Sat Oct 8 17:26:52 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 Sat Oct 8 2011 at 17:26:52 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3469 !!! WARNING: ILE 377 has a net charge of -0.2720 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: 0.5513141 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): 37.14500 94.28100 ymin,ymax (A): 16.11100 80.68400 zmin,zma (A): -22.98600 26.31000 x,y,z range (A): 57.13600 64.57300 49.29600 scale (grids/A): 0.5513141 object centre (A): 65.71300 48.39750 1.662000 number of atom coordinates read : 3469 total number of charged atoms : 3323 net assigned charge : -5.271987 assigned positive charge : 521.8031 centred at (gu) : 90.13153 90.04752 89.46173 assigned negative charge : -527.0768 centred at (gu) : 90.15759 90.03957 89.43027 start vw surface at 0.1600000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 6906 nv = 96 ne = 84 npr = 69842 no. pairs analyzed = 69842 no. exposed pairs = 4331 no. arc points = 29289 no. surface atoms = 1467 nbur = 2002 mkacc time = 0.1600000 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 = 1.568000 m= 276 mr = 3711 m= 2 mr = 25 m= 0 mr = 0 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3700000 number of dielectric boundary points 3448 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2974 ## 369 charges are in solution ## iepsmp to db, and charging done at 0.5300000 number of grid points assigned charge 8882 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -8.0402895E-10 -9.0305596E-11 midg,1,midg; midg,igrid,midg -4.7274773E-10 -3.2909878E-10 1,midg,midg; igrid,midg,midg -1.4795803E-10 -6.7398415E-10 gauss-seidel spectral radius is 0.9830694 estimated iterations to convergence 63 setup time was (sec) 0.7100000 now iterating at: 17:26:53 rms-change max change #iterations 8.6637169E-02 16.91943 at 10iterations 5.9871352E-03 0.8469172 at 20iterations 5.0454796E-04 8.3401680E-02 at 30iterations 8.7897199E-05 1.5323639E-02 at 40iterations 2.3820457E-05 4.5814514E-03 at 50iterations finished qdiffx linear iterations at : 17:26:57 total time elapsed so far: 4.850000 # loops : 50 mean,max change (kT/e) : 2.3820457E-05 4.5814514E-03 energy calculations done at 4.850000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 5.020000 DelPhi exited at 17:26:57 5.022u 0.384s 0:05.74 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 Sat Oct 8 2011 at 17:26:57 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 = 3469 !!! WARNING: ILE 377 has a net charge of -0.2720 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1300000 grid size : 179 scale,in grids/A, set to be: 1.653942 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): 37.14500 94.28100 ymin,ymax (A): 16.11100 80.68400 zmin,zma (A): -22.98600 26.31000 x,y,z range (A): 57.13600 64.57300 49.29600 scale (grids/A): 1.653942 object centre (A): 65.71300 48.39750 1.662000 number of atom coordinates read : 3469 total number of charged atoms : 3323 net assigned charge : -5.271987 assigned positive charge : 521.8031 centred at (gu) : 90.39378 90.14146 88.38436 assigned negative charge : -527.0768 centred at (gu) : 90.47227 90.11851 88.29057 start vw surface at 0.2300000 fill in re-entrant regions at 0.3200000 boundary points on vw surface= 75909 reading accessible surface arcs data from file ARCDAT no. of arc points read = 29289 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 25433 mr = 52841 m= 2886 mr = 18018 m= 87 mr = 1506 m= 0 mr = 8 time to grow re-entrant surface = 0.2600000 no. cavity mid-points inaccessible to solvent = 306 time to turn everything in is 0.6300000 number of dielectric boundary points 31942 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 324 ## 4 charges are in solution ## iepsmp to db, and charging done at 0.7400000 number of grid points assigned charge 25535 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) : 0.5513141 object centre at (A) : 65.71300 48.39750 1.662000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -5.6774658E-03 -4.3562087E-03 