Wed Dec 21 14:21:38 PST 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 Wed Dec 21 2011 at 14:21:39 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: 259 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1861 !!! WARNING: GLN 7 has a net charge of 0.0170 !!! WARNING: ARG 14 has a net charge of 0.0400 !!! WARNING: LYS 20 has a net charge of 0.0200 !!! WARNING: LYS 41 has a net charge of 0.0200 !!! WARNING: LYS 43 has a net charge of 0.0200 !!! WARNING: LYS 55 has a net charge of 0.0200 !!! WARNING: LYS 70 has a net charge of 0.0200 !!! WARNING: VAL 82 has a net charge of -0.0120 !!! WARNING: GLN 106 has a net charge of 0.0170 !!! WARNING: GLN 117 has a net charge of 0.0170 !!! WARNING: LYS 140 has a net charge of 0.0200 !!! WARNING: LYS 142 has a net charge of 0.0200 !!! WARNING: LYS 144 has a net charge of 0.0200 !!! WARNING: LYS 154 has a net charge of 0.0200 !!! WARNING: LYS 169 has a net charge of 0.0200 !!! WARNING: VAL 181 has a net charge of -0.0120 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: 0.6099650 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): -23.86100 34.50300 ymin,ymax (A): -18.51500 20.62200 zmin,zma (A): -3.312000 38.67000 x,y,z range (A): 58.36400 39.13700 41.98200 scale (grids/A): 0.6099650 object centre (A): 5.321001 1.053500 17.67900 number of atom coordinates read : 1861 total number of charged atoms : 1729 net assigned charge : -5.732985 assigned positive charge : 272.6771 centred at (gu) : 89.78355 90.17233 90.51074 assigned negative charge : -278.4103 centred at (gu) : 89.84436 90.25898 90.58276 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 4757 nv = 96 ne = 84 npr = 38379 no. pairs analyzed = 38379 no. exposed pairs = 2478 no. arc points = 16875 no. surface atoms = 838 nbur = 1023 mkacc time = 0.1100000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 265 mr = 2549 m= 0 mr = 22 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 2451 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1656 ## 144 charges are in solution ## iepsmp to db, and charging done at 0.4300000 number of grid points assigned charge 5654 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -7.5546708E-10 -6.6510353E-09 midg,1,midg; midg,igrid,midg -3.1244948E-10 -6.7194263E-09 1,midg,midg; igrid,midg,midg -1.2726494E-09 -5.2766795E-09 gauss-seidel spectral radius is 0.9860243 estimated iterations to convergence 69 setup time was (sec) 0.6200000 now iterating at: 14:21:41 rms-change max change #iterations 9.9942088E-02 18.22295 at 10iterations 8.8628922E-03 1.492386 at 20iterations 7.5636338E-04 0.1353760 at 30iterations 6.7295849E-05 1.1724472E-02 at 40iterations 5.9817980E-06 9.6893311E-04 at 50iterations finished qdiffx linear iterations at : 14:21:45 total time elapsed so far: 4.850000 # loops : 50 mean,max change (kT/e) : 5.9817980E-06 9.6893311E-04 energy calculations done at 4.850000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 5.040000 DelPhi exited at 14:21:49 5.044u 0.392s 0:10.99 49.4% 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 Wed Dec 21 2011 at 14:21:51 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: 259 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1861 !!! WARNING: GLN 7 has a net charge of 0.0170 !!! WARNING: ARG 14 has a net charge of 0.0400 !!! WARNING: LYS 20 has a net charge of 0.0200 !!! WARNING: LYS 41 has a net charge of 0.0200 !!! WARNING: LYS 43 has a net charge of 0.0200 !!! WARNING: LYS 55 has a net charge of 0.0200 !!! WARNING: LYS 70 has a net charge of 0.0200 !!! WARNING: VAL 82 has a net charge of -0.0120 !!! WARNING: GLN 106 has a net charge of 0.0170 !!! WARNING: GLN 117 has a net charge of 0.0170 !!! WARNING: LYS 140 has a net charge of 0.0200 !!! WARNING: LYS 142 has a net charge of 0.0200 !!! WARNING: LYS 144 has a net charge of 0.0200 !!! WARNING: LYS 154 has a net charge of 0.0200 !!! WARNING: LYS 169 has a net charge of 0.0200 !!! WARNING: VAL 181 has a net charge of -0.0120 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: 1.829895 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): -23.86100 34.50300 ymin,ymax (A): -18.51500 20.62200 zmin,zma (A): -3.312000 38.67000 x,y,z range (A): 58.36400 39.13700 41.98200 scale (grids/A): 1.829895 object centre (A): 5.321001 1.053500 17.67900 number of atom coordinates read : 1861 total number of charged atoms : 1729 net assigned charge : -5.732985 assigned positive charge : 272.6771 centred at (gu) : 89.35081 90.51719 91.53249 assigned negative charge : -278.4103 centred at (gu) : 89.53328 90.77723 91.74842 start vw surface at 0.1300000 fill in re-entrant regions at 0.2200000 boundary points on vw surface= 51019 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16875 grid for indexing accessible points = 1.400000 m= 18602 mr = 34566 m= 2829 mr = 13836 m= 115 mr = 1775 m= 2 mr = 23 m= 0 mr = 0 time to grow re-entrant surface = 0.2300000 no. cavity mid-points inaccessible to solvent = 331 time to turn everything in is 0.4800000 number of dielectric boundary points 22367 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 