Sat Oct 8 11:38:20 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 Sat Oct 8 2011 at 11:38:20 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 = 2798 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 0.5974658 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): -53.39300 -7.215000 ymin,ymax (A): -12.02800 47.55700 zmin,zma (A): -45.48200 7.524000 x,y,z range (A): 46.17800 59.58500 53.00600 scale (grids/A): 0.5974658 object centre (A): -30.30400 17.76450 -18.97900 number of atom coordinates read : 2798 total number of charged atoms : 2646 net assigned charge : -2.999992 assigned positive charge : 410.8222 centred at (gu) : 90.34434 89.53020 91.13641 assigned negative charge : -413.8230 centred at (gu) : 90.42161 89.52273 91.16194 start vw surface at 0.1600000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 6647 nv = 96 ne = 84 npr = 56461 no. pairs analyzed = 56461 no. exposed pairs = 3703 no. arc points = 25935 no. surface atoms = 1247 nbur = 1551 mkacc time = 0.1800000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 314 mr = 3367 m= 1 mr = 18 m= 0 mr = 0 time to grow re-entrant surface = 0.2200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4100000 number of dielectric boundary points 3577 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2602 ## 267 charges are in solution ## iepsmp to db, and charging done at 0.5300000 number of grid points assigned charge 8358 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.9853244E-10 -2.6874225E-09 midg,1,midg; midg,igrid,midg -1.5826411E-09 -8.0259194E-10 1,midg,midg; igrid,midg,midg 1.4669067E-09 -4.2811132E-09 gauss-seidel spectral radius is 0.9855250 estimated iterations to convergence 68 setup time was (sec) 0.7100000 now iterating at: 11:38:22 rms-change max change #iterations 0.1112941 15.93752 at 10iterations 9.4916243E-03 1.438023 at 20iterations 8.5863454E-04 0.1138649 at 30iterations 1.2006220E-04 1.7524719E-02 at 40iterations 3.2367039E-05 4.1351318E-03 at 50iterations finished qdiffx linear iterations at : 11:38:25 total time elapsed so far: 4.250000 # loops : 50 mean,max change (kT/e) : 3.2367039E-05 4.1351318E-03 energy calculations done at 4.250000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.480000 DelPhi exited at 11:38:26 4.483u 0.415s 0:05.44 89.8% 0+0k 0+0io 6pf+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 11:38:26 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 = 2798 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 1.792397 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): -53.39300 -7.215000 ymin,ymax (A): -12.02800 47.55700 zmin,zma (A): -45.48200 7.524000 x,y,z range (A): 46.17800 59.58500 53.00600 scale (grids/A): 1.792397 object centre (A): -30.30400 17.76450 -18.97900 number of atom coordinates read : 2798 total number of charged atoms : 2646 net assigned charge : -2.999992 assigned positive charge : 410.8222 centred at (gu) : 91.03217 88.58957 93.40842 assigned negative charge : -413.8230 centred at (gu) : 91.26444 88.56783 93.48541 start vw surface at 0.1700000 fill in re-entrant regions at 0.3100000 boundary points on vw surface= 72877 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25935 grid for indexing accessible points = 1.400000 m= 23189 mr = 48648 m= 2901 mr = 15935 m= 113 mr = 1474 m= 1 mr = 13 m= 0 mr = 0 time to grow re-entrant surface = 0.3600000 no. cavity mid-points inaccessible to solvent = 116 time to turn everything in is 0.7300000 number of dielectric boundary points 33011 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 201 iepsmp to db, and charging done at 0.8600000 number of grid points assigned charge 20667 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) : 0.5974658 object centre at (A) : -30.30400 17.76450 -18.97900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 5.8938847E-03 -2.6957167E-03 midg,1,midg; midg,igrid,midg -2.3474585E-02 1.0124924E-02 1,midg,midg; igrid,midg,midg -5.3215859E-04 -1.1415393E-02 gauss-seidel spectral radius is 0.9984914 estimated iterations to convergence 204 setup time was (sec) 1.060000 now iterating at: 11:38:27 rms-change max change #iterations 3.867340 158.9919 at 10iterations 1.734344 67.45449 at 20iterations 0.7786146 28.21288 at 30iterations 0.3501945 11.42072 at 40iterations 0.1571977 5.541569 at 50iterations 7.1079180E-02 2.484074 at 60iterations 3.1834833E-02 1.103836 at 70iterations 1.4329790E-02 0.4763627 at 80iterations 6.4938962E-03 0.2247844 at 90iterations 2.9323676E-03 9.7755432E-02 at 100iterations 1.3275717E-03 4.5518875E-02 at 110iterations 6.0888741E-04 1.9294739E-02 at 120iterations finished qdiffx linear iterations at : 11:38:37 total time elapsed so far: 10.08000 # loops : 120 mean,max change (kT/e) : 6.0888741E-04 1.9294739E-02 energy calculations done at 10.08000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.31000 DelPhi exited at 11:38:37 10.318u 0.465s 0:11.36 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 Sat Oct 8 2011 at 11:38:37 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 = 2798 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 2.688596 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): -53.39300 -7.215000 ymin,ymax (A): -12.02800 47.55700 zmin,zma (A): -45.48200 7.524000 x,y,z range (A): 46.17800 59.58500 53.00600 scale (grids/A): 2.688596 object centre (A): -30.30400 17.76450 -18.97900 number of atom coordinates read : 2798 total number of charged atoms : 2646 net assigned charge : -2.999992 assigned positive charge : 410.8222 centred at (gu) : 91.54824 87.88413 95.11240 assigned negative charge : -413.8230 centred at (gu) : 91.89651 87.85175 95.22807 start vw surface at 0.1600000 fill in re-entrant regions at 0.6200000 boundary points on vw surface= 168989 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25935 grid for indexing accessible points = 1.400000 m= 78032 mr = 119091 m= 24267 mr = 61242 m= 4785 mr = 18353 m= 443 mr = 3240 m= 11 mr = 222 m= 0 mr = 4 time to grow re-entrant surface = 1.110000 no. cavity mid-points inaccessible to solvent = 369 time to turn everything in is 1.850000 number of dielectric boundary points 74375 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3 iepsmp to db, and charging done at 2.000000 number of grid points assigned charge 21164 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) : 1.792397 object centre at (A) : -30.30400 17.76450 -18.97900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1497587 -2.5375020E-02 midg,1,midg; midg,igrid,midg -0.3331122 0.3547886 1,midg,midg; igrid,midg,midg -3.7297521E-02 -0.1569938 gauss-seidel spectral radius is 0.9992347 estimated iterations to convergence 285 setup time was (sec) 2.210000 now iterating at: 11:38:40 rms-change max change #iterations 9.611369 335.9456 at 10iterations 5.717041 135.3967 at 20iterations 3.346526 82.40335 at 30iterations 1.946065 41.65418 at 40iterations 1.128628 25.98190 at 50iterations 0.6495702 13.70705 at 60iterations 0.3753218 8.212382 at 70iterations 0.2153017 4.242460 at 80iterations 0.1237232 2.560371 at 90iterations 7.0895545E-02 1.498083 at 100iterations 4.0563062E-02 0.8746433 at 110iterations 2.3172200E-02 0.4620504 at 120iterations 1.3233747E-02 0.2489831 at 130iterations 7.5652902E-03 0.1412849 at 140iterations 4.3366421E-03 8.9935303E-02 at 150iterations 2.4813588E-03 5.0365686E-02 at 160iterations 1.4253849E-03 2.8381586E-02 at 170iterations 8.2078087E-04 1.5968323E-02 at 180iterations finished qdiffx linear iterations at : 11:38:55 total time elapsed so far: 17.35000 # loops : 180 mean,max change (kT/e) : 8.2078087E-04 1.5968323E-02 energy calculations done at 17.35000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 17.57000 DelPhi exited at 11:38:56 17.578u 0.487s 0:18.36 98.3% 0+0k 0+0io 0pf+0w