Sun Oct 9 07:46:39 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+sph2.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 = amb2.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 07:46:39 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: 260 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2570 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: 0.5480717 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): -3.797000 42.16200 ymin,ymax (A): 35.71700 88.87400 zmin,zma (A): -3.168000 61.78700 x,y,z range (A): 45.95900 53.15700 64.95500 scale (grids/A): 0.5480717 object centre (A): 19.18250 62.29550 29.30950 number of atom coordinates read : 2570 total number of charged atoms : 2425 net assigned charge : -8.499981 assigned positive charge : 385.4618 centred at (gu) : 90.48186 88.88768 89.81654 assigned negative charge : -393.9623 centred at (gu) : 90.62700 88.59780 89.73402 start vw surface at 0.1000000 fill in re-entrant regions at 0.1000000 boundary points on vw surface= 5092 nv = 96 ne = 84 npr = 51497 no. pairs analyzed = 51497 no. exposed pairs = 3541 no. arc points = 25407 no. surface atoms = 1194 nbur = 1376 mkacc time = 8.9999996E-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 = 1.568000 m= 216 mr = 2393 m= 1 mr = 10 m= 0 mr = 0 time to grow re-entrant surface = 9.9999987E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2100000 number of dielectric boundary points 2906 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2546 ## 317 charges are in solution ## iepsmp to db, and charging done at 0.2800000 number of grid points assigned charge 6530 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.1192787E-09 -2.1961061E-11 midg,1,midg; midg,igrid,midg -3.2369989E-09 9.3119318E-10 1,midg,midg; igrid,midg,midg 3.2050743E-10 -1.6665231E-09 gauss-seidel spectral radius is 0.9828105 estimated iterations to convergence 63 setup time was (sec) 0.4000000 now iterating at: 07:46:40 rms-change max change #iterations 6.8767339E-02 12.63760 at 10iterations 4.4890447E-03 0.8074932 at 20iterations 2.9314269E-04 5.4822922E-02 at 30iterations 1.9955591E-05 3.6468506E-03 at 40iterations 1.4288511E-06 2.2411346E-04 at 50iterations finished qdiffx linear iterations at : 07:46:42 total time elapsed so far: 3.260000 # loops : 50 mean,max change (kT/e) : 1.4288511E-06 2.2411346E-04 energy calculations done at 3.260000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.390000 DelPhi exited at 07:46:43 3.392u 0.222s 0:04.06 88.9% 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 Sun Oct 9 2011 at 07:46:43 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: 260 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2570 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: 1.644215 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): -3.797000 42.16200 ymin,ymax (A): 35.71700 88.87400 zmin,zma (A): -3.168000 61.78700 x,y,z range (A): 45.95900 53.15700 64.95500 scale (grids/A): 1.644215 object centre (A): 19.18250 62.29550 29.30950 number of atom coordinates read : 2570 total number of charged atoms : 2425 net assigned charge : -8.499981 assigned positive charge : 385.4618 centred at (gu) : 91.44474 86.66241 89.44916 assigned negative charge : -393.9623 centred at (gu) : 91.88055 85.79312 89.20164 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 55740 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25407 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 16748 mr = 35541 m= 1635 mr = 11154 m= 53 mr = 739 m= 0 mr = 0 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3100000 number of dielectric boundary points 26742 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 282 ## 3 charges are in solution ## iepsmp to db, and charging done at 0.3900000 number of grid points assigned charge 18574 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) : 0.5480717 object centre at (A) : 19.18250 62.29550 29.30950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -3.2653697E-02 