139 iepsmp to db, and charging done at 0.6100000 number of grid points assigned charge 13574 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) : 0.6099650 object centre at (A) : 5.321001 1.053500 17.67900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -3.5286194E-03 -1.1164878E-02 midg,1,midg; midg,igrid,midg -8.6639216E-04 -6.3062171E-03 1,midg,midg; igrid,midg,midg 1.4653499E-02 -1.2363605E-02 gauss-seidel spectral radius is 0.9984388 estimated iterations to convergence 201 setup time was (sec) 0.7700000 now iterating at: 14:21:52 rms-change max change #iterations 3.258472 174.2426 at 10iterations 1.448066 55.61870 at 20iterations 0.6435704 25.56728 at 30iterations 0.2852749 11.28023 at 40iterations 0.1268087 4.622604 at 50iterations 5.6287639E-02 2.208382 at 60iterations 2.4881728E-02 0.9501496 at 70iterations 1.1086343E-02 0.4396973 at 80iterations 4.9198475E-03 0.1942663 at 90iterations 2.1860427E-03 9.0207100E-02 at 100iterations 9.7199850E-04 4.3218374E-02 at 110iterations 4.3140716E-04 1.7211914E-02 at 120iterations finished qdiffx linear iterations at : 14:22:01 total time elapsed so far: 9.980000 # loops : 120 mean,max change (kT/e) : 4.3140716E-04 1.7211914E-02 energy calculations done at 9.980000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.16000 DelPhi exited at 14:22:06 10.165u 0.309s 0:16.32 64.0% 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 Wed Dec 21 2011 at 14:22:07 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: 259 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1861 !!! WARNING: GLN 7 has a net charge of 0.0170 !!! WARNING: ARG 14 has a net charge of 0.0400 !!! WARNING: LYS 20 has a net charge of 0.0200 !!! WARNING: LYS 41 has a net charge of 0.0200 !!! WARNING: LYS 43 has a net charge of 0.0200 !!! WARNING: LYS 55 has a net charge of 0.0200 !!! WARNING: LYS 70 has a net charge of 0.0200 !!! WARNING: VAL 82 has a net charge of -0.0120 !!! WARNING: GLN 106 has a net charge of 0.0170 !!! WARNING: GLN 117 has a net charge of 0.0170 !!! WARNING: LYS 140 has a net charge of 0.0200 !!! WARNING: LYS 142 has a net charge of 0.0200 !!! WARNING: LYS 144 has a net charge of 0.0200 !!! WARNING: LYS 154 has a net charge of 0.0200 !!! WARNING: LYS 169 has a net charge of 0.0200 !!! WARNING: VAL 181 has a net charge of -0.0120 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: 2.744843 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): -23.86100 34.50300 ymin,ymax (A): -18.51500 20.62200 zmin,zma (A): -3.312000 38.67000 x,y,z range (A): 58.36400 39.13700 41.98200 scale (grids/A): 2.744843 object centre (A): 5.321001 1.053500 17.67900 number of atom coordinates read : 1861 total number of charged atoms : 1729 net assigned charge : -5.732985 assigned positive charge : 272.6771 centred at (gu) : 89.02630 90.77567 92.29876 assigned negative charge : -278.4103 centred at (gu) : 89.30004 91.16574 92.62273 start vw surface at 0.1400000 fill in re-entrant regions at 0.4100000 boundary points on vw surface= 117827 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16875 grid for indexing accessible points = 1.400000 m= 59940 mr = 83882 m= 21889 mr = 49098 m= 5074 mr = 17773 m= 482 mr = 3855 m= 13 mr = 262 m= 0 mr = 0 time to grow re-entrant surface = 0.7199999 no. cavity mid-points inaccessible to solvent = 1087 time to turn everything in is 1.220000 number of dielectric boundary points 50355 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3 iepsmp to db, and charging done at 1.380000 number of grid points assigned charge 13831 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) : 1.829895 object centre at (A) : 5.321001 1.053500 17.67900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -3.4086715E-02 -9.9335238E-02 midg,1,midg; midg,igrid,midg -2.5710149E-03 -4.2993404E-02 1,midg,midg; igrid,midg,midg 0.2176769 -0.1602962 gauss-seidel spectral radius is 0.9991882 estimated iterations to convergence 277 setup time was (sec) 1.610000 now iterating at: 14:22:10 rms-change max change #iterations 7.892872 360.1832 at 10iterations 4.504171 131.6171 at 20iterations 2.548244 72.89168 at 30iterations 1.434692 32.45435 at 40iterations 0.8068854 22.36983 at 50iterations 0.4522812 11.17235 at 60iterations 0.2528733 5.445679 at 70iterations 0.1419462 3.192665 at 80iterations 7.9297930E-02 1.690926 at 90iterations 4.4455174E-02 1.022069 at 100iterations 2.4838950E-02 0.5527191 at 110iterations 1.3877654E-02 0.2905874 at 120iterations 7.7517671E-03 0.1780319 at 130iterations 4.3441611E-03 9.4737053E-02 at 140iterations 2.4209172E-03 4.9911499E-02 at 150iterations 1.3529741E-03 3.2112122E-02 at 160iterations 7.5645087E-04 1.7158508E-02 at 170iterations 4.2278497E-04 1.0531902E-02 at 180iterations finished qdiffx linear iterations at : 14:22:25 total time elapsed so far: 17.15000 # loops : 180 mean,max change (kT/e) : 4.2278497E-04 1.0531902E-02 energy calculations done at 17.15000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 17.33000 DelPhi exited at 14:22:29 17.328u 0.546s 0:21.16 84.4% 0+0k 0+0io 0pf+0w