Sat Oct 15 13:41:54 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 15 2011 at 13:41:54 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: 252 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3070 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: 0.5062355 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): 2.162000 68.31900 ymin,ymax (A): 42.02800 112.3510 zmin,zma (A): 27.28500 83.39500 x,y,z range (A): 66.15700 70.32300 56.11000 scale (grids/A): 0.5062355 object centre (A): 35.24050 77.18950 55.34000 number of atom coordinates read : 3070 total number of charged atoms : 2891 net assigned charge : -7.999985 assigned positive charge : 460.9957 centred at (gu) : 88.33206 87.80565 90.53290 assigned negative charge : -468.9969 centred at (gu) : 88.42096 87.87708 90.33553 start vw surface at 9.0000004E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 5277 nv = 96 ne = 84 npr = 56613 no. pairs analyzed = 56613 no. exposed pairs = 4602 no. arc points = 34290 no. surface atoms = 1525 nbur = 1545 mkacc time = 9.9999994E-02 writing accessible surface arcs data to file ARCDAT initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.680000 m= 194 mr = 2199 m= 0 mr = 3 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 8 time to turn everything in is 0.2100000 number of dielectric boundary points 3269 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3267 ## 512 charges are in solution ## iepsmp to db, and charging done at 0.2800000 number of grid points assigned charge 6960 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -3.3125888E-10 1.9735601E-10 midg,1,midg; midg,igrid,midg 5.3001483E-12 -1.1237315E-10 1,midg,midg; igrid,midg,midg 4.1295866E-11 -1.4471270E-10 gauss-seidel spectral radius is 0.9799491 estimated iterations to convergence 58 setup time was (sec) 0.4100000 now iterating at: 13:41:54 rms-change max change #iterations 4.9551882E-02 10.98125 at 10iterations 2.6855075E-03 0.4892273 at 20iterations 1.5157276E-04 2.4902344E-02 at 30iterations 9.7189877E-06 1.7642975E-03 at 40iterations 8.1070800E-07 1.7166138E-04 at 50iterations finished qdiffx linear iterations at : 13:41:59 total time elapsed so far: 3.550000 # loops : 50 mean,max change (kT/e) : 8.1070800E-07 1.7166138E-04 energy calculations done at 3.550000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.680000 DelPhi exited at 13:41:59 3.682u 0.258s 0:05.78 67.9% 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 15 2011 at 13:41:59 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: 252 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3070 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: 1.518707 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): 2.162000 68.31900 ymin,ymax (A): 42.02800 112.3510 zmin,zma (A): 27.28500 83.39500 x,y,z range (A): 66.15700 70.32300 56.11000 scale (grids/A): 1.518707 object centre (A): 35.24050 77.18950 55.34000 number of atom coordinates read : 3070 total number of charged atoms : 2891 net assigned charge : -7.999985 assigned positive charge : 460.9957 centred at (gu) : 84.99514 83.41608 91.59780 assigned negative charge : -468.9969 centred at (gu) : 85.26262 83.63093 91.00634 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 58218 reading accessible surface arcs data from file ARCDAT no. of arc points read = 34290 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.568000 m= 15227 mr = 34850 m= 1317 mr = 9156 m= 28 mr = 499 m= 0 mr = 2 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 495 time to turn everything in is 0.3200000 number of dielectric boundary points 30283 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 437 ## 8 charges are in solution ## iepsmp to db, and charging done at 0.4400000 number of grid points assigned charge 21595 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) : 0.5062355 object centre at (A) : 35.24050 77.18950 55.34000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -9.4584301E-03 7.9061044E-03 