midg,1,midg; midg,igrid,midg 8.8581732E-03 1.4947141E-02 1,midg,midg; igrid,midg,midg -1.4473410E-02 -7.1748565E-03 gauss-seidel spectral radius is 0.9982792 estimated iterations to convergence 191 setup time was (sec) 0.8900000 now iterating at: 17:26:58 rms-change max change #iterations 3.737145 154.6633 at 10iterations 1.594350 60.91021 at 20iterations 0.6808047 22.12291 at 30iterations 0.2915601 9.414742 at 40iterations 0.1239793 4.297781 at 50iterations 5.3009223E-02 1.720259 at 60iterations 2.2675216E-02 0.8114824 at 70iterations 9.7272163E-03 0.3275690 at 80iterations 4.1822167E-03 0.1391354 at 90iterations 1.8037403E-03 6.4579010E-02 at 100iterations 7.9043454E-04 2.7526855E-02 at 110iterations 3.5475884E-04 1.2983322E-02 at 120iterations finished qdiffx linear iterations at : 17:27:05 total time elapsed so far: 7.100000 # loops : 120 mean,max change (kT/e) : 3.5475884E-04 1.2983322E-02 energy calculations done at 7.100000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.270000 DelPhi exited at 17:27:05 7.272u 0.206s 0:07.76 96.2% 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 Sat Oct 8 2011 at 17:27:05 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 = 3469 !!! WARNING: ILE 377 has a net charge of -0.2720 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 2.480913 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): 37.14500 94.28100 ymin,ymax (A): 16.11100 80.68400 zmin,zma (A): -22.98600 26.31000 x,y,z range (A): 57.13600 64.57300 49.29600 scale (grids/A): 2.480913 object centre (A): 65.71300 48.39750 1.662000 number of atom coordinates read : 3469 total number of charged atoms : 3323 net assigned charge : -5.271987 assigned positive charge : 521.8031 centred at (gu) : 90.59013 90.21193 87.57641 assigned negative charge : -527.0768 centred at (gu) : 90.70811 90.17750 87.43574 start vw surface at 0.1500000 fill in re-entrant regions at 0.4200000 boundary points on vw surface= 176086 reading accessible surface arcs data from file ARCDAT no. of arc points read = 29289 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 86345 mr = 128887 m= 26677 mr = 69385 m= 4575 mr = 20439 m= 365 mr = 3015 m= 8 mr = 170 m= 1 mr = 1 m= 0 mr = 0 time to grow re-entrant surface = 0.7700000 no. cavity mid-points inaccessible to solvent = 1085 time to turn everything in is 1.290000 number of dielectric boundary points 72160 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 16 iepsmp to db, and charging done at 1.420000 number of grid points assigned charge 26553 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) : 1.653942 object centre at (A) : 65.71300 48.39750 1.662000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -6.4878561E-02 -3.9321963E-02 midg,1,midg; midg,igrid,midg 0.2766968 0.4957035 1,midg,midg; igrid,midg,midg -0.2313950 -7.2324574E-02 gauss-seidel spectral radius is 0.9991744 estimated iterations to convergence 275 setup time was (sec) 1.590000 now iterating at: 17:27:07 rms-change max change #iterations 9.603871 300.4495 at 10iterations 5.452467 118.4391 at 20iterations 3.085106 72.26743 at 30iterations 1.742988 34.65314 at 40iterations 0.9792718 20.70941 at 50iterations 0.5487059 10.47177 at 60iterations 0.3069952 6.298221 at 70iterations 0.1716917 3.284996 at 80iterations 9.5803857E-02 1.760120 at 90iterations 5.3471539E-02 0.9899158 at 100iterations 2.9824749E-02 0.5620956 at 110iterations 1.6653446E-02 0.3144646 at 120iterations 9.3060359E-03 0.1689072 at 130iterations 5.1888274E-03 0.1040058 at 140iterations 2.9065253E-03 5.3146362E-02 at 150iterations 1.6336489E-03 3.4601212E-02 at 160iterations 9.2458545E-04 1.9065857E-02 at 170iterations 5.3211651E-04 1.0181427E-02 at 180iterations finished qdiffx linear iterations at : 17:27:17 total time elapsed so far: 11.30000 # loops : 180 mean,max change (kT/e) : 5.3211651E-04 1.0181427E-02 energy calculations done at 11.30000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.48000 DelPhi exited at 17:27:17 11.479u 0.202s 0:11.95 97.6% 0+0k 0+0io 0pf+0w