8.4164599E-03 midg,1,midg; midg,igrid,midg -2.4193550E-02 3.8109096E-03 1,midg,midg; igrid,midg,midg -3.0844870E-03 -9.9458406E-03 gauss-seidel spectral radius is 0.9981678 estimated iterations to convergence 186 setup time was (sec) 0.5400000 now iterating at: 07:46:44 rms-change max change #iterations 3.134148 170.1314 at 10iterations 1.299513 58.63279 at 20iterations 0.5355878 20.12566 at 30iterations 0.2222374 8.929146 at 40iterations 9.1864020E-02 3.639940 at 50iterations 3.8268905E-02 1.454894 at 60iterations 1.5833322E-02 0.5886898 at 70iterations 6.5690647E-03 0.2451239 at 80iterations 2.7191234E-03 0.1101761 at 90iterations 1.1324962E-03 4.8892975E-02 at 100iterations 4.6988510E-04 1.7814636E-02 at 110iterations 1.9521805E-04 7.7772141E-03 at 120iterations finished qdiffx linear iterations at : 07:46:51 total time elapsed so far: 8.300000 # loops : 120 mean,max change (kT/e) : 1.9521805E-04 7.7772141E-03 energy calculations done at 8.300000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.440000 DelPhi exited at 07:46:52 8.439u 0.210s 0:08.96 96.4% 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 07:46:52 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: 260 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2570 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.466323 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): -3.797000 42.16200 ymin,ymax (A): 35.71700 88.87400 zmin,zma (A): -3.168000 61.78700 x,y,z range (A): 45.95900 53.15700 64.95500 scale (grids/A): 2.466323 object centre (A): 19.18250 62.29550 29.30950 number of atom coordinates read : 2570 total number of charged atoms : 2425 net assigned charge : -8.499981 assigned positive charge : 385.4618 centred at (gu) : 92.16694 84.99343 89.17344 assigned negative charge : -393.9623 centred at (gu) : 92.82078 83.68959 88.80240 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 129301 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25407 grid for indexing accessible points = 1.400000 m= 57928 mr = 87459 m= 15966 mr = 44855 m= 2408 mr = 11532 m= 148 mr = 1462 m= 2 mr = 61 m= 1 mr = 0 m= 0 mr = 0 time to grow re-entrant surface = 0.3700000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.6700000 number of dielectric boundary points 60385 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 27 iepsmp to db, and charging done at 0.7600000 number of grid points assigned charge 19377 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) : 1.644215 object centre at (A) : 19.18250 62.29550 29.30950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.8610707 8.7285675E-02 midg,1,midg; midg,igrid,midg -0.3084009 7.1892537E-02 1,midg,midg; igrid,midg,midg -5.0051305E-02 -0.1363370 gauss-seidel spectral radius is 0.9991263 estimated iterations to convergence 267 setup time was (sec) 0.9000000 now iterating at: 07:46:53 rms-change max change #iterations 8.138098 327.5173 at 10iterations 4.527905 147.4519 at 20iterations 2.529584 63.55551 at 30iterations 1.398815 34.38903 at 40iterations 0.7751905 21.25840 at 50iterations 0.4269348 10.70762 at 60iterations 0.2357754 5.767819 at 70iterations 0.1294874 2.963127 at 80iterations 7.1085691E-02 1.544729 at 90iterations 3.9117385E-02 0.9396019 at 100iterations 2.1406842E-02 0.5100698 at 110iterations 1.1736280E-02 0.2830982 at 120iterations 6.4234431E-03 0.1583705 at 130iterations 3.5247938E-03 8.0904961E-02 at 140iterations 1.9267316E-03 4.2297363E-02 at 150iterations 1.0577680E-03 2.3090363E-02 at 160iterations 5.7621428E-04 1.3019323E-02 at 170iterations 3.1529347E-04 6.7069530E-03 at 180iterations finished qdiffx linear iterations at : 07:47:04 total time elapsed so far: 11.85000 # loops : 180 mean,max change (kT/e) : 3.1529347E-04 6.7069530E-03 energy calculations done at 11.85000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.99000 DelPhi exited at 07:47:04 11.990u 0.205s 0:12.50 97.5% 0+0k 0+0io 0pf+0w