Sat Oct 8 21:28:03 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 21:28:03 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 = 2016 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6732351 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): 6.904000 59.78300 ymin,ymax (A): 77.34000 124.0690 zmin,zma (A): -7.364000 33.69600 x,y,z range (A): 52.87900 46.72900 41.06000 scale (grids/A): 0.6732351 object centre (A): 33.34350 100.7045 13.16600 number of atom coordinates read : 2016 total number of charged atoms : 1880 net assigned charge : 3.0249357E-06 assigned positive charge : 298.9908 centred at (gu) : 88.11117 90.19205 90.93395 assigned negative charge : -298.9909 centred at (gu) : 88.23028 90.17368 90.87897 start vw surface at 7.9999998E-02 fill in re-entrant regions at 7.9999998E-02 boundary points on vw surface= 6346 nv = 96 ne = 84 npr = 40394 no. pairs analyzed = 40394 no. exposed pairs = 2508 no. arc points = 17682 no. surface atoms = 853 nbur = 1163 mkacc time = 7.0000008E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 414 mr = 3542 m= 2 mr = 63 m= 0 mr = 0 time to grow re-entrant surface = 9.0000004E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.1700000 number of dielectric boundary points 3157 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1563 ## 127 charges are in solution ## iepsmp to db, and charging done at 0.2300000 number of grid points assigned charge 7049 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.0175065E-08 1.3292960E-08 midg,1,midg; midg,igrid,midg -4.3621315E-09 3.3678000E-09 1,midg,midg; igrid,midg,midg 3.6143533E-08 -1.7725830E-08 gauss-seidel spectral radius is 0.9885109 estimated iterations to convergence 76 setup time was (sec) 0.3600000 now iterating at: 21:28:04 rms-change max change #iterations 0.1644544 23.62249 at 10iterations 1.8043535E-02 3.309265 at 20iterations 2.0099075E-03 0.3021736 at 30iterations 2.3169383E-04 3.0441284E-02 at 40iterations 2.9974537E-05 4.1770935E-03 at 50iterations finished qdiffx linear iterations at : 21:28:07 total time elapsed so far: 3.340000 # loops : 50 mean,max change (kT/e) : 2.9974537E-05 4.1770935E-03 energy calculations done at 3.340000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.480000 DelPhi exited at 21:28:07 3.484u 0.184s 0:03.94 92.8% 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 21:28:07 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2016 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.019705 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): 6.904000 59.78300 ymin,ymax (A): 77.34000 124.0690 zmin,zma (A): -7.364000 33.69600 x,y,z range (A): 52.87900 46.72900 41.06000 scale (grids/A): 2.019705 object centre (A): 33.34350 100.7045 13.16600 number of atom coordinates read : 2016 total number of charged atoms : 1880 net assigned charge : 3.0249357E-06 assigned positive charge : 298.9908 centred at (gu) : 84.33332 90.57612 92.80194 assigned negative charge : -298.9909 centred at (gu) : 84.69080 90.52093 92.63676 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 67304 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17682 grid for indexing accessible points = 1.400000 m= 26112 mr = 46836 m= 4813 mr = 19522 m= 378 mr = 3113 m= 7 mr = 169 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 0.3500000 number of dielectric boundary points 28974 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 78 iepsmp to db, and charging done at 0.4300000 number of grid points assigned charge 14870 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) : 0.6732351 object centre at (A) : 33.34350 100.7045 13.16600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -6.3125850E-03 1.1339566E-02 midg,1,midg; midg,igrid,midg 3.5050346E-03 2.1430412E-02 1,midg,midg; igrid,midg,midg -2.7618252E-02 -2.9021576E-02 gauss-seidel spectral radius is 0.9987223 estimated iterations to convergence 222 setup time was (sec) 0.5800000 now iterating at: 21:28:08 rms-change max change #iterations 4.136405 229.3405 at 10iterations 1.992431 74.03897 at 20iterations 0.9533934 35.10468 at 30iterations 0.4598846 16.69221 at 40iterations 0.2212900 7.545519 at 50iterations 0.1062343 3.283577 at 60iterations 5.1141184E-02 1.788300 at 70iterations 2.4565902E-02 0.8124452 at 80iterations 1.1834483E-02 0.4514093 at 90iterations 5.6791566E-03 0.1912689 at 100iterations 2.7316432E-03 8.6097717E-02 at 110iterations 1.3135108E-03 4.2025328E-02 at 120iterations finished qdiffx linear iterations at : 21:28:16 total time elapsed so far: 8.240000 # loops : 120 mean,max change (kT/e) : 1.3135108E-03 4.2025328E-02 energy calculations done at 8.240000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.370000 DelPhi exited at 21:28:16 8.374u 0.245s 0:08.92 96.5% 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 21:28:16 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 = 2016 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 3.029558 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): 6.904000 59.78300 ymin,ymax (A): 77.34000 124.0690 zmin,zma (A): -7.364000 33.69600 x,y,z range (A): 52.87900 46.72900 41.06000 scale (grids/A): 3.029558 object centre (A): 33.34350 100.7045 13.16600 number of atom coordinates read : 2016 total number of charged atoms : 1880 net assigned charge : 3.0249357E-06 assigned positive charge : 298.9908 centred at (gu) : 81.49991 90.86435 94.20271 assigned negative charge : -298.9909 centred at (gu) : 82.03620 90.78132 93.95519 start vw surface at 7.0000000E-02 fill in re-entrant regions at 0.3100000 boundary points on vw surface= 155384 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17682 grid for indexing accessible points = 1.400000 m= 82033 mr = 113102 m= 32308 mr = 67822 m= 8999 mr = 26148 m= 1613 mr = 6887 m= 130 mr = 1138 m= 4 mr = 71 m= 0 mr = 4 time to grow re-entrant surface = 0.5300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.9200000 number of dielectric boundary points 65299 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.030000 number of grid points assigned charge 15040 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) : 2.019705 object centre at (A) : 33.34350 100.7045 13.16600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -6.8950571E-02 0.1339158 midg,1,midg; midg,igrid,midg -5.4879609E-02 0.1853666 1,midg,midg; igrid,midg,midg -0.3854656 -0.2236734 gauss-seidel spectral radius is 0.9992704 estimated iterations to convergence 292 setup time was (sec) 1.200000 now iterating at: 21:28:18 rms-change max change #iterations 9.466637 362.7670 at 10iterations 5.555212 160.1706 at 20iterations 3.241542 75.53246 at 30iterations 1.894502 39.84084 at 40iterations 1.103174 22.59066 at 50iterations 0.6396754 12.57533 at 60iterations 0.3711696 7.153131 at 70iterations 0.2153277 4.403711 at 80iterations 0.1247380 2.290525 at 90iterations 7.2259545E-02 1.371955 at 100iterations 4.1751646E-02 0.8355865 at 110iterations 2.4165677E-02 0.4609680 at 120iterations 1.3963102E-02 0.2654266 at 130iterations 8.0693942E-03 0.1445951 at 140iterations 4.6664067E-03 8.3583832E-02 at 150iterations 2.7097419E-03 5.1292419E-02 at 160iterations 1.5705269E-03 2.8948545E-02 at 170iterations 9.1361045E-04 1.8873930E-02 at 180iterations finished qdiffx linear iterations at : 21:28:31 total time elapsed so far: 14.00000 # loops : 180 mean,max change (kT/e) : 9.1361045E-04 1.8873930E-02 energy calculations done at 14.00000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 14.14000 DelPhi exited at 21:28:31 14.139u 0.262s 0:14.68 98.0% 0+0k 0+0io 0pf+0w