14:20:56 PST 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 Wed Dec 21 2011 at 14:20:56 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: 263 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1966 !!! WARNING: ASH 25 has a net charge of -0.3190 !!! WARNING: ASH 125 has a net charge of -0.3190 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6472257 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): -6.559000 34.47600 ymin,ymax (A): -3.525000 48.11900 zmin,zma (A): -24.07500 30.92900 x,y,z range (A): 41.03500 51.64400 55.00400 scale (grids/A): 0.6472257 object centre (A): 13.95850 22.29700 3.427001 number of atom coordinates read : 1966 total number of charged atoms : 1832 net assigned charge : 3.362005 assigned positive charge : 287.8021 centred at (gu) : 91.01990 92.53313 90.10111 assigned negative charge : -284.4403 centred at (gu) : 91.15234 92.69098 90.04534 start vw surface at 7.0000000E-02 fill in re-entrant regions at 7.0000000E-02 boundary points on vw surface= 5546 nv = 96 ne = 84 npr = 40959 no. pairs analyzed = 40959 no. exposed pairs = 2404 no. arc points = 16847 no. surface atoms = 814 nbur = 1152 mkacc time = 8.0000006E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 280 mr = 3121 m= 2 mr = 32 m= 0 mr = 0 time to grow re-entrant surface = 8.9999996E-02 no. cavity mid-points inaccessible to solvent = 44 time to turn everything in is 0.1600000 number of dielectric boundary points 2675 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1680 ## 159 charges are in solution ## iepsmp to db, and charging done at 0.2600000 number of grid points assigned charge 6593 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 8.1697238E-10 1.2566335E-08 midg,1,midg; midg,igrid,midg 1.3270169E-08 -1.7628304E-08 1,midg,midg; igrid,midg,midg 1.6150860E-08 -9.1077803E-09 gauss-seidel spectral radius is 0.9875715 estimated iterations to convergence 73 setup time was (sec) 0.4700000 now iterating at: 14:20:57 rms-change max change #iterations 0.1315430 23.75157 at 10iterations 1.3262430E-02 2.022759 at 20iterations 1.3463735E-03 0.2408090 at 30iterations 1.3594430E-04 2.1144867E-02 at 40iterations 1.3837775E-05 2.6912689E-03 at 50iterations finished qdiffx linear iterations at : 14:21:01 total time elapsed so far: 4.640000 # loops : 50 mean,max change (kT/e) : 1.3837775E-05 2.6912689E-03 energy calculations done at 4.640000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.770000 DelPhi exited at 14:21:03 4.777u 0.335s 0:06.83 74.6% 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 Wed Dec 21 2011 at 14:21:04 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: 263 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1966 !!! WARNING: ASH 25 has a net charge of -0.3190 !!! WARNING: ASH 125 has a net charge of -0.3190 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: 1.941677 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): -6.559000 34.47600 ymin,ymax (A): -3.525000 48.11900 zmin,zma (A): -24.07500 30.92900 x,y,z range (A): 41.03500 51.64400 55.00400 scale (grids/A): 1.941677 object centre (A): 13.95850 22.29700 3.427001 number of atom coordinates read : 1966 total number of charged atoms : 1832 net assigned charge : 3.362005 assigned positive charge : 287.8021 centred at (gu) : 93.05954 97.59944 90.30333 assigned negative charge : -284.4403 centred at (gu) : 93.45742 98.07309 90.13638 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 59589 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16847 grid for indexing accessible points = 1.400000 m= 22161 mr = 41339 m= 3573 mr = 17020 m= 216 mr = 2378 m= 4 mr = 103 m= 0 mr = 0 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 2876 time to turn everything in is 0.3100000 number of dielectric boundary points 24703 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 97 iepsmp to db, and charging done at 0.4100000 number of grid points assigned charge 14459 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) : 0.6472257 object centre at (A) : 13.95850 22.29700 3.427001 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.7416229E-02 