Tue Nov 22 14:12:23 PST 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 Tue Nov 22 2011 at 14:12:28 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: 228 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1942 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: 0.6449742 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): -34.67000 10.64300 ymin,ymax (A): 1.399000 41.71500 zmin,zma (A): -0.2900000 54.90600 x,y,z range (A): 45.31300 40.31600 55.19600 scale (grids/A): 0.6449742 object centre (A): -12.01350 21.55700 27.30800 number of atom coordinates read : 1942 total number of charged atoms : 1810 net assigned charge : 3.000004 assigned positive charge : 285.2440 centred at (gu) : 90.08852 89.26743 90.39362 assigned negative charge : -282.2443 centred at (gu) : 90.01140 89.40495 90.37699 start vw surface at 0.1200000 fill in re-entrant regions at 0.1200000 boundary points on vw surface= 5485 nv = 96 ne = 84 npr = 40116 no. pairs analyzed = 40116 no. exposed pairs = 2404 no. arc points = 16687 no. surface atoms = 814 nbur = 1128 mkacc time = 8.0000006E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 273 mr = 3062 m= 2 mr = 33 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 0.2200000 number of dielectric boundary points 2665 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1695 ## 172 charges are in solution ## iepsmp to db, and charging done at 0.3400000 number of grid points assigned charge 6428 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 3.0549585E-09 7.0892594E-09 midg,1,midg; midg,igrid,midg 2.1144050E-08 -7.3280719E-09 1,midg,midg; igrid,midg,midg -2.5724922E-09 1.2576434E-08 gauss-seidel spectral radius is 0.9874849 estimated iterations to convergence 73 setup time was (sec) 0.4500000 now iterating at: 14:12:32 rms-change max change #iterations 0.1282599 20.82440 at 10iterations 1.2641739E-02 1.720280 at 20iterations 1.2549250E-03 0.2001538 at 30iterations 1.2513905E-04 1.8199921E-02 at 40iterations 1.2845879E-05 1.9593239E-03 at 50iterations finished qdiffx linear iterations at : 14:12:40 total time elapsed so far: 2.930000 # loops : 50 mean,max change (kT/e) : 1.2845879E-05 1.9593239E-03 energy calculations done at 2.930000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.110000 DelPhi exited at 14:12:44 3.114u 0.153s 0:16.40 19.8% 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 Tue Nov 22 2011 at 14:12:48 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: 228 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1942 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: 1.934923 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): -34.67000 10.64300 ymin,ymax (A): 1.399000 41.71500 zmin,zma (A): -0.2900000 54.90600 x,y,z range (A): 45.31300 40.31600 55.19600 scale (grids/A): 1.934923 object centre (A): -12.01350 21.55700 27.30800 number of atom coordinates read : 1942 total number of charged atoms : 1810 net assigned charge : 3.000004 assigned positive charge : 285.2440 centred at (gu) : 90.26572 87.80243 91.18109 assigned negative charge : -282.2443 centred at (gu) : 90.03431 88.21494 91.13111 start vw surface at 0.1000000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 58480 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16687 grid for indexing accessible points = 1.400000 m= 22459 mr = 40376 m= 3787 mr = 17266 m= 221 mr = 2491 m= 1 mr = 71 m= 0 mr = 0 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4100000 number of dielectric boundary points 24744 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 102 iepsmp to db, and charging done at 0.5200000 number of grid points assigned charge 14267 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) : 0.6449742 object centre at (A) : -12.01350 21.55700 27.30800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.1824421E-02 5.2762188E-02 midg,1,midg; midg,igrid,midg 9.2865173E-03 -1.1345692E-02 1,midg,midg; igrid,midg,midg -2.3860596E-03 -4.0170010E-03 gauss-seidel spectral radius is 0.9985982 estimated iterations to convergence 212 setup time was (sec) 0.6900000 now iterating at: 14:12:53 rms-change max change #iterations 3.646526 171.1562 at 10iterations 1.692351 63.39954 at 20iterations 0.7883423 29.44306 at 30iterations 0.3654274 12.33733 at 40iterations 0.1696530 5.802567 at 50iterations 7.8326382E-02 2.849136 at 60iterations 3.6205910E-02 1.299229 at 70iterations 1.6823214E-02 0.6078005 at 80iterations 7.8044003E-03 0.2539005 at 90iterations 3.6184303E-03 0.1255226 at 100iterations 1.6785040E-03 5.9822083E-02 at 110iterations 7.7697437E-04 2.7264118E-02 at 120iterations finished qdiffx linear iterations at : 14:13:12 total time elapsed so far: 6.930000 # loops : 120 mean,max change (kT/e) : 7.7697437E-04 2.7264118E-02 energy calculations done at 6.930000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.110000 DelPhi exited at 14:13:14 7.110u 0.208s 0:26.70 27.3% 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 Tue Nov 22 2011 at 14:13:15 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: 228 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1942 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: 2.902384 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): -34.67000 10.64300 ymin,ymax (A): 1.399000 41.71500 zmin,zma (A): -0.2900000 54.90600 x,y,z range (A): 45.31300 40.31600 55.19600 scale (grids/A): 2.902384 object centre (A): -12.01350 21.55700 27.30800 number of atom coordinates read : 1942 total number of charged atoms : 1810 net assigned charge : 3.000004 assigned positive charge : 285.2440 centred at (gu) : 90.39854 86.70359 91.77168 assigned negative charge : -282.2443 centred at (gu) : 90.05155 87.32253 91.69686 start vw surface at 0.1000000 fill in re-entrant regions at 0.3500000 boundary points on vw surface= 134832 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16687 grid for indexing accessible points = 1.400000 m= 70968 mr = 97363 m= 27895 mr = 59190 m= 6908 mr = 23279 m= 922 mr = 5348 m= 55 mr = 589 m= 1 mr = 32 m= 0 mr = 0 time to grow re-entrant surface = 0.6199999 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.070000 number of dielectric boundary points 55780 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.200000 number of grid points assigned charge 14480 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) : 1.934923 object centre at (A) : -12.01350 21.55700 27.30800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -6.8688720E-02 0.4067809 midg,1,midg; midg,igrid,midg 4.6571597E-02 -0.1370134 1,midg,midg; igrid,midg,midg -7.3702991E-02 -7.7028163E-02 gauss-seidel spectral radius is 0.9992321 estimated iterations to convergence 285 setup time was (sec) 1.370000 now iterating at: 14:13:22 rms-change max change #iterations 8.540496 364.2596 at 10iterations 4.907725 114.9592 at 20iterations 2.798842 55.58002 at 30iterations 1.596644 36.06016 at 40iterations 0.9102456 17.35862 at 50iterations 0.5172027 10.41126 at 60iterations 0.2940555 5.763857 at 70iterations 0.1672456 3.155151 at 80iterations 9.4878457E-02 1.984188 at 90iterations 5.3960033E-02 1.114270 at 100iterations 3.0609898E-02 0.6114388 at 110iterations 1.7371655E-02 0.3565931 at 120iterations 9.8470608E-03 0.1873283 at 130iterations 5.6016548E-03 0.1088257 at 140iterations 3.1797178E-03 6.3201904E-02 at 150iterations 1.8056317E-03 3.6434174E-02 at 160iterations 1.0275228E-03 2.0239830E-02 at 170iterations 5.8445288E-04 1.2460709E-02 at 180iterations finished qdiffx linear iterations at : 14:13:56 total time elapsed so far: 11.64000 # loops : 180 mean,max change (kT/e) : 5.8445288E-04 1.2460709E-02 energy calculations done at 11.64000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.81000 DelPhi exited at 14:14:04 11.816u 0.240s 0:48.84 24.6% 0+0k 0+0io 0pf+0w