Tue Oct 11 07:07:12 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 07:07:12 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 = 3761 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: 0.5418322 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): -10.67100 55.03200 ymin,ymax (A): -35.16700 23.05500 zmin,zma (A): 66.77400 118.7020 x,y,z range (A): 65.70300 58.22200 51.92800 scale (grids/A): 0.5418322 object centre (A): 22.18050 -6.056000 92.73801 number of atom coordinates read : 3761 total number of charged atoms : 3619 net assigned charge : 9.500031 assigned positive charge : 572.2283 centred at (gu) : 90.04345 89.38960 90.75653 assigned negative charge : -562.7307 centred at (gu) : 90.03014 89.23802 90.80017 start vw surface at 0.1100000 fill in re-entrant regions at 0.1100000 boundary points on vw surface= 7110 nv = 96 ne = 84 npr = 76110 no. pairs analyzed = 76110 no. exposed pairs = 4479 no. arc points = 30769 no. surface atoms = 1506 nbur = 2255 mkacc time = 0.1300000 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 = 1.596000 m= 262 mr = 3952 m= 1 mr = 10 m= 0 mr = 0 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2600000 number of dielectric boundary points 3411 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3140 ## 427 charges are in solution ## iepsmp to db, and charging done at 0.3100000 number of grid points assigned charge 9340 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 6.8530559E-10 2.3406591E-10 midg,1,midg; midg,igrid,midg -7.0299416E-10 1.3592703E-09 1,midg,midg; igrid,midg,midg 4.1288881E-10 6.1501482E-10 gauss-seidel spectral radius is 0.9824951 estimated iterations to convergence 62 setup time was (sec) 0.4300000 now iterating at: 07:07:12 rms-change max change #iterations 7.8010395E-02 14.00119 at 10iterations 6.0438048E-03 0.8843231 at 20iterations 9.7102451E-04 0.1873703 at 30iterations 2.7547887E-04 5.5282593E-02 at 40iterations 8.2511047E-05 1.6567230E-02 at 50iterations finished qdiffx linear iterations at : 07:07:15 total time elapsed so far: 3.280000 # loops : 50 mean,max change (kT/e) : 8.2511047E-05 1.6567230E-02 energy calculations done at 3.280000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.420000 DelPhi exited at 07:07:16 3.424u 0.179s 0:03.98 90.2% 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 Tue Oct 11 2011 at 07:07:16 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 = 3761 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: 1.625497 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): -10.67100 55.03200 ymin,ymax (A): -35.16700 23.05500 zmin,zma (A): 66.77400 118.7020 x,y,z range (A): 65.70300 58.22200 51.92800 scale (grids/A): 1.625497 object centre (A): 22.18050 -6.056000 92.73801 number of atom coordinates read : 3761 total number of charged atoms : 3619 net assigned charge : 9.500031 assigned positive charge : 572.2283 centred at (gu) : 90.12933 88.16747 92.26816 assigned negative charge : -562.7307 centred at (gu) : 90.08987 87.71356 92.40014 start vw surface at 0.1100000 fill in re-entrant regions at 0.1900000 boundary points on vw surface= 78958 reading accessible surface arcs data from file ARCDAT no. of arc points read = 30769 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 25788 mr = 55691 m= 2598 mr = 18714 m= 51 mr = 1340 m= 0 mr = 0 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 839 time to turn everything in is 0.3900000 number of dielectric boundary points 31650 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 385 ## 4 charges are in solution ## iepsmp to db, and charging done at 0.4700000 number of grid points assigned charge 27691 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) : 0.5418322 object centre at (A) : 22.18050 -6.056000 92.73801 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 8.9831147E-03 -1.2853234E-03 midg,1,midg; midg,igrid,midg -1.3039947E-02 