1.9250382E-02 midg,1,midg; midg,igrid,midg 3.9169233E-02 -8.6202165E-03 1,midg,midg; igrid,midg,midg 9.9223545E-03 -7.0259920E-03 gauss-seidel spectral radius is 0.9986035 estimated iterations to convergence 212 setup time was (sec) 0.5800000 now iterating at: 14:21:05 rms-change max change #iterations 3.674732 166.1346 at 10iterations 1.708376 57.71782 at 20iterations 0.7961639 28.41436 at 30iterations 0.3695809 12.72863 at 40iterations 0.1713192 6.590878 at 50iterations 7.9358213E-02 3.010300 at 60iterations 3.6840275E-02 1.378121 at 70iterations 1.7139196E-02 0.5541000 at 80iterations 7.9195797E-03 0.2691879 at 90iterations 3.6885855E-03 0.1280460 at 100iterations 1.7152409E-03 6.2454224E-02 at 110iterations 7.9273258E-04 2.7776718E-02 at 120iterations finished qdiffx linear iterations at : 14:21:17 total time elapsed so far: 12.34000 # loops : 120 mean,max change (kT/e) : 7.9273258E-04 2.7776718E-02 energy calculations done at 12.34000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.47000 DelPhi exited at 14:21:26 12.475u 0.380s 0:22.19 57.9% 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 Wed Dec 21 2011 at 14:21:26 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: 263 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1966 !!! WARNING: ASH 25 has a net charge of -0.3190 !!! WARNING: ASH 125 has a net charge of -0.3190 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.912516 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): -6.559000 34.47600 ymin,ymax (A): -3.525000 48.11900 zmin,zma (A): -24.07500 30.92900 x,y,z range (A): 41.03500 51.64400 55.00400 scale (grids/A): 2.912516 object centre (A): 13.95850 22.29700 3.427001 number of atom coordinates read : 1966 total number of charged atoms : 1832 net assigned charge : 3.362005 assigned positive charge : 287.8021 centred at (gu) : 94.58934 101.3991 90.45499 assigned negative charge : -284.4403 centred at (gu) : 95.18624 102.1096 90.20466 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.3000000 boundary points on vw surface= 137582 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16847 grid for indexing accessible points = 1.400000 m= 70863 mr = 99847 m= 26555 mr = 59204 m= 6520 mr = 22047 m= 996 mr = 5114 m= 65 mr = 730 m= 0 mr = 22 time to grow re-entrant surface = 0.4300000 no. cavity mid-points inaccessible to solvent = 10188 time to turn everything in is 0.8100000 number of dielectric boundary points 55617 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 0.9000000 number of grid points assigned charge 14656 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) : 1.941677 object centre at (A) : 13.95850 22.29700 3.427001 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.9970386 6.4465210E-02 midg,1,midg; midg,igrid,midg 0.3791876 -0.1051731 1,midg,midg; igrid,midg,midg 6.5992273E-02 -4.2000275E-02 gauss-seidel spectral radius is 0.9992359 estimated iterations to convergence 286 setup time was (sec) 1.080000 now iterating at: 14:21:29 rms-change max change #iterations 8.601073 420.6047 at 10iterations 4.954107 133.4716 at 20iterations 2.823695 81.51286 at 30iterations 1.604213 35.63526 at 40iterations 0.9159688 19.90137 at 50iterations 0.5223733 12.66584 at 60iterations 0.2960038 5.870723 at 70iterations 0.1688289 3.668996 at 80iterations 9.6006341E-02 2.148168 at 90iterations 5.4476663E-02 1.002220 at 100iterations 3.0964203E-02 0.6306766 at 110iterations 1.7589044E-02 0.3752890 at 120iterations 1.0023007E-02 0.2186375 at 130iterations 5.6882040E-03 0.1199293 at 140iterations 3.2393083E-03 6.7199767E-02 at 150iterations 1.8372331E-03 3.9596558E-02 at 160iterations 1.0453109E-03 2.0752907E-02 at 170iterations 5.9367949E-04 1.1368752E-02 at 180iterations finished qdiffx linear iterations at : 14:21:45 total time elapsed so far: 16.96000 # loops : 180 mean,max change (kT/e) : 5.9367949E-04 1.1368752E-02 energy calculations done at 16.96000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 17.10000 DelPhi exited at 14:22:04 17.100u 0.294s 0:37.56 46.2% 0+0k 0+0io 0pf+0w