Sun Oct 9 13:37:11 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 Sun Oct 9 2011 at 13:37:11 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 = 2339 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: 0.7059290 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): -18.51800 30.39000 ymin,ymax (A): -20.71400 29.71600 zmin,zma (A): 4.075000 48.01100 x,y,z range (A): 48.90800 50.43000 43.93600 scale (grids/A): 0.7059290 object centre (A): 5.936000 4.500999 26.04300 number of atom coordinates read : 2339 total number of charged atoms : 2199 net assigned charge : 3.500011 assigned positive charge : 354.5672 centred at (gu) : 90.66609 90.33996 90.36456 assigned negative charge : -351.0676 centred at (gu) : 90.74267 90.49460 90.49603 start vw surface at 0.1100000 fill in re-entrant regions at 0.1200000 boundary points on vw surface= 7957 nv = 96 ne = 84 npr = 47225 no. pairs analyzed = 47225 no. exposed pairs = 2954 no. arc points = 20415 no. surface atoms = 1001 nbur = 1338 mkacc time = 0.1200000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 499 mr = 4407 m= 2 mr = 79 m= 0 mr = 0 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 52 time to turn everything in is 0.2900000 number of dielectric boundary points 3972 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1965 ## 208 charges are in solution ## iepsmp to db, and charging done at 0.4300000 number of grid points assigned charge 8863 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 9.2439763E-08 -4.5414001E-08 midg,1,midg; midg,igrid,midg 1.0419772E-07 -5.8905560E-08 1,midg,midg; igrid,midg,midg 6.1837092E-08 -1.3924240E-08 gauss-seidel spectral radius is 0.9895689 estimated iterations to convergence 80 setup time was (sec) 0.6100000 now iterating at: 13:37:12 rms-change max change #iterations 0.2090017 27.19248 at 10iterations 2.6055444E-02 3.593925 at 20iterations 3.8134409E-03 0.5674744 at 30iterations 8.9021918E-04 0.1397228 at 40iterations 3.1399020E-04 5.1620483E-02 at 50iterations finished qdiffx linear iterations at : 13:37:16 total time elapsed so far: 4.820000 # loops : 50 mean,max change (kT/e) : 3.1399020E-04 5.1620483E-02 energy calculations done at 4.820000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.990000 DelPhi exited at 13:37:17 4.996u 0.460s 0:05.75 94.7% 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 Sun Oct 9 2011 at 13:37:17 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 = 2339 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: 2.117787 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): -18.51800 30.39000 ymin,ymax (A): -20.71400 29.71600 zmin,zma (A): 4.075000 48.01100 x,y,z range (A): 48.90800 50.43000 43.93600 scale (grids/A): 2.117787 object centre (A): 5.936000 4.500999 26.04300 number of atom coordinates read : 2339 total number of charged atoms : 2199 net assigned charge : 3.500011 assigned positive charge : 354.5672 centred at (gu) : 91.99790 91.01926 91.09328 assigned negative charge : -351.0676 centred at (gu) : 92.22791 91.48365 91.48792 start vw surface at 0.1100000 fill in re-entrant regions at 0.2700000 boundary points on vw surface= 83802 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20415 grid for indexing accessible points = 1.400000 m= 33152 mr = 58352 m= 6400 mr = 24876 m= 594 mr = 4117 m= 17 mr = 298 m= 0 mr = 0 time to grow re-entrant surface = 0.3800000 no. cavity mid-points inaccessible to solvent = 1420 time to turn everything in is 0.7100000 number of dielectric boundary points 36322 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 86 iepsmp to db, and charging done at 0.8900000 number of grid points assigned charge 17452 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) : 0.7059290 object centre at (A) : 5.936000 4.500999 26.04300 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 6.2800974E-02 7.0613888E-03 