Tue Oct 11 05:13:39 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 05:13:39 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: 255 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2247 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6784570 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): 1.506000 46.68800 ymin,ymax (A): 0.5820001 41.57000 zmin,zma (A): -2.435000 50.03700 x,y,z range (A): 45.18200 40.98800 52.47200 scale (grids/A): 0.6784570 object centre (A): 24.09700 21.07600 23.80100 number of atom coordinates read : 2247 total number of charged atoms : 1949 net assigned charge : 7.500009 assigned positive charge : 315.2170 centred at (gu) : 90.79819 90.23376 89.49542 assigned negative charge : -307.7172 centred at (gu) : 90.96796 90.22298 89.53476 start vw surface at 0.1400000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 6418 nv = 96 ne = 84 npr = 40567 no. pairs analyzed = 40567 no. exposed pairs = 2550 no. arc points = 17346 no. surface atoms = 869 nbur = 1378 mkacc time = 0.1100000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 405 mr = 3617 m= 2 mr = 50 m= 0 mr = 0 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2900000 number of dielectric boundary points 3158 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1697 ## 144 charges are in solution ## iepsmp to db, and charging done at 0.4000000 number of grid points assigned charge 7392 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 4.5404917E-08 1.9565661E-08 midg,1,midg; midg,igrid,midg 2.7387157E-08 3.5614512E-08 1,midg,midg; igrid,midg,midg 6.1972834E-08 -1.4021002E-08 gauss-seidel spectral radius is 0.9886831 estimated iterations to convergence 77 setup time was (sec) 0.5500000 now iterating at: 05:13:40 rms-change max change #iterations 0.1652163 26.82096 at 10iterations 1.8416939E-02 2.813124 at 20iterations 2.2879422E-03 0.3287821 at 30iterations 3.5315985E-04 5.1640511E-02 at 40iterations 8.1614540E-05 1.0204315E-02 at 50iterations finished qdiffx linear iterations at : 05:13:44 total time elapsed so far: 3.840000 # loops : 50 mean,max change (kT/e) : 8.1614540E-05 1.0204315E-02 energy calculations done at 3.840000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.030000 DelPhi exited at 05:13:45 4.030u 0.284s 0:05.78 74.5% 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 05:13:45 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: 255 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2247 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.035371 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): 1.506000 46.68800 ymin,ymax (A): 0.5820001 41.57000 zmin,zma (A): -2.435000 50.03700 x,y,z range (A): 45.18200 40.98800 52.47200 scale (grids/A): 2.035371 object centre (A): 24.09700 21.07600 23.80100 number of atom coordinates read : 2247 total number of charged atoms : 1949 net assigned charge : 7.500009 assigned positive charge : 315.2170 centred at (gu) : 92.39441 90.70090 88.48621 assigned negative charge : -307.7172 centred at (gu) : 92.90395 90.66912 88.60429 start vw surface at 0.1300000 fill in re-entrant regions at 0.2600000 boundary points on vw surface= 68425 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17346 grid for indexing accessible points = 1.400000 m= 27173 mr = 48343 m= 4950 mr = 20349 m= 373 mr = 3207 m= 7 mr = 138 m= 0 mr = 2 time to grow re-entrant surface = 0.3200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.6200000 number of dielectric boundary points 28889 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 97 iepsmp to db, and charging done at 0.7500000 number of grid points assigned charge 15429 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) : 0.6784570 object centre at (A) : 24.09700 21.07600 23.80100 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 5.0939642E-02 5.4517891E-02 midg,1,midg; midg,igrid,midg 4.3805866E-03 2.2495426E-02 1,midg,midg; igrid,midg,midg 3.4651186E-02 2.2373896E-04 gauss-seidel spectral radius is 0.9987394 estimated iterations to convergence 223 setup time was (sec) 0.9200000 now iterating at: 05:13:47 rms-change max change #iterations 4.185081 186.4080 at 10iterations 2.033581 64.59625 at 20iterations 0.9827339 30.81239 at 30iterations 0.4729237 15.65130 at 40iterations 0.2295267 7.319916 at 50iterations 0.1111424 3.622517 at 60iterations 5.3752299E-02 1.800430 at 70iterations 2.6023114E-02 0.9140968 at 80iterations 1.2635750E-02 0.3974323 at 90iterations 6.1676838E-03 0.2133703 at 100iterations 3.0383922E-03 9.5911026E-02 at 110iterations 1.5341794E-03 4.9819469E-02 at 120iterations finished qdiffx linear iterations at : 05:13:55 total time elapsed so far: 9.200000 # loops : 120 mean,max change (kT/e) : 1.5341794E-03 4.9819469E-02 energy calculations done at 9.200000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.370000 DelPhi exited at 05:13:55 9.377u 0.320s 0:10.11 95.8% 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 05:13:56 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: 255 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2247 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 3.053057 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): 1.506000 46.68800 ymin,ymax (A): 0.5820001 41.57000 zmin,zma (A): -2.435000 50.03700 x,y,z range (A): 45.18200 40.98800 52.47200 scale (grids/A): 3.053057 object centre (A): 24.09700 21.07600 23.80100 number of atom coordinates read : 2247 total number of charged atoms : 1949 net assigned charge : 7.500009 assigned positive charge : 315.2170 centred at (gu) : 93.59174 91.05141 87.72929 assigned negative charge : -307.7172 centred at (gu) : 94.35580 91.00359 87.90649 start vw surface at 0.1400000 fill in re-entrant regions at 0.5400000 boundary points on vw surface= 157669 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17346 grid for indexing accessible points = 1.400000 m= 85045 mr = 116497 m= 33688 mr = 70306 m= 9150 mr = 27412 m= 1591 mr = 6932 m= 132 mr = 1109 m= 5 mr = 71 m= 0 mr = 2 time to grow re-entrant surface = 1.010000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.660000 number of dielectric boundary points 64951 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.800000 number of grid points assigned charge 15592 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) : 2.035371 object centre at (A) : 24.09700 21.07600 23.80100 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.3953832 0.7812952 midg,1,midg; midg,igrid,midg 1.2025838E-02 0.1987699 1,midg,midg; igrid,midg,midg 0.2815931 5.3076502E-02 gauss-seidel spectral radius is 0.9992722 estimated iterations to convergence 293 setup time was (sec) 1.980000 now iterating at: 05:13:58 rms-change max change #iterations 9.660617 358.8784 at 10iterations 5.666533 125.9688 at 20iterations 3.328636 75.94742 at 30iterations 1.944690 42.46400 at 40iterations 1.134651 26.27149 at 50iterations 0.6618999 14.87505 at 60iterations 0.3851832 7.830244 at 70iterations 0.2240087 4.098807 at 80iterations 0.1299194 2.777100 at 90iterations 7.5693727E-02 1.550470 at 100iterations 4.3949191E-02 0.8449202 at 110iterations 2.5602669E-02 0.5541544 at 120iterations 1.4999897E-02 0.2933311 at 130iterations 8.8753086E-03 0.1658936 at 140iterations 5.3157266E-03 0.1199722 at 150iterations 3.2953350E-03 6.3075066E-02 at 160iterations 2.1364014E-03 3.9268494E-02 at 170iterations 1.4607849E-03 2.8486252E-02 at 180iterations finished qdiffx linear iterations at : 05:14:11 total time elapsed so far: 15.53000 # loops : 180 mean,max change (kT/e) : 1.4607849E-03 2.8486252E-02 energy calculations done at 15.53000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.70000 DelPhi exited at 05:14:12 15.698u 0.329s 0:16.58 96.5% 0+0k 0+0io 0pf+0w