1.3445495E-02 1,midg,midg; igrid,midg,midg 1.7255759E-02 9.5289461E-03 gauss-seidel spectral radius is 0.9982455 estimated iterations to convergence 190 setup time was (sec) 0.6100000 now iterating at: 07:07:17 rms-change max change #iterations 3.794544 159.3536 at 10iterations 1.599575 60.03635 at 20iterations 0.6806218 23.21795 at 30iterations 0.2887235 9.139214 at 40iterations 0.1227088 4.437944 at 50iterations 5.2079335E-02 1.720210 at 60iterations 2.2223840E-02 0.8132915 at 70iterations 9.5021389E-03 0.3074532 at 80iterations 4.1080401E-03 0.1447105 at 90iterations 1.8302773E-03 6.9353104E-02 at 100iterations 8.4553380E-04 3.1860352E-02 at 110iterations 4.1332471E-04 1.7303467E-02 at 120iterations finished qdiffx linear iterations at : 07:07:24 total time elapsed so far: 7.790000 # loops : 120 mean,max change (kT/e) : 4.1332471E-04 1.7303467E-02 energy calculations done at 7.790000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.910000 DelPhi exited at 07:07:24 7.908u 0.222s 0:08.58 94.6% 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 07:07:24 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 = 3761 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: 2.438245 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): -10.67100 55.03200 ymin,ymax (A): -35.16700 23.05500 zmin,zma (A): 66.77400 118.7020 x,y,z range (A): 65.70300 58.22200 51.92800 scale (grids/A): 2.438245 object centre (A): 22.18050 -6.056000 92.73801 number of atom coordinates read : 3761 total number of charged atoms : 3619 net assigned charge : 9.500031 assigned positive charge : 572.2283 centred at (gu) : 90.19354 87.25095 93.40202 assigned negative charge : -562.7307 centred at (gu) : 90.13480 86.57022 93.60000 start vw surface at 0.1000000 fill in re-entrant regions at 0.3300000 boundary points on vw surface= 183413 reading accessible surface arcs data from file ARCDAT no. of arc points read = 30769 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 88136 mr = 135385 m= 26425 mr = 71799 m= 4044 mr = 20794 m= 208 mr = 2734 m= 4 mr = 84 m= 0 mr = 0 time to grow re-entrant surface = 0.5300000 no. cavity mid-points inaccessible to solvent = 2727 time to turn everything in is 0.9400000 number of dielectric boundary points 71434 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 24 iepsmp to db, and charging done at 1.030000 number of grid points assigned charge 28910 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) : 1.625497 object centre at (A) : 22.18050 -6.056000 92.73801 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 9.7665370E-02 -5.9538517E-02 midg,1,midg; midg,igrid,midg -0.1383145 0.1627641 1,midg,midg; igrid,midg,midg 0.2737950 -0.2095303 gauss-seidel spectral radius is 0.9991702 estimated iterations to convergence 274 setup time was (sec) 1.160000 now iterating at: 07:07:26 rms-change max change #iterations 9.559717 429.9830 at 10iterations 5.383638 141.2069 at 20iterations 3.010857 60.28092 at 30iterations 1.682469 31.87313 at 40iterations 0.9394863 18.81467 at 50iterations 0.5226471 10.16860 at 60iterations 0.2918030 5.207047 at 70iterations 0.1623863 3.178593 at 80iterations 9.0365119E-02 1.694729 at 90iterations 5.0369170E-02 1.026730 at 100iterations 2.7939061E-02 0.5679169 at 110iterations 1.5601830E-02 0.2887688 at 120iterations 8.6765941E-03 0.1694195 at 130iterations 4.8563434E-03 0.1070209 at 140iterations 2.7358434E-03 5.4140091E-02 at 150iterations 1.5508271E-03 3.0044556E-02 at 160iterations 8.9120498E-04 1.8099785E-02 at 170iterations 5.2633270E-04 1.2111664E-02 at 180iterations finished qdiffx linear iterations at : 07:07:37 total time elapsed so far: 12.34000 # loops : 180 mean,max change (kT/e) : 5.2633270E-04 1.2111664E-02 energy calculations done at 12.34000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.47000 DelPhi exited at 07:07:38 12.469u 0.213s 0:13.32 95.1% 0+0k 0+0io 0pf+0w