Tue Oct 11 04:29:35 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 Tue Oct 11 2011 at 04:29:35 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: 254 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2731 !!! WARNING: TYS 1 has a net charge of -0.3380 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 0.6388744 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): -12.37700 36.51600 ymin,ymax (A): -25.82100 22.59900 zmin,zma (A): -10.43100 45.29200 x,y,z range (A): 48.89300 48.42000 55.72300 scale (grids/A): 0.6388744 object centre (A): 12.06950 -1.611000 17.43050 number of atom coordinates read : 2731 total number of charged atoms : 2579 net assigned charge : 3.162011 assigned positive charge : 411.6007 centred at (gu) : 90.47061 90.31858 91.93993 assigned negative charge : -408.4393 centred at (gu) : 90.22270 90.15220 91.87688 start vw surface at 0.1000000 fill in re-entrant regions at 0.1100000 boundary points on vw surface= 7388 nv = 96 ne = 84 npr = 55782 no. pairs analyzed = 55782 no. exposed pairs = 3304 no. arc points = 22789 no. surface atoms = 1108 nbur = 1623 mkacc time = 9.0000004E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 389 mr = 4192 m= 1 mr = 42 m= 0 mr = 0 time to grow re-entrant surface = 0.1000000 no. cavity mid-points inaccessible to solvent = 41 time to turn everything in is 0.2200000 number of dielectric boundary points 3544 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2237 ## 204 charges are in solution ## iepsmp to db, and charging done at 0.2900000 number of grid points assigned charge 8914 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -2.1813895E-09 1.7563281E-08 midg,1,midg; midg,igrid,midg -1.4898029E-08 2.5169319E-08 1,midg,midg; igrid,midg,midg -2.3535458E-08 3.6259472E-08 gauss-seidel spectral radius is 0.9873130 estimated iterations to convergence 73 setup time was (sec) 0.4100000 now iterating at: 04:29:35 rms-change max change #iterations 0.1459258 20.47937 at 10iterations 1.4723426E-02 2.166380 at 20iterations 1.5992697E-03 0.2554379 at 30iterations 2.2712935E-04 3.0323029E-02 at 40iterations 5.2920408E-05 7.3909760E-03 at 50iterations finished qdiffx linear iterations at : 04:29:38 total time elapsed so far: 3.320000 # loops : 50 mean,max change (kT/e) : 5.2920408E-05 7.3909760E-03 energy calculations done at 3.320000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.450000 DelPhi exited at 04:29:39 3.453u 0.180s 0:04.10 88.5% 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 Tue Oct 11 2011 at 04:29:39 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: 254 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2731 !!! WARNING: TYS 1 has a net charge of -0.3380 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 1.916623 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): -12.37700 36.51600 ymin,ymax (A): -25.82100 22.59900 zmin,zma (A): -10.43100 45.29200 x,y,z range (A): 48.89300 48.42000 55.72300 scale (grids/A): 1.916623 object centre (A): 12.06950 -1.611000 17.43050 number of atom coordinates read : 2731 total number of charged atoms : 2579 net assigned charge : 3.162011 assigned positive charge : 411.6007 centred at (gu) : 91.41125 90.95537 95.81919 assigned negative charge : -408.4393 centred at (gu) : 90.66780 90.45615 95.63038 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 79868 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22789 grid for indexing accessible points = 1.400000 m= 28963 mr = 56526 m= 4301 mr = 21473 m= 242 mr = 2644 m= 3 mr = 69 m= 0 mr = 0 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 967 time to turn everything in is 0.4000000 number of dielectric boundary points 32665 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 147 iepsmp to db, and charging done at 0.4800000 number of grid points assigned charge 20268 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) : 0.6388744 object centre at (A) : 12.06950 -1.611000 17.43050 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -3.6553252E-02 