Sat Oct 8 19:36:51 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+sph2.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 = amb2.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 19:36:51 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: 280 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2606 !!! WARNING: HIZ 94 has a net charge of 0.2000 !!! WARNING: HIZ 96 has a net charge of 0.2000 !!! WARNING: HIY 119 has a net charge of 0.2000 !!! WARNING: ZN7 701 has a net charge of 1.4000 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: 0.6186033 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): -31.93900 17.55700 ymin,ymax (A): -23.43600 23.39300 zmin,zma (A): -12.35600 45.19300 x,y,z range (A): 49.49600 46.82900 57.54900 scale (grids/A): 0.6186033 object centre (A): -7.191001 -2.1499634E-02 16.41850 number of atom coordinates read : 2606 total number of charged atoms : 2466 net assigned charge : 4.500007 assigned positive charge : 394.5950 centred at (gu) : 88.69288 89.09118 89.50622 assigned negative charge : -390.0956 centred at (gu) : 88.58343 89.14456 89.39516 start vw surface at 0.1200000 fill in re-entrant regions at 0.1300000 boundary points on vw surface= 6454 nv = 96 ne = 84 npr = 54800 no. pairs analyzed = 54800 no. exposed pairs = 3022 no. arc points = 21740 no. surface atoms = 1004 nbur = 1602 mkacc time = 0.1500000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 327 mr = 3596 m= 1 mr = 32 m= 0 mr = 0 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 176 time to turn everything in is 0.3200000 number of dielectric boundary points 3154 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2226 ## 257 charges are in solution ## iepsmp to db, and charging done at 0.4700000 number of grid points assigned charge 8093 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -4.0637467E-09 9.5008241E-09 midg,1,midg; midg,igrid,midg 8.5180671E-09 1.4753082E-10 1,midg,midg; igrid,midg,midg -4.7944453E-09 7.8779223E-09 gauss-seidel spectral radius is 0.9864640 estimated iterations to convergence 70 setup time was (sec) 0.6300000 now iterating at: 19:36:52 rms-change max change #iterations 0.1272244 20.18314 at 10iterations 1.1609292E-02 1.996595 at 20iterations 1.0749379E-03 0.1553097 at 30iterations 9.9439771E-05 1.4915466E-02 at 40iterations 9.3553981E-06 1.3160706E-03 at 50iterations finished qdiffx linear iterations at : 19:36:56 total time elapsed so far: 4.590000 # loops : 50 mean,max change (kT/e) : 9.3553981E-06 1.3160706E-03 energy calculations done at 4.590000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.750000 DelPhi exited at 19:36:56 4.751u 0.382s 0:05.40 95.0% 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 19:36:56 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: 280 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2606 !!! WARNING: HIZ 94 has a net charge of 0.2000 !!! WARNING: HIZ 96 has a net charge of 0.2000 !!! WARNING: HIY 119 has a net charge of 0.2000 !!! WARNING: ZN7 701 has a net charge of 1.4000 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: 1.855810 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): -31.93900 17.55700 ymin,ymax (A): -23.43600 23.39300 zmin,zma (A): -12.35600 45.19300 x,y,z range (A): 49.49600 46.82900 57.54900 scale (grids/A): 1.855810 object centre (A): -7.191001 -2.1499634E-02 16.41850 number of atom coordinates read : 2606 total number of charged atoms : 2466 net assigned charge : 4.500007 assigned positive charge : 394.5950 centred at (gu) : 86.07853 87.27299 88.51823 assigned negative charge : -390.0956 centred at (gu) : 85.74986 87.43326 88.18546 start vw surface at 0.1300000 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 70311 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21740 grid for indexing accessible points = 1.400000 m= 24231 mr = 48909 m= 3470 mr = 18010 m= 177 mr = 2155 m= 0 mr = 57 time to grow re-entrant surface = 0.2800000 no. cavity mid-points inaccessible to solvent = 7746 time to turn everything in is 0.5800000 number of dielectric boundary points 29058 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 195 iepsmp to db, and charging done at 0.6900000 number of grid points assigned charge 19345 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) : 0.6186033 object centre at (A) : -7.191001 -2.1499634E-02 16.41850 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.3651113E-02 2.7522679E-02 midg,1,midg; midg,igrid,midg 1.3444217E-02 -5.9286773E-04 1,midg,midg; igrid,midg,midg -3.3144143E-03 3.5560470E-02 gauss-seidel spectral radius is 0.9985611 estimated iterations to convergence 209 setup time was (sec) 0.8700000 now iterating at: 19:36:58 rms-change max change #iterations 4.051634 145.2544 at 10iterations 1.852219 67.77773 at 20iterations 0.8499722 27.26530 at 30iterations 0.3895985 14.20122 at 40iterations 0.1793229 6.163839 at 50iterations 8.2342148E-02 2.822318 at 60iterations 3.7903935E-02 1.286646 at 70iterations 1.7420914E-02 0.5615768 at 80iterations 7.9981899E-03 0.2791824 at 90iterations 3.6608605E-03 0.1228027 at 100iterations 1.6820404E-03 5.3089142E-02 at 110iterations 7.7270356E-04 2.6852608E-02 at 120iterations finished qdiffx linear iterations at : 19:37:07 total time elapsed so far: 10.66000 # loops : 120 mean,max change (kT/e) : 7.7270356E-04 2.6852608E-02 energy calculations done at 10.66000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.83000 DelPhi exited at 19:37:08 10.830u 0.427s 0:11.55 97.4% 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 Sat Oct 8 2011 at 19:37:08 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: 280 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2606 !!! WARNING: HIZ 94 has a net charge of 0.2000 !!! WARNING: HIZ 96 has a net charge of 0.2000 !!! WARNING: HIY 119 has a net charge of 0.2000 !!! WARNING: ZN7 701 has a net charge of 1.4000 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: 2.783715 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): -31.93900 17.55700 ymin,ymax (A): -23.43600 23.39300 zmin,zma (A): -12.35600 45.19300 x,y,z range (A): 49.49600 46.82900 57.54900 scale (grids/A): 2.783715 object centre (A): -7.191001 -2.1499634E-02 16.41850 number of atom coordinates read : 2606 total number of charged atoms : 2466 net assigned charge : 4.500007 assigned positive charge : 394.5950 centred at (gu) : 84.11761 85.90918 87.77705 assigned negative charge : -390.0956 centred at (gu) : 83.62479 86.14977 87.27812 start vw surface at 0.1200000 fill in re-entrant regions at 0.4900000 boundary points on vw surface= 162489 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21740 grid for indexing accessible points = 1.400000 m= 80213 mr = 118377 m= 27411 mr = 65918 m= 6186 mr = 22146 m= 753 mr = 4718 m= 48 mr = 504 m= 1 mr = 23 m= 0 mr = 0 time to grow re-entrant surface = 0.8699999 no. cavity mid-points inaccessible to solvent = 25929 time to turn everything in is 1.460000 number of dielectric boundary points 65415 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2 iepsmp to db, and charging done at 1.590000 number of grid points assigned charge 19725 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) : 1.855810 object centre at (A) : -7.191001 -2.1499634E-02 16.41850 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.0018384E-04 0.3400775 midg,1,midg; midg,igrid,midg 0.1488290 -4.2801439E-03 1,midg,midg; igrid,midg,midg -3.9427012E-02 0.4539196 gauss-seidel spectral radius is 0.9992327 estimated iterations to convergence 285 setup time was (sec) 1.810000 now iterating at: 19:37:10 rms-change max change #iterations 9.479554 290.3210 at 10iterations 5.440880 127.4838 at 20iterations 3.103997 63.58421 at 30iterations 1.772685 41.14276 at 40iterations 1.011609 19.76504 at 50iterations 0.5757788 11.16169 at 60iterations 0.3281711 6.522231 at 70iterations 0.1864019 3.679956 at 80iterations 0.1060598 1.944974 at 90iterations 6.0253877E-02 1.134827 at 100iterations 3.4218464E-02 0.6248121 at 110iterations 1.9486729E-02 0.3821163 at 120iterations 1.1071330E-02 0.1969035 at 130iterations 6.2949802E-03 0.1282482 at 140iterations 3.5778836E-03 7.0160389E-02 at 150iterations 2.0391240E-03 3.6653519E-02 at 160iterations 1.1591868E-03 2.1848679E-02 at 170iterations 6.5767858E-04 1.2180328E-02 at 180iterations finished qdiffx linear iterations at : 19:37:27 total time elapsed so far: 18.24000 # loops : 180 mean,max change (kT/e) : 6.5767858E-04 1.2180328E-02 energy calculations done at 18.24000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 18.40000 DelPhi exited at 19:37:27 18.407u 0.506s 0:19.22 98.3% 0+0k 0+0io 0pf+0w