Tue Oct 11 06:18:19 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 06:18:19 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 = 2053 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: 0.7044065 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): -20.65000 29.88900 ymin,ymax (A): -11.84200 30.68000 zmin,zma (A): -8.494000 38.19300 x,y,z range (A): 50.53900 42.52200 46.68700 scale (grids/A): 0.7044065 object centre (A): 4.619500 9.419001 14.84950 number of atom coordinates read : 2053 total number of charged atoms : 1925 net assigned charge : 6.500009 assigned positive charge : 311.0290 centred at (gu) : 91.00607 89.84882 91.02085 assigned negative charge : -304.5292 centred at (gu) : 90.94243 89.77711 90.91867 start vw surface at 0.1400000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 6944 nv = 96 ne = 84 npr = 40551 no. pairs analyzed = 40551 no. exposed pairs = 2537 no. arc points = 17497 no. surface atoms = 860 nbur = 1193 mkacc time = 0.1100000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 484 mr = 3950 m= 2 mr = 112 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 3368 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1608 ## 154 charges are in solution ## iepsmp to db, and charging done at 0.4100000 number of grid points assigned charge 7723 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 3.5286605E-09 1.1686342E-07 midg,1,midg; midg,igrid,midg 1.8117342E-08 7.9879399E-08 1,midg,midg; igrid,midg,midg 1.7966963E-08 9.5619427E-08 gauss-seidel spectral radius is 0.9894948 estimated iterations to convergence 79 setup time was (sec) 0.5600000 now iterating at: 06:18:20 rms-change max change #iterations 0.1905893 27.93340 at 10iterations 2.3166349E-02 3.132393 at 20iterations 2.9660102E-03 0.4121094 at 30iterations 4.3482386E-04 6.2404633E-02 at 40iterations 9.1370668E-05 1.1732101E-02 at 50iterations finished qdiffx linear iterations at : 06:18:23 total time elapsed so far: 3.820000 # loops : 50 mean,max change (kT/e) : 9.1370668E-05 1.1732101E-02 energy calculations done at 3.820000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.990000 DelPhi exited at 06:18:24 3.998u 0.279s 0:04.61 92.4% 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 06:18:24 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 = 2053 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: 2.113219 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): -20.65000 29.88900 ymin,ymax (A): -11.84200 30.68000 zmin,zma (A): -8.494000 38.19300 x,y,z range (A): 50.53900 42.52200 46.68700 scale (grids/A): 2.113219 object centre (A): 4.619500 9.419001 14.84950 number of atom coordinates read : 2053 total number of charged atoms : 1925 net assigned charge : 6.500009 assigned positive charge : 311.0290 centred at (gu) : 93.01804 89.54655 93.06273 assigned negative charge : -304.5292 centred at (gu) : 92.82744 89.33151 92.75636 start vw surface at 0.1500000 fill in re-entrant regions at 0.3000000 boundary points on vw surface= 74157 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17497 grid for indexing accessible points = 1.400000 m= 30275 mr = 52690 m= 6065 mr = 23067 m= 585 mr = 4016 m= 14 mr = 286 m= 0 mr = 2 time to grow re-entrant surface = 0.3600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.7000000 number of dielectric boundary points 31035 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 80 iepsmp to db, and charging done at 0.8400000 number of grid points assigned charge 15298 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) : 0.7044065 object centre at (A) : 4.619500 9.419001 14.84950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -4.4795148E-02 3.7849251E-02 midg,1,midg; midg,igrid,midg 2.4370495E-02 2.5418200E-02 1,midg,midg; igrid,midg,midg 5.5629767E-02 4.3272454E-02 gauss-seidel spectral radius is 0.9988226 estimated iterations to convergence 231 setup time was (sec) 1.000000 now iterating at: 06:18:25 rms-change max change #iterations 4.494940 204.1710 at 10iterations 2.214238 75.90831 at 20iterations 1.098681 34.28531 at 30iterations 0.5420574 16.63223 at 40iterations 0.2689130 8.734978 at 50iterations 0.1328778 4.008704 at 60iterations 6.5883785E-02 2.025650 at 70iterations 3.2649197E-02 0.9116001 at 80iterations 1.6236018E-02 0.5054874 at 90iterations 8.1033017E-03 0.2407990 at 100iterations 4.0455568E-03 0.1251221 at 110iterations 2.0539507E-03 6.0439229E-02 at 120iterations finished qdiffx linear iterations at : 06:18:33 total time elapsed so far: 9.310000 # loops : 120 mean,max change (kT/e) : 2.0539507E-03 6.0439229E-02 energy calculations done at 9.310000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.490000 DelPhi exited at 06:18:34 9.495u 0.276s 0:10.41 93.7% 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 06:18:34 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2053 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: 3.169829 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): -20.65000 29.88900 ymin,ymax (A): -11.84200 30.68000 zmin,zma (A): -8.494000 38.19300 x,y,z range (A): 50.53900 42.52200 46.68700 scale (grids/A): 3.169829 object centre (A): 4.619500 9.419001 14.84950 number of atom coordinates read : 2053 total number of charged atoms : 1925 net assigned charge : 6.500009 assigned positive charge : 311.0290 centred at (gu) : 94.52715 89.31966 94.59411 assigned negative charge : -304.5292 centred at (gu) : 94.24123 88.99731 94.13456 start vw surface at 0.1600000 fill in re-entrant regions at 0.9700000 boundary points on vw surface= 170846 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17497 grid for indexing accessible points = 1.400000 m= 93658 mr = 126668 m= 38747 mr = 78042 m= 11211 mr = 31866 m= 2278 mr = 8634 m= 264 mr = 1633 m= 9 mr = 156 m= 1 mr = 0 m= 0 mr = 0 time to grow re-entrant surface = 1.120000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 2.200000 number of dielectric boundary points 70015 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.340000 number of grid points assigned charge 15400 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) : 2.113219 object centre at (A) : 4.619500 9.419001 14.84950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.4917900 0.3811684 midg,1,midg; midg,igrid,midg 0.1853584 0.1695896 1,midg,midg; igrid,midg,midg 0.5039756 0.2719869 gauss-seidel spectral radius is 0.9992962 estimated iterations to convergence 297 setup time was (sec) 2.510000 now iterating at: 06:18:37 rms-change max change #iterations 10.12667 410.0318 at 10iterations 5.975023 118.0218 at 20iterations 3.533766 76.55241 at 30iterations 2.078099 38.56558 at 40iterations 1.222069 22.25793 at 50iterations 0.7188332 14.58337 at 60iterations 0.4213619 9.018044 at 70iterations 0.2471541 4.687082 at 80iterations 0.1446429 2.600395 at 90iterations 8.4952906E-02 1.556065 at 100iterations 4.9850926E-02 0.8924471 at 110iterations 2.9331181E-02 0.5077868 at 120iterations 1.7347289E-02 0.3545418 at 130iterations 1.0382583E-02 0.2024155 at 140iterations 6.3371588E-03 0.1357212 at 150iterations 3.9791036E-03 8.2077026E-02 at 160iterations 2.6316454E-03 5.3977966E-02 at 170iterations 1.8359664E-03 4.0908813E-02 at 180iterations finished qdiffx linear iterations at : 06:18:51 total time elapsed so far: 16.16000 # loops : 180 mean,max change (kT/e) : 1.8359664E-03 4.0908813E-02 energy calculations done at 16.16000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 16.34000 DelPhi exited at 06:18:52 16.340u 0.316s 0:17.20 96.8% 0+0k 0+0io 0pf+0w