Tue Oct 11 00:35:27 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 00:35:27 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2651 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: 0.5733335 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): 18.09600 80.18900 ymin,ymax (A): -12.76000 44.35400 zmin,zma (A): -7.574000 35.14200 x,y,z range (A): 62.09300 57.11400 42.71600 scale (grids/A): 0.5733335 object centre (A): 49.14250 15.79700 13.78400 number of atom coordinates read : 2651 total number of charged atoms : 2508 net assigned charge : 5.000021 assigned positive charge : 399.4387 centred at (gu) : 87.61639 90.16259 89.71496 assigned negative charge : -394.4395 centred at (gu) : 87.90131 90.29728 89.88428 start vw surface at 0.1100000 fill in re-entrant regions at 0.1100000 boundary points on vw surface= 5700 nv = 96 ne = 84 npr = 53616 no. pairs analyzed = 53616 no. exposed pairs = 3109 no. arc points = 22200 no. surface atoms = 1054 nbur = 1597 mkacc time = 9.0000004E-02 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= 222 mr = 3130 m= 0 mr = 15 time to grow re-entrant surface = 9.0000004E-02 no. cavity mid-points inaccessible to solvent = 56 time to turn everything in is 0.2100000 number of dielectric boundary points 2777 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2205 ## 246 charges are in solution ## iepsmp to db, and charging done at 0.2800000 number of grid points assigned charge 7248 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 3.5584398E-09 -1.8083368E-09 midg,1,midg; midg,igrid,midg 2.7000340E-09 -1.4383912E-09 1,midg,midg; igrid,midg,midg 8.9513508E-09 -2.1626949E-09 gauss-seidel spectral radius is 0.9842700 estimated iterations to convergence 66 setup time was (sec) 0.4000000 now iterating at: 00:35:28 rms-change max change #iterations 8.7712198E-02 14.55018 at 10iterations 7.5909961E-03 1.304741 at 20iterations 9.8910043E-04 0.2399178 at 30iterations 2.1410415E-04 5.5233002E-02 at 40iterations 4.9731443E-05 1.3065338E-02 at 50iterations finished qdiffx linear iterations at : 00:35:31 total time elapsed so far: 3.320000 # loops : 50 mean,max change (kT/e) : 4.9731443E-05 1.3065338E-02 energy calculations done at 3.320000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.440000 DelPhi exited at 00:35:32 3.446u 0.176s 0:04.21 85.7% 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 00:35:32 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2651 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: 1.720001 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): 18.09600 80.18900 ymin,ymax (A): -12.76000 44.35400 zmin,zma (A): -7.574000 35.14200 x,y,z range (A): 62.09300 57.11400 42.71600 scale (grids/A): 1.720001 object centre (A): 49.14250 15.79700 13.78400 number of atom coordinates read : 2651 total number of charged atoms : 2508 net assigned charge : 5.000021 assigned positive charge : 399.4387 centred at (gu) : 82.84860 90.48688 89.14423 assigned negative charge : -394.4395 centred at (gu) : 83.70383 90.89162 89.65235 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 63249 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22200 grid for indexing accessible points = 1.400000 m= 19870 mr = 44244 m= 2295 mr = 14340 m= 43 mr = 1224 m= 0 mr = 5 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 3335 time to turn everything in is 0.3100000 number of dielectric boundary points 25644 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 201 iepsmp to db, and charging done at 0.3900000 number of grid points assigned charge 19424 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) : 0.5733335 object centre at (A) : 49.14250 15.79700 13.78400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.6004214E-02 4.3027023E-05 midg,1,midg; midg,igrid,midg 1.8821573E-02 -1.8692009E-02 