Mon Oct 10 14:15:48 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 Mon Oct 10 2011 at 14:15:48 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: 250 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2968 !!! WARNING: MG3 357 has a net charge of 1.4000 !!! WARNING: MG3 358 has a net charge of 1.4000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 0.5722737 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): -15.03300 34.51800 ymin,ymax (A): 14.71700 73.66700 zmin,zma (A): 15.66000 77.86800 x,y,z range (A): 49.55100 58.95000 62.20800 scale (grids/A): 0.5722737 object centre (A): 9.742500 44.19200 46.76400 number of atom coordinates read : 2968 total number of charged atoms : 2829 net assigned charge : -1.199981 assigned positive charge : 438.7001 centred at (gu) : 89.65382 89.15392 89.85377 assigned negative charge : -439.9008 centred at (gu) : 89.67902 89.07909 89.93285 start vw surface at 0.1700000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 6526 nv = 96 ne = 84 npr = 59526 no. pairs analyzed = 59526 no. exposed pairs = 3725 no. arc points = 26983 no. surface atoms = 1266 nbur = 1702 mkacc time = 0.1200000 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 = 1.512000 m= 304 mr = 3410 m= 1 mr = 6 m= 0 mr = 0 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 18 time to turn everything in is 0.3200000 number of dielectric boundary points 3415 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2837 ## 364 charges are in solution ## iepsmp to db, and charging done at 0.4400000 number of grid points assigned charge 8311 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.1663382E-09 -1.4789985E-09 midg,1,midg; midg,igrid,midg -1.7894415E-09 8.5996804E-10 1,midg,midg; igrid,midg,midg 2.5261107E-10 -5.6652033E-10 gauss-seidel spectral radius is 0.9842486 estimated iterations to convergence 65 setup time was (sec) 0.5500000 now iterating at: 14:15:49 rms-change max change #iterations 9.3581572E-02 15.79168 at 10iterations 7.1401475E-03 1.199934 at 20iterations 5.3351233E-04 8.3595276E-02 at 30iterations 4.1567622E-05 7.4577332E-03 at 40iterations 3.1410734E-06 4.7302246E-04 at 50iterations finished qdiffx linear iterations at : 14:15:52 total time elapsed so far: 3.060000 # loops : 50 mean,max change (kT/e) : 3.1410734E-06 4.7302246E-04 energy calculations done at 3.060000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.230000 DelPhi exited at 14:15:52 3.237u 0.148s 0:03.80 88.6% 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 Mon Oct 10 2011 at 14:15:52 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: 250 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2968 !!! WARNING: MG3 357 has a net charge of 1.4000 !!! WARNING: MG3 358 has a net charge of 1.4000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1000000 grid size : 179 scale,in grids/A, set to be: 1.716821 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): -15.03300 34.51800 ymin,ymax (A): 14.71700 73.66700 zmin,zma (A): 15.66000 77.86800 x,y,z range (A): 49.55100 58.95000 62.20800 scale (grids/A): 1.716821 object centre (A): 9.742500 44.19200 46.76400 number of atom coordinates read : 2968 total number of charged atoms : 2829 net assigned charge : -1.199981 assigned positive charge : 438.7001 centred at (gu) : 88.96047 87.46118 89.56051 assigned negative charge : -439.9008 centred at (gu) : 89.03654 87.23684 89.79814 start vw surface at 0.1700000 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 71815 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26983 grid for indexing accessible points = 1.400000 m= 22804 mr = 48732 m= 2613 mr = 15682 m= 90 mr = 1287 m= 3 mr = 8 m= 0 mr = 0 time to grow re-entrant surface = 0.2100000 no. cavity mid-points inaccessible to solvent = 2085 time to turn everything in is 0.5000000 number of dielectric boundary points 31616 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 266 ## 3 charges are in solution ## iepsmp to db, and charging done at 0.6100000 number of grid points assigned charge 21911 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) : 0.5722737 object centre at (A) : 9.742500 44.19200 46.76400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.6393428E-03 -1.8008199E-02 midg,1,midg; midg,igrid,midg -1.1343325E-02 1.1009302E-03 1,midg,midg; igrid,midg,midg 4.2973710E-03 -1.2569519E-02 gauss-seidel spectral radius is 0.9983630 estimated iterations to convergence 196 setup time was (sec) 0.7600000 now iterating at: 14:15:53 rms-change max change #iterations 3.669156 176.1482 at 10iterations 1.600374 53.64368 at 20iterations 0.6955700 24.33873 at 30iterations 0.3027931 10.28014 at 40iterations 0.1317729 4.740065 at 50iterations 5.7585862E-02 1.915212 at 60iterations 2.5089135E-02 0.9535446 at 70iterations 1.0881661E-02 0.3796678 at 80iterations 4.7659837E-03 0.1548152 at 90iterations 2.0789830E-03 6.4585596E-02 at 100iterations 9.0576743E-04 3.5923958E-02 at 110iterations 3.9525772E-04 1.3748169E-02 at 120iterations finished qdiffx linear iterations at : 14:15:59 total time elapsed so far: 6.960000 # loops : 120 mean,max change (kT/e) : 3.9525772E-04 1.3748169E-02 energy calculations done at 6.960000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.160000 DelPhi exited at 14:16:01 7.161u 0.212s 0:08.19 89.9% 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 Mon Oct 10 2011 at 14:16:01 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: 250 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2968 !!! WARNING: MG3 357 has a net charge of 1.4000 !!! WARNING: MG3 358 has a net charge of 1.4000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1100000 grid size : 179 scale,in grids/A, set to be: 2.575232 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): -15.03300 34.51800 ymin,ymax (A): 14.71700 73.66700 zmin,zma (A): 15.66000 77.86800 x,y,z range (A): 49.55100 58.95000 62.20800 scale (grids/A): 2.575232 object centre (A): 9.742500 44.19200 46.76400 number of atom coordinates read : 2968 total number of charged atoms : 2829 net assigned charge : -1.199981 assigned positive charge : 438.7001 centred at (gu) : 88.44051 86.19162 89.34071 assigned negative charge : -439.9008 centred at (gu) : 88.55479 85.85501 89.69705 start vw surface at 0.2000000 fill in re-entrant regions at 0.5300000 boundary points on vw surface= 166497 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26983 grid for indexing accessible points = 1.400000 m= 78392 mr = 118962 m= 23243 mr = 62287 m= 4103 mr = 17208 m= 316 mr = 2695 m= 6 mr = 141 m= 0 mr = 0 time to grow re-entrant surface = 0.6600000 no. cavity mid-points inaccessible to solvent = 6868 time to turn everything in is 1.310000 number of dielectric boundary points 71264 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 8 iepsmp to db, and charging done at 1.440000 number of grid points assigned charge 22625 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) : 1.716821 object centre at (A) : 9.742500 44.19200 46.76400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -9.3135975E-02 -0.2791982 midg,1,midg; midg,igrid,midg -0.2417446 1.9081276E-02 1,midg,midg; igrid,midg,midg 6.4286411E-02 -0.2060148 gauss-seidel spectral radius is 0.9991962 estimated iterations to convergence 279 setup time was (sec) 1.600000 now iterating at: 14:16:03 rms-change max change #iterations 9.281941 351.4528 at 10iterations 5.346484 174.8839 at 20iterations 3.051749 66.95667 at 30iterations 1.729229 43.30167 at 40iterations 0.9811811 23.92724 at 50iterations 0.5559201 12.53900 at 60iterations 0.3132278 6.523124 at 70iterations 0.1762579 3.520201 at 80iterations 9.9035375E-02 2.042069 at 90iterations 5.5812813E-02 1.123035 at 100iterations 3.1318281E-02 0.5903187 at 110iterations 1.7579902E-02 0.3520508 at 120iterations 9.8479884E-03 0.1966000 at 130iterations 5.5384613E-03 0.1120815 at 140iterations 3.1073492E-03 6.7382813E-02 at 150iterations 1.7391938E-03 3.2967091E-02 at 160iterations 9.7614445E-04 2.1167755E-02 at 170iterations 5.4766191E-04 1.0337830E-02 at 180iterations finished qdiffx linear iterations at : 14:16:13 total time elapsed so far: 11.61000 # loops : 180 mean,max change (kT/e) : 5.4766191E-04 1.0337830E-02 energy calculations done at 11.61000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.79000 DelPhi exited at 14:16:13 11.789u 0.195s 0:12.47 95.9% 0+0k 0+0io 0pf+0w