Mon Oct 10 13:54:21 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 Mon Oct 10 2011 at 13:54:21 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: 252 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4974 !!! WARNING: PLP 999 has a net charge of -0.3790 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 0.5627391 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): 3.309000 65.09600 ymin,ymax (A): -8.516000 52.46900 zmin,zma (A): -1.186000 62.07600 x,y,z range (A): 61.78700 60.98500 63.26200 scale (grids/A): 0.5627391 object centre (A): 34.20250 21.97650 30.44500 number of atom coordinates read : 4974 total number of charged atoms : 4836 net assigned charge : 1.121042 assigned positive charge : 763.0548 centred at (gu) : 88.37203 89.35812 89.15599 assigned negative charge : -761.9396 centred at (gu) : 88.24755 89.38604 89.14040 start vw surface at 0.1300000 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 10234 nv = 96 ne = 84 npr = 100701 no. pairs analyzed = 100701 no. exposed pairs = 5766 no. arc points = 39041 no. surface atoms = 1968 nbur = 3006 mkacc time = 0.1800000 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= 500 mr = 5890 m= 1 mr = 25 m= 0 mr = 0 time to grow re-entrant surface = 0.2000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3400000 number of dielectric boundary points 4820 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4031 ## 406 charges are in solution ## iepsmp to db, and charging done at 0.4100000 number of grid points assigned charge 13485 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.8157330E-10 4.1052206E-10 midg,1,midg; midg,igrid,midg 8.8683916E-10 -3.4484218E-10 1,midg,midg; igrid,midg,midg -3.6757226E-09 1.8428661E-09 gauss-seidel spectral radius is 0.9838566 estimated iterations to convergence 65 setup time was (sec) 0.5300000 now iterating at: 13:54:22 rms-change max change #iterations 0.1164260 14.04057 at 10iterations 1.0953177E-02 1.356369 at 20iterations 3.1285461E-03 0.3100128 at 30iterations 1.4631812E-03 0.1418772 at 40iterations 7.2202558E-04 7.8847885E-02 at 50iterations finished qdiffx linear iterations at : 13:54:25 total time elapsed so far: 3.370000 # loops : 50 mean,max change (kT/e) : 7.2202558E-04 7.8847885E-02 energy calculations done at 3.370000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.500000 DelPhi exited at 13:54:25 3.505u 0.160s 0:04.01 91.2% 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 13:54:25 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: 252 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4974 !!! WARNING: PLP 999 has a net charge of -0.3790 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 1.688217 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): 3.309000 65.09600 ymin,ymax (A): -8.516000 52.46900 zmin,zma (A): -1.186000 62.07600 x,y,z range (A): 61.78700 60.98500 63.26200 scale (grids/A): 1.688217 object centre (A): 34.20250 21.97650 30.44500 number of atom coordinates read : 4974 total number of charged atoms : 4836 net assigned charge : 1.121042 assigned positive charge : 763.0548 centred at (gu) : 85.11479 88.07295 87.46659 assigned negative charge : -761.9396 centred at (gu) : 84.74239 88.15794 87.42093 start vw surface at 0.1200000 fill in re-entrant regions at 0.2300000 boundary points on vw surface= 114841 reading accessible surface arcs data from file ARCDAT no. of arc points read = 39041 grid for indexing accessible points = 1.400000 m= 41306 mr = 83701 m= 5380 mr = 30072 m= 187 mr = 3003 m= 0 mr = 27 time to grow re-entrant surface = 0.2600000 no. cavity mid-points inaccessible to solvent = 264 time to turn everything in is 0.5400000 number of dielectric boundary points 44911 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 362 ## 2 charges are in solution ## iepsmp to db, and charging done at 0.6300000 number of grid points assigned charge 37313 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) : 0.5627391 object centre at (A) : 34.20250 21.97650 30.44500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -3.0029103E-02 -2.5061818E-02 midg,1,midg; midg,igrid,midg 1.7402327E-02 8.7629762E-03 1,midg,midg; igrid,midg,midg -2.3676874E-02 3.4146320E-02 gauss-seidel spectral radius is 0.9984860 estimated iterations to convergence 204 setup time was (sec) 0.7800000 now iterating at: 13:54:26 rms-change max change #iterations 4.926353 165.7914 at 10iterations 2.209943 59.53991 at 20iterations 0.9983783 28.74118 at 30iterations 0.4504878 14.29489 at 40iterations 0.2035659 6.045517 at 50iterations 9.2585035E-02 2.553310 at 60iterations 4.2301603E-02 1.180012 at 70iterations 1.9870060E-02 0.5434875 at 80iterations 9.9058570E-03 0.3039429 at 90iterations 5.5173333E-03 0.1788559 at 100iterations 3.5499178E-03 9.4955444E-02 at 110iterations 2.5389157E-03 6.2122345E-02 at 120iterations finished qdiffx linear iterations at : 13:54:33 total time elapsed so far: 8.070000 # loops : 120 mean,max change (kT/e) : 2.5389157E-03 6.2122345E-02 energy calculations done at 8.070000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.220000 DelPhi exited at 13:54:34 8.220u 0.218s 0:08.79 95.9% 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 13:54:34 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: 252 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4974 !!! WARNING: PLP 999 has a net charge of -0.3790 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: 2.532326 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): 3.309000 65.09600 ymin,ymax (A): -8.516000 52.46900 zmin,zma (A): -1.186000 62.07600 x,y,z range (A): 61.78700 60.98500 63.26200 scale (grids/A): 2.532326 object centre (A): 34.20250 21.97650 30.44500 number of atom coordinates read : 4974 total number of charged atoms : 4836 net assigned charge : 1.121042 assigned positive charge : 763.0548 centred at (gu) : 82.67202 87.10908 86.19961 assigned negative charge : -761.9396 centred at (gu) : 82.11362 87.23705 86.13142 start vw surface at 0.1300000 fill in re-entrant regions at 0.4500000 boundary points on vw surface= 266531 reading accessible surface arcs data from file ARCDAT no. of arc points read = 39041 grid for indexing accessible points = 1.400000 m= 137692 mr = 203005 m= 46192 mr = 112859 m= 8996 mr = 36093 m= 796 mr = 6335 m= 26 mr = 404 m= 0 mr = 4 time to grow re-entrant surface = 0.8400000 no. cavity mid-points inaccessible to solvent = 832 time to turn everything in is 1.410000 number of dielectric boundary points 101533 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 12 iepsmp to db, and charging done at 1.510000 number of grid points assigned charge 38653 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) : 1.688217 object centre at (A) : 34.20250 21.97650 30.44500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.4946256 -0.5931164 midg,1,midg; midg,igrid,midg 6.6393144E-02 -1.3460370E-02 1,midg,midg; igrid,midg,midg -0.4458542 0.4115836 gauss-seidel spectral radius is 0.9992665 estimated iterations to convergence 291 setup time was (sec) 1.670000 now iterating at: 13:54:36 rms-change max change #iterations 12.39960 280.3697 at 10iterations 7.358398 142.7368 at 20iterations 4.336018 79.43738 at 30iterations 2.545314 53.36927 at 40iterations 1.490261 29.91091 at 50iterations 0.8696147 15.22521 at 60iterations 0.5057353 8.245132 at 70iterations 0.2938135 4.477327 at 80iterations 0.1703716 2.783346 at 90iterations 9.9048704E-02 1.712938 at 100iterations 5.7587322E-02 0.9380960 at 110iterations 3.3554718E-02 0.5418668 at 120iterations 1.9755207E-02 0.3019238 at 130iterations 1.1854128E-02 0.1866112 at 140iterations 7.3587289E-03 0.1281128 at 150iterations 4.8524956E-03 8.5937500E-02 at 160iterations 3.4368341E-03 5.4397583E-02 at 170iterations 2.6242665E-03 4.2285919E-02 at 180iterations finished qdiffx linear iterations at : 13:54:48 total time elapsed so far: 13.71000 # loops : 180 mean,max change (kT/e) : 2.6242665E-03 4.2285919E-02 energy calculations done at 13.71000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.84000 DelPhi exited at 13:54:48 13.839u 0.227s 0:14.55 96.5% 0+0k 0+0io 0pf+0w