1,midg,midg; igrid,midg,midg 4.3379418E-03 -1.2601884E-02 gauss-seidel spectral radius is 0.9983283 estimated iterations to convergence 194 setup time was (sec) 0.5200000 now iterating at: 00:35:32 rms-change max change #iterations 3.441281 141.2119 at 10iterations 1.480101 56.04016 at 20iterations 0.6391522 22.80344 at 30iterations 0.2772127 11.36981 at 40iterations 0.1198675 4.543882 at 50iterations 5.1876821E-02 1.870718 at 60iterations 2.2652555E-02 0.8484306 at 70iterations 9.9292397E-03 0.3620567 at 80iterations 4.3909359E-03 0.1810055 at 90iterations 1.9993649E-03 7.9578400E-02 at 100iterations 9.4540534E-04 4.0866852E-02 at 110iterations 4.7293428E-04 2.0732880E-02 at 120iterations finished qdiffx linear iterations at : 00:35:40 total time elapsed so far: 7.640000 # loops : 120 mean,max change (kT/e) : 4.7293428E-04 2.0732880E-02 energy calculations done at 7.640000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.770000 DelPhi exited at 00:35:40 7.777u 0.210s 0:08.60 92.7% 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 00:35:40 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2651 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: 2.580001 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): 18.09600 80.18900 ymin,ymax (A): -12.76000 44.35400 zmin,zma (A): -7.574000 35.14200 x,y,z range (A): 62.09300 57.11400 42.71600 scale (grids/A): 2.580001 object centre (A): 49.14250 15.79700 13.78400 number of atom coordinates read : 2651 total number of charged atoms : 2508 net assigned charge : 5.000021 assigned positive charge : 399.4387 centred at (gu) : 79.27284 90.73025 88.71610 assigned negative charge : -394.4395 centred at (gu) : 80.55572 91.33743 89.47867 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.2700000 boundary points on vw surface= 147015 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22200 grid for indexing accessible points = 1.400000 m= 68498 mr = 107529 m= 20301 mr = 55679 m= 3604 mr = 16009 m= 263 mr = 2558 m= 4 mr = 141 m= 0 mr = 0 time to grow re-entrant surface = 0.4100000 no. cavity mid-points inaccessible to solvent = 11192 time to turn everything in is 0.7500000 number of dielectric boundary points 57769 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 12 iepsmp to db, and charging done at 0.8400000 number of grid points assigned charge 20058 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) : 1.720001 object centre at (A) : 49.14250 15.79700 13.78400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1814876 9.9796122E-03 midg,1,midg; midg,igrid,midg 0.1839430 -0.4217421 1,midg,midg; igrid,midg,midg -6.1948039E-02 -0.1829743 gauss-seidel spectral radius is 0.9991680 estimated iterations to convergence 274 setup time was (sec) 0.9800000 now iterating at: 00:35:42 rms-change max change #iterations 8.550647 330.6932 at 10iterations 4.777070 134.2019 at 20iterations 2.663984 55.19847 at 30iterations 1.487550 31.61226 at 40iterations 0.8242705 19.11691 at 50iterations 0.4595000 9.793446 at 60iterations 0.2552430 5.254909 at 70iterations 0.1417840 2.883635 at 80iterations 7.8866042E-02 1.801689 at 90iterations 4.3925609E-02 0.9525146 at 100iterations 2.4414858E-02 0.5091629 at 110iterations 1.3647348E-02 0.3031921 at 120iterations 7.6585985E-03 0.1629677 at 130iterations 4.3364861E-03 0.1003113 at 140iterations 2.4848711E-03 6.2705994E-02 at 150iterations 1.4652285E-03 3.4851074E-02 at 160iterations 8.9352025E-04 2.2865295E-02 at 170iterations 5.6960428E-04 1.6143799E-02 at 180iterations finished qdiffx linear iterations at : 00:35:53 total time elapsed so far: 12.02000 # loops : 180 mean,max change (kT/e) : 5.6960428E-04 1.6143799E-02 energy calculations done at 12.02000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.15000 DelPhi exited at 00:35:53 12.156u 0.220s 0:12.84 96.3% 0+0k 0+0io 0pf+0w