Mon Oct 10 17:00:33 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 Mon Oct 10 2011 at 17:00:33 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: 320 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4612 !!! WARNING: HEM 818 has a net charge of -3.4000 !!! WARNING: FE 2 has a net charge of 1.4000 !!! WARNING: FE 3 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= 0.1300000 grid size : 179 scale,in grids/A, set to be: 0.5121418 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): -18.26900 36.06900 ymin,ymax (A): -30.35400 31.48700 zmin,zma (A): -4.014000 65.49800 x,y,z range (A): 54.33800 61.84100 69.51200 scale (grids/A): 0.5121418 object centre (A): 8.900001 0.5664997 30.74200 number of atom coordinates read : 4612 total number of charged atoms : 4410 net assigned charge : 5.400050 assigned positive charge : 694.3746 centred at (gu) : 90.45786 90.72337 88.17239 assigned negative charge : -688.9789 centred at (gu) : 90.37549 90.76391 88.22958 start vw surface at 0.2100000 fill in re-entrant regions at 0.2200000 boundary points on vw surface= 7475 nv = 96 ne = 84 npr = 94644 no. pairs analyzed = 94644 no. exposed pairs = 5867 no. arc points = 41118 no. surface atoms = 1959 nbur = 2653 mkacc time = 0.2200000 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 = 1.652000 m= 278 mr = 3796 m= 1 mr = 0 m= 0 mr = 0 time to grow re-entrant surface = 0.2400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4700000 number of dielectric boundary points 3958 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3919 ## 552 charges are in solution ## iepsmp to db, and charging done at 0.5800000 number of grid points assigned charge 10127 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 3.7275702E-10 -4.5136422E-11 midg,1,midg; midg,igrid,midg 1.5377222E-10 -3.7274225E-11 1,midg,midg; igrid,midg,midg -1.2631206E-10 3.3311787E-10 gauss-seidel spectral radius is 0.9804860 estimated iterations to convergence 59 setup time was (sec) 0.7200000 now iterating at: 17:00:34 rms-change max change #iterations 6.7262650E-02 10.18627 at 10iterations 3.8539337E-03 0.6748962 at 20iterations 2.8108168E-04 3.5285950E-02 at 30iterations 6.4571846E-05 1.0011673E-02 at 40iterations 2.3189685E-05 3.5278797E-03 at 50iterations finished qdiffx linear iterations at : 17:00:37 total time elapsed so far: 3.630000 # loops : 50 mean,max change (kT/e) : 2.3189685E-05 3.5278797E-03 energy calculations done at 3.630000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.820000 DelPhi exited at 17:00:38 3.819u 0.227s 0:04.46 90.3% 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 Mon Oct 10 2011 at 17:00:38 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: 320 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4612 !!! WARNING: HEM 818 has a net charge of -3.4000 !!! WARNING: FE 2 has a net charge of 1.4000 !!! WARNING: FE 3 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= 0.1400000 grid size : 179 scale,in grids/A, set to be: 1.536425 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): -18.26900 36.06900 ymin,ymax (A): -30.35400 31.48700 zmin,zma (A): -4.014000 65.49800 x,y,z range (A): 54.33800 61.84100 69.51200 scale (grids/A): 1.536425 object centre (A): 8.900001 0.5664997 30.74200 number of atom coordinates read : 4612 total number of charged atoms : 4410 net assigned charge : 5.400050 assigned positive charge : 694.3746 centred at (gu) : 91.37199 92.16879 84.51548 assigned negative charge : -688.9789 centred at (gu) : 91.12617 92.29124 84.68851 start vw surface at 0.2200000 fill in re-entrant regions at 0.3300000 boundary points on vw surface= 84699 reading accessible surface arcs data from file ARCDAT no. of arc points read = 41118 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.568000 m= 23600 mr = 57549 m= 2036 mr = 15265 m= 46 mr = 836 m= 0 mr = 3 time to grow re-entrant surface = 0.2900000 no. cavity mid-points inaccessible to solvent = 324 time to turn everything in is 0.6600000 number of dielectric boundary points 36728 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 512 ## 7 charges are in solution ## iepsmp to db, and charging done at 0.7800000 number of grid points assigned charge 33140 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) : 0.5121418 object centre at (A) : 8.900001 0.5664997 30.74200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 5.0166608E-03 -5.1491610E-03 midg,1,midg; midg,igrid,midg 8.7119499E-03 -7.9630120E-03 1,midg,midg; igrid,midg,midg -1.3103865E-03 1.1233482E-02 gauss-seidel spectral radius is 0.9981043 estimated iterations to convergence 183 setup time was (sec) 0.9400000 now iterating at: 17:00:39 rms-change max change #iterations 3.742174 150.7604 at 10iterations 1.526190 59.06374 at 20iterations 0.6236271 19.96677 at 30iterations 0.2557666 8.374192 at 40iterations 0.1045170 3.563753 at 50iterations 4.2814013E-02 1.672005 at 60iterations 1.7556235E-02 0.5946503 at 70iterations 7.2115306E-03 0.2369537 at 80iterations 2.9650023E-03 9.8533630E-02 at 90iterations 1.2286934E-03 4.0196419E-02 at 100iterations 5.1232585E-04 1.9378662E-02 at 110iterations 2.2103483E-04 7.5988770E-03 at 120iterations finished qdiffx linear iterations at : 17:00:46 total time elapsed so far: 8.000000 # loops : 120 mean,max change (kT/e) : 2.2103483E-04 7.5988770E-03 energy calculations done at 8.000000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.200000 DelPhi exited at 17:00:47 8.206u 0.174s 0:08.82 94.8% 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 Mon Oct 10 2011 at 17:00:47 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: 320 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4612 !!! WARNING: HEM 818 has a net charge of -3.4000 !!! WARNING: FE 2 has a net charge of 1.4000 !!! WARNING: FE 3 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= 0.1300000 grid size : 179 scale,in grids/A, set to be: 2.304638 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): -18.26900 36.06900 ymin,ymax (A): -30.35400 31.48700 zmin,zma (A): -4.014000 65.49800 x,y,z range (A): 54.33800 61.84100 69.51200 scale (grids/A): 2.304638 object centre (A): 8.900001 0.5664997 30.74200 number of atom coordinates read : 4612 total number of charged atoms : 4410 net assigned charge : 5.400050 assigned positive charge : 694.3746 centred at (gu) : 92.05756 93.25289 81.77282 assigned negative charge : -688.9789 centred at (gu) : 91.68935 93.43670 82.03265 start vw surface at 0.2200000 fill in re-entrant regions at 0.5300000 boundary points on vw surface= 197340 reading accessible surface arcs data from file ARCDAT no. of arc points read = 41118 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.540000 m= 85112 mr = 141476 m= 20656 mr = 65538 m= 2787 mr = 14396 m= 124 mr = 1598 m= 0 mr = 24 time to grow re-entrant surface = 0.8600000 no. cavity mid-points inaccessible to solvent = 1098 time to turn everything in is 1.490000 number of dielectric boundary points 82987 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 67 iepsmp to db, and charging done at 1.640000 number of grid points assigned charge 35201 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) : 1.536425 object centre at (A) : 8.900001 0.5664997 30.74200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1543358 -0.1555239 midg,1,midg; midg,igrid,midg 0.1244495 -0.2219127 1,midg,midg; igrid,midg,midg -2.2724295E-02 0.1657784 gauss-seidel spectral radius is 0.9991539 estimated iterations to convergence 272 setup time was (sec) 1.800000 now iterating at: 17:00:49 rms-change max change #iterations 10.13177 272.3801 at 10iterations 5.792898 127.0511 at 20iterations 3.281782 74.54581 at 30iterations 1.847826 40.74360 at 40iterations 1.038791 22.52861 at 50iterations 0.5803997 12.35018 at 60iterations 0.3247904 7.007847 at 70iterations 0.1808929 4.585562 at 80iterations 0.1007603 2.005989 at 90iterations 5.5981960E-02 1.047592 at 100iterations 3.1122534E-02 0.6390915 at 110iterations 1.7255556E-02 0.3227897 at 120iterations 9.5908018E-03 0.1869335 at 130iterations 5.3070323E-03 0.1049929 at 140iterations 2.9387982E-03 5.6482315E-02 at 150iterations 1.6291523E-03 3.3136368E-02 at 160iterations 9.0358517E-04 1.7260551E-02 at 170iterations 4.9970997E-04 9.4242096E-03 at 180iterations finished qdiffx linear iterations at : 17:01:00 total time elapsed so far: 12.96000 # loops : 180 mean,max change (kT/e) : 4.9970997E-04 9.4242096E-03 energy calculations done at 12.96000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.18000 DelPhi exited at 17:01:01 13.178u 0.196s 0:14.56 91.7% 0+0k 0+0io 0pf+0w