Mon Oct 10 17:02:05 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 17:02:05 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 = 2283 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: 0.6391611 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): -6.154000 39.56500 ymin,ymax (A): 15.97300 71.67101 zmin,zma (A): -0.7520000 48.13500 x,y,z range (A): 45.71900 55.69801 48.88700 scale (grids/A): 0.6391611 object centre (A): 16.70550 43.82200 23.69150 number of atom coordinates read : 2283 total number of charged atoms : 2209 net assigned charge : -3.999991 assigned positive charge : 335.7743 centred at (gu) : 90.39691 89.65749 88.28139 assigned negative charge : -339.7748 centred at (gu) : 90.44827 89.65669 88.22762 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 6316 nv = 96 ne = 84 npr = 46052 no. pairs analyzed = 46052 no. exposed pairs = 2982 no. arc points = 20514 no. surface atoms = 1017 nbur = 1266 mkacc time = 0.1300000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 341 mr = 3379 m= 0 mr = 47 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3100000 number of dielectric boundary points 3231 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1985 ## 176 charges are in solution ## iepsmp to db, and charging done at 0.4300000 number of grid points assigned charge 7648 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.5790873E-08 -2.3003224E-10 midg,1,midg; midg,igrid,midg -6.0300223E-09 -5.0863478E-09 1,midg,midg; igrid,midg,midg -4.4431314E-10 -1.1615062E-08 gauss-seidel spectral radius is 0.9872937 estimated iterations to convergence 73 setup time was (sec) 0.5800000 now iterating at: 17:02:06 rms-change max change #iterations 0.1353736 19.56433 at 10iterations 1.3208847E-02 2.673552 at 20iterations 1.3593399E-03 0.1967478 at 30iterations 1.6068805E-04 2.7421951E-02 at 40iterations 2.7119009E-05 3.7164688E-03 at 50iterations finished qdiffx linear iterations at : 17:02:09 total time elapsed so far: 3.860000 # loops : 50 mean,max change (kT/e) : 2.7119009E-05 3.7164688E-03 energy calculations done at 3.860000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.030000 DelPhi exited at 17:02:10 4.038u 0.261s 0:04.75 90.3% 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 17:02:10 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 = 2283 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: 1.917483 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): -6.154000 39.56500 ymin,ymax (A): 15.97300 71.67101 zmin,zma (A): -0.7520000 48.13500 x,y,z range (A): 45.71900 55.69801 48.88700 scale (grids/A): 1.917483 object centre (A): 16.70550 43.82200 23.69150 number of atom coordinates read : 2283 total number of charged atoms : 2209 net assigned charge : -3.999991 assigned positive charge : 335.7743 centred at (gu) : 91.19030 88.97206 84.84354 assigned negative charge : -339.7748 centred at (gu) : 91.34470 88.96997 84.68289 start vw surface at 0.1500000 fill in re-entrant regions at 0.2800000 boundary points on vw surface= 68410 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20514 grid for indexing accessible points = 1.400000 m= 24321 mr = 46998 m= 4194 mr = 17599 m= 292 mr = 2608 m= 5 mr = 107 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 0.6200000 number of dielectric boundary points 29910 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 132 iepsmp to db, and charging done at 0.7500000 number of grid points assigned charge 17406 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) : 0.6391611 object centre at (A) : 16.70550 43.82200 23.69150 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.9043807E-02 1.0549400E-02 midg,1,midg; midg,igrid,midg 1.6691223E-02 -8.1930179E-03 1,midg,midg; igrid,midg,midg -2.9965690E-03 -3.1584110E-02 gauss-seidel spectral radius is 0.9986274 estimated iterations to convergence 214 setup time was (sec) 0.9200000 now iterating at: 17:02:11 rms-change max change #iterations 3.974514 185.3560 at 10iterations 1.856653 66.10375 at 20iterations 0.8692055 33.42094 at 30iterations 0.4074906 15.82709 at 40iterations 0.1908448 6.530012 at 50iterations 8.9190982E-02 2.752764 at 60iterations 4.1941736E-02 1.317127 at 70iterations 1.9559659E-02 0.6261764 at 80iterations 9.1478555E-03 0.2982922 at 90iterations 4.3061827E-03 0.1530743 at 100iterations 2.0214927E-03 6.9208145E-02 at 110iterations 9.5187780E-04 3.5575867E-02 at 120iterations finished qdiffx linear iterations at : 17:02:19 total time elapsed so far: 9.130000 # loops : 120 mean,max change (kT/e) : 9.5187780E-04 3.5575867E-02 energy calculations done at 9.130000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.310000 DelPhi exited at 17:02:20 9.308u 0.301s 0:09.92 96.7% 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 17:02:20 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 = 2283 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: 2.876225 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): -6.154000 39.56500 ymin,ymax (A): 15.97300 71.67101 zmin,zma (A): -0.7520000 48.13500 x,y,z range (A): 45.71900 55.69801 48.88700 scale (grids/A): 2.876225 object centre (A): 16.70550 43.82200 23.69150 number of atom coordinates read : 2283 total number of charged atoms : 2209 net assigned charge : -3.999991 assigned positive charge : 335.7743 centred at (gu) : 91.78529 88.45800 82.26515 assigned negative charge : -339.7748 centred at (gu) : 92.01696 88.45493 82.02426 start vw surface at 0.1500000 fill in re-entrant regions at 0.5300000 boundary points on vw surface= 158476 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20514 grid for indexing accessible points = 1.400000 m= 78454 mr = 114476 m= 28996 mr = 63340 m= 7433 mr = 22993 m= 1300 mr = 5573 m= 111 mr = 900 m= 4 mr = 45 m= 0 mr = 0 time to grow re-entrant surface = 0.9500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.600000 number of dielectric boundary points 67447 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.750000 number of grid points assigned charge 17667 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) : 1.917483 object centre at (A) : 16.70550 43.82200 23.69150 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.3083842 0.1639469 midg,1,midg; midg,igrid,midg 0.1992665 -3.9353758E-02 1,midg,midg; igrid,midg,midg -3.7278645E-02 -0.3030593 gauss-seidel spectral radius is 0.9992551 estimated iterations to convergence 289 setup time was (sec) 1.920000 now iterating at: 17:02:22 rms-change max change #iterations 9.358043 451.0724 at 10iterations 5.474062 142.7982 at 20iterations 3.195309 64.45421 at 30iterations 1.853089 41.04985 at 40iterations 1.075625 20.60822 at 50iterations 0.6218424 11.93944 at 60iterations 0.3592190 7.153141 at 70iterations 0.2069024 4.311295 at 80iterations 0.1190988 2.173597 at 90iterations 6.8599083E-02 1.310360 at 100iterations 3.9493456E-02 0.8417258 at 110iterations 2.2706626E-02 0.4141636 at 120iterations 1.3052090E-02 0.2293692 at 130iterations 7.4913488E-03 0.1454277 at 140iterations 4.3014945E-03 8.0114365E-02 at 150iterations 2.4744563E-03 4.4681549E-02 at 160iterations 1.4294832E-03 2.7816772E-02 at 170iterations 8.2934322E-04 1.5631199E-02 at 180iterations finished qdiffx linear iterations at : 17:02:36 total time elapsed so far: 15.36000 # loops : 180 mean,max change (kT/e) : 8.2934322E-04 1.5631199E-02 energy calculations done at 15.36000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.54000 DelPhi exited at 17:02:36 15.539u 0.298s 0:16.35 96.7% 0+0k 0+0io 0pf+0w