midg,1,midg; midg,igrid,midg -1.5703926E-02 -0.1044644 1,midg,midg; igrid,midg,midg -5.5369339E-04 9.9475132E-03 gauss-seidel spectral radius is 0.9988589 estimated iterations to convergence 234 setup time was (sec) 1.100000 now iterating at: 13:37:18 rms-change max change #iterations 4.945170 218.4565 at 10iterations 2.460604 75.57703 at 20iterations 1.223355 37.33281 at 30iterations 0.6116782 17.43827 at 40iterations 0.3063137 8.806681 at 50iterations 0.1533215 4.961173 at 60iterations 7.6513924E-02 2.497009 at 70iterations 3.8476184E-02 1.066780 at 80iterations 1.9423367E-02 0.5404053 at 90iterations 9.8522436E-03 0.2828846 at 100iterations 5.1028719E-03 0.1738663 at 110iterations 2.7356837E-03 8.3562851E-02 at 120iterations finished qdiffx linear iterations at : 13:37:30 total time elapsed so far: 12.19000 # loops : 120 mean,max change (kT/e) : 2.7356837E-03 8.3562851E-02 energy calculations done at 12.19000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.36000 DelPhi exited at 13:37:30 12.364u 0.506s 0:13.15 97.7% 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 Sun Oct 9 2011 at 13:37:30 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 = 2339 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: 3.176681 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): -18.51800 30.39000 ymin,ymax (A): -20.71400 29.71600 zmin,zma (A): 4.075000 48.01100 x,y,z range (A): 48.90800 50.43000 43.93600 scale (grids/A): 3.176681 object centre (A): 5.936000 4.500999 26.04300 number of atom coordinates read : 2339 total number of charged atoms : 2199 net assigned charge : 3.500011 assigned positive charge : 354.5672 centred at (gu) : 92.99671 91.52870 91.63985 assigned negative charge : -351.0676 centred at (gu) : 93.34188 92.22534 92.23180 start vw surface at 0.1100000 fill in re-entrant regions at 0.8700000 boundary points on vw surface= 192931 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20415 grid for indexing accessible points = 1.400000 m= 103072 mr = 140520 m= 41989 mr = 84997 m= 11934 mr = 34236 m= 2406 mr = 9086 m= 251 mr = 1713 m= 11 mr = 118 m= 0 mr = 6 time to grow re-entrant surface = 1.210000 no. cavity mid-points inaccessible to solvent = 4959 time to turn everything in is 2.210000 number of dielectric boundary points 81918 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.370000 number of grid points assigned charge 17592 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) : 2.117787 object centre at (A) : 5.936000 4.500999 26.04300 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.5678899 3.5046645E-02 midg,1,midg; midg,igrid,midg -0.5667194 -1.167782 1,midg,midg; igrid,midg,midg -8.6166523E-02 1.5970113E-02 gauss-seidel spectral radius is 0.9993081 estimated iterations to convergence 300 setup time was (sec) 2.590000 now iterating at: 13:37:33 rms-change max change #iterations 11.04230 455.6353 at 10iterations 6.618107 154.7437 at 20iterations 3.949482 77.26840 at 30iterations 2.346907 42.94118 at 40iterations 1.392978 25.80740 at 50iterations 0.8244713 15.48945 at 60iterations 0.4864595 8.408257 at 70iterations 0.2873296 5.370292 at 80iterations 0.1692317 2.911313 at 90iterations 0.1000054 1.870790 at 100iterations 5.9000365E-02 0.9247055 at 110iterations 3.4880199E-02 0.6015892 at 120iterations 2.0767545E-02 0.3901978 at 130iterations 1.2530608E-02 0.2044907 at 140iterations 7.7579827E-03 0.1503067 at 150iterations 4.9993661E-03 9.6290588E-02 at 160iterations 3.4219606E-03 6.9408417E-02 at 170iterations 2.5076601E-03 5.4525375E-02 at 180iterations finished qdiffx linear iterations at : 13:37:52 total time elapsed so far: 21.11000 # loops : 180 mean,max change (kT/e) : 2.5076601E-03 5.4525375E-02 energy calculations done at 21.11000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 21.26000 DelPhi exited at 13:37:52 21.265u 0.556s 0:22.08 98.7% 0+0k 0+0io 0pf+0w