Mon Oct 10 14:39:59 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 14:39:59 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: 247 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2406 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: 0.6210313 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): -6.693000 44.61000 ymin,ymax (A): 13.15400 70.47800 zmin,zma (A): 55.88900 107.5780 x,y,z range (A): 51.30300 57.32401 51.68900 scale (grids/A): 0.6210313 object centre (A): 18.95850 41.81600 81.73351 number of atom coordinates read : 2406 total number of charged atoms : 2248 net assigned charge : -3.999988 assigned positive charge : 353.1772 centred at (gu) : 89.56243 90.58144 89.93551 assigned negative charge : -357.1775 centred at (gu) : 89.32240 90.52863 89.90603 start vw surface at 0.1400000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 6292 nv = 96 ne = 84 npr = 47719 no. pairs analyzed = 47719 no. exposed pairs = 3249 no. arc points = 22914 no. surface atoms = 1098 nbur = 1308 mkacc time = 0.1300000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 336 mr = 3174 m= 5 mr = 14 m= 0 mr = 0 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3100000 number of dielectric boundary points 3445 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2242 ## 210 charges are in solution ## iepsmp to db, and charging done at 0.4400000 number of grid points assigned charge 7549 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -5.1836566E-09 -1.3779955E-09 midg,1,midg; midg,igrid,midg -5.8121077E-09 9.6213433E-11 1,midg,midg; igrid,midg,midg -2.0716811E-08 1.0396428E-08 gauss-seidel spectral radius is 0.9865645 estimated iterations to convergence 71 setup time was (sec) 0.5800000 now iterating at: 14:40:00 rms-change max change #iterations 0.1180519 18.83670 at 10iterations 1.0964124E-02 1.599598 at 20iterations 1.0833400E-03 0.1568356 at 30iterations 1.5212633E-04 3.0159101E-02 at 40iterations 3.7848167E-05 7.7075958E-03 at 50iterations finished qdiffx linear iterations at : 14:40:03 total time elapsed so far: 3.850000 # loops : 50 mean,max change (kT/e) : 3.7848167E-05 7.7075958E-03 energy calculations done at 3.850000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.020000 DelPhi exited at 14:40:04 4.022u 0.297s 0:04.72 91.3% 0+0k 0+0io 5pf+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 14:40:04 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: 247 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2406 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: 1.863094 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): -6.693000 44.61000 ymin,ymax (A): 13.15400 70.47800 zmin,zma (A): 55.88900 107.5780 x,y,z range (A): 51.30300 57.32401 51.68900 scale (grids/A): 1.863094 object centre (A): 18.95850 41.81600 81.73351 number of atom coordinates read : 2406 total number of charged atoms : 2248 net assigned charge : -3.999988 assigned positive charge : 353.1772 centred at (gu) : 88.68736 91.74386 89.80630 assigned negative charge : -357.1775 centred at (gu) : 87.96690 91.58544 89.71774 start vw surface at 0.1500000 fill in re-entrant regions at 0.2700000 boundary points on vw surface= 67960 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22914 grid for indexing accessible points = 1.400000 m= 23512 mr = 45163 m= 3254 mr = 16355 m= 150 mr = 1604 m= 1 mr = 21 m= 0 mr = 0 time to grow re-entrant surface = 0.3000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.6100000 number of dielectric boundary points 31734 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 151 iepsmp to db, and charging done at 0.7500000 number of grid points assigned charge 17665 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) : 0.6210313 object centre at (A) : 18.95850 41.81600 81.73351 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.5749130E-02 3.1479672E-03 midg,1,midg; midg,igrid,midg -8.9932354E-03 2.6785212E-03 1,midg,midg; igrid,midg,midg -3.9434124E-02 7.9122456E-03 gauss-seidel spectral radius is 0.9985660 estimated iterations to convergence 209 setup time was (sec) 0.9200000 now iterating at: 14:40:05 rms-change max change #iterations 3.848598 166.5161 at 10iterations 1.764930 64.79842 at 20iterations 0.8106442 28.84546 at 30iterations 0.3726968 13.96539 at 40iterations 0.1707269 5.664650 at 50iterations 7.8516074E-02 2.642101 at 60iterations 3.6057658E-02 1.257264 at 70iterations 1.6579108E-02 0.5944061 at 80iterations 7.6221712E-03 0.2473173 at 90iterations 3.5181358E-03 0.1241283 at 100iterations 1.6345930E-03 5.8002472E-02 at 110iterations 7.7355810E-04 2.7663708E-02 at 120iterations finished qdiffx linear iterations at : 14:40:14 total time elapsed so far: 9.180000 # loops : 120 mean,max change (kT/e) : 7.7355810E-04 2.7663708E-02 energy calculations done at 9.180000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.350000 DelPhi exited at 14:40:14 9.357u 0.291s 0:10.07 95.7% 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 14:40:14 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: 247 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2406 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: 2.794641 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): -6.693000 44.61000 ymin,ymax (A): 13.15400 70.47800 zmin,zma (A): 55.88900 107.5780 x,y,z range (A): 51.30300 57.32401 51.68900 scale (grids/A): 2.794641 object centre (A): 18.95850 41.81600 81.73351 number of atom coordinates read : 2406 total number of charged atoms : 2248 net assigned charge : -3.999988 assigned positive charge : 353.1772 centred at (gu) : 88.03088 92.61567 89.70918 assigned negative charge : -357.1775 centred at (gu) : 86.95020 92.37814 89.57649 start vw surface at 0.1600000 fill in re-entrant regions at 0.5200000 boundary points on vw surface= 156905 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22914 grid for indexing accessible points = 1.400000 m= 76685 mr = 109947 m= 26316 mr = 60682 m= 5324 mr = 20055 m= 508 mr = 3389 m= 47 mr = 231 m= 1 mr = 23 m= 0 mr = 0 time to grow re-entrant surface = 0.9299999 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.570000 number of dielectric boundary points 71459 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.740000 number of grid points assigned charge 17981 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) : 1.863094 object centre at (A) : 18.95850 41.81600 81.73351 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.2715585 7.2317526E-02 midg,1,midg; midg,igrid,midg -5.0078988E-02 9.7031156E-03 1,midg,midg; igrid,midg,midg -0.4421350 4.0217493E-02 gauss-seidel spectral radius is 0.9992449 estimated iterations to convergence 287 setup time was (sec) 1.900000 now iterating at: 14:40:16 rms-change max change #iterations 9.355717 298.0096 at 10iterations 5.496441 131.5803 at 20iterations 3.206590 78.49075 at 30iterations 1.859281 40.49831 at 40iterations 1.074607 24.37733 at 50iterations 0.6212204 13.19540 at 60iterations 0.3577147 9.514191 at 70iterations 0.2056953 4.464063 at 80iterations 0.1180246 2.507058 at 90iterations 6.7827255E-02 1.469534 at 100iterations 3.8835835E-02 0.7819219 at 110iterations 2.2250185E-02 0.4943237 at 120iterations 1.2764688E-02 0.2589784 at 130iterations 7.3066382E-03 0.1464043 at 140iterations 4.2108214E-03 9.1517448E-02 at 150iterations 2.4315710E-03 5.7296216E-02 at 160iterations 1.4183215E-03 3.2027245E-02 at 170iterations 8.4522110E-04 2.1450043E-02 at 180iterations finished qdiffx linear iterations at : 14:40:30 total time elapsed so far: 15.45000 # loops : 180 mean,max change (kT/e) : 8.4522110E-04 2.1450043E-02 energy calculations done at 15.45000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.62000 DelPhi exited at 14:40:31 15.621u 0.297s 0:16.33 97.4% 0+0k 0+0io 0pf+0w