midg,1,midg; midg,igrid,midg 3.0714381E-03 -1.4627022E-03 1,midg,midg; igrid,midg,midg -4.3958449E-03 -1.2596923E-02 gauss-seidel spectral radius is 0.9979222 estimated iterations to convergence 174 setup time was (sec) 0.6200000 now iterating at: 13:42:00 rms-change max change #iterations 2.885366 143.2510 at 10iterations 1.121136 55.67321 at 20iterations 0.4367944 19.41975 at 30iterations 0.1704279 6.643423 at 40iterations 6.6342220E-02 2.635810 at 50iterations 2.5923362E-02 1.094695 at 60iterations 1.0139300E-02 0.4084892 at 70iterations 3.9593964E-03 0.1518254 at 80iterations 1.5509296E-03 6.0101032E-02 at 90iterations 6.0797000E-04 2.4354935E-02 at 100iterations 2.3827187E-04 9.9964142E-03 at 110iterations 9.3883056E-05 4.2042732E-03 at 120iterations finished qdiffx linear iterations at : 13:42:10 total time elapsed so far: 8.680000 # loops : 120 mean,max change (kT/e) : 9.3883056E-05 4.2042732E-03 energy calculations done at 8.680000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.800000 DelPhi exited at 13:42:10 8.807u 0.315s 0:10.71 85.0% 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 Sat Oct 15 2011 at 13:42:10 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: 252 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3070 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: 2.278060 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): 2.162000 68.31900 ymin,ymax (A): 42.02800 112.3510 zmin,zma (A): 27.28500 83.39500 x,y,z range (A): 66.15700 70.32300 56.11000 scale (grids/A): 2.278060 object centre (A): 35.24050 77.18950 55.34000 number of atom coordinates read : 3070 total number of charged atoms : 2891 net assigned charge : -7.999985 assigned positive charge : 460.9957 centred at (gu) : 82.49249 80.12391 92.39680 assigned negative charge : -468.9969 centred at (gu) : 82.89368 80.44637 91.50935 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 135384 reading accessible surface arcs data from file ARCDAT no. of arc points read = 34290 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.568000 m= 53824 mr = 86844 m= 13248 mr = 38988 m= 1774 mr = 8965 m= 60 mr = 946 m= 3 mr = 11 m= 0 mr = 0 time to grow re-entrant surface = 0.3700000 no. cavity mid-points inaccessible to solvent = 1655 time to turn everything in is 0.7100000 number of dielectric boundary points 68539 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 54 iepsmp to db, and charging done at 0.8000000 number of grid points assigned charge 23046 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) : 1.518707 object centre at (A) : 35.24050 77.18950 55.34000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1937008 0.1228546 midg,1,midg; midg,igrid,midg 0.1091439 -7.5057559E-02 1,midg,midg; igrid,midg,midg 2.3843425E-03 -0.2441370 gauss-seidel spectral radius is 0.9990584 estimated iterations to convergence 258 setup time was (sec) 0.9400000 now iterating at: 13:42:12 rms-change max change #iterations 8.021563 276.0260 at 10iterations 4.463210 164.8943 at 20iterations 2.453160 85.20961 at 30iterations 1.337416 39.10427 at 40iterations 0.7264507 18.80338 at 50iterations 0.3920321 9.792356 at 60iterations 0.2109666 5.441040 at 70iterations 0.1135572 3.124336 at 80iterations 6.1042260E-02 1.375946 at 90iterations 3.2750562E-02 0.7763600 at 100iterations 1.7553745E-02 0.4391899 at 110iterations 9.4049890E-03 0.2266846 at 120iterations 5.0288527E-03 0.1123886 at 130iterations 2.6912480E-03 5.9278488E-02 at 140iterations 1.4401582E-03 3.2212257E-02 at 150iterations 7.7306764E-04 1.6942978E-02 at 160iterations 4.1366369E-04 9.1819763E-03 at 170iterations 2.2191601E-04 5.0539970E-03 at 180iterations finished qdiffx linear iterations at : 13:42:32 total time elapsed so far: 13.22000 # loops : 180 mean,max change (kT/e) : 2.2191601E-04 5.0539970E-03 energy calculations done at 13.22000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.35000 DelPhi exited at 13:42:32 13.351u 0.273s 0:22.27 61.1% 0+0k 0+0io 0pf+0w