1.0056589E-02 midg,1,midg; midg,igrid,midg -1.0143963E-02 2.7289886E-02 1,midg,midg; igrid,midg,midg -9.4253048E-03 5.0342493E-02 gauss-seidel spectral radius is 0.9986621 estimated iterations to convergence 217 setup time was (sec) 0.6200000 now iterating at: 04:29:40 rms-change max change #iterations 4.416802 210.0274 at 10iterations 2.084901 78.89385 at 20iterations 0.9866583 31.10328 at 30iterations 0.4675382 15.18050 at 40iterations 0.2205502 6.811338 at 50iterations 0.1039931 3.241120 at 60iterations 4.9280103E-02 1.732802 at 70iterations 2.3303254E-02 0.7988014 at 80iterations 1.1015019E-02 0.3586748 at 90iterations 5.2100774E-03 0.1686115 at 100iterations 2.4831609E-03 7.3701859E-02 at 110iterations 1.1811140E-03 3.5892487E-02 at 120iterations finished qdiffx linear iterations at : 04:29:47 total time elapsed so far: 7.820000 # loops : 120 mean,max change (kT/e) : 1.1811140E-03 3.5892487E-02 energy calculations done at 7.820000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.960000 DelPhi exited at 04:29:47 7.967u 0.195s 0:08.67 94.0% 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 Tue Oct 11 2011 at 04:29:47 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: 254 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2731 !!! WARNING: TYS 1 has a net charge of -0.3380 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 2.874935 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): -12.37700 36.51600 ymin,ymax (A): -25.82100 22.59900 zmin,zma (A): -10.43100 45.29200 x,y,z range (A): 48.89300 48.42000 55.72300 scale (grids/A): 2.874935 object centre (A): 12.06950 -1.611000 17.43050 number of atom coordinates read : 2731 total number of charged atoms : 2579 net assigned charge : 3.162011 assigned positive charge : 411.6007 centred at (gu) : 92.11687 91.43295 98.72855 assigned negative charge : -408.4393 centred at (gu) : 91.00156 90.68413 98.44547 start vw surface at 0.1000000 fill in re-entrant regions at 0.3600000 boundary points on vw surface= 184952 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22789 grid for indexing accessible points = 1.400000 m= 94812 mr = 136865 m= 33199 mr = 78211 m= 7563 mr = 26676 m= 886 mr = 5516 m= 49 mr = 534 m= 0 mr = 12 time to grow re-entrant surface = 0.5900000 no. cavity mid-points inaccessible to solvent = 3240 time to turn everything in is 1.030000 number of dielectric boundary points 73647 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.120000 number of grid points assigned charge 20620 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) : 1.916623 object centre at (A) : 12.06950 -1.611000 17.43050 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.7121421 0.2947645 midg,1,midg; midg,igrid,midg -0.1253332 0.3217612 1,midg,midg; igrid,midg,midg -7.6597914E-02 0.4066755 gauss-seidel spectral radius is 0.9992655 estimated iterations to convergence 291 setup time was (sec) 1.270000 now iterating at: 04:29:49 rms-change max change #iterations 10.34501 307.9968 at 10iterations 6.054917 138.4860 at 20iterations 3.541072 71.13607 at 30iterations 2.063017 41.99023 at 40iterations 1.198794 24.55360 at 50iterations 0.6949434 12.43489 at 60iterations 0.4013188 7.711060 at 70iterations 0.2333263 4.484570 at 80iterations 0.1347942 2.451775 at 90iterations 7.7977031E-02 1.411785 at 100iterations 4.5013607E-02 0.8514271 at 110iterations 2.6060158E-02 0.5257378 at 120iterations 1.5060508E-02 0.2672234 at 130iterations 8.7255659E-03 0.1498146 at 140iterations 5.0761998E-03 8.6141586E-02 at 150iterations 2.9638223E-03 5.4191113E-02 at 160iterations 1.7419339E-03 3.6911011E-02 at 170iterations 1.0428755E-03 1.9493103E-02 at 180iterations finished qdiffx linear iterations at : 04:30:00 total time elapsed so far: 12.57000 # loops : 180 mean,max change (kT/e) : 1.0428755E-03 1.9493103E-02 energy calculations done at 12.57000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.71000 DelPhi exited at 04:30:01 12.708u 0.213s 0:13.33 96.8% 0+0k 0+0io 0pf+0w