Mon Oct 10 11:34:22 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 11:34:22 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 = 2171 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: 0.6987517 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): 5.265000 54.88300 ymin,ymax (A): -8.535000 36.48200 zmin,zma (A): 17.38800 68.33600 x,y,z range (A): 49.61800 45.01700 50.94800 scale (grids/A): 0.6987517 object centre (A): 30.07400 13.97350 42.86200 number of atom coordinates read : 2171 total number of charged atoms : 2031 net assigned charge : -4.999979 assigned positive charge : 325.6908 centred at (gu) : 89.50256 90.32633 91.30012 assigned negative charge : -330.6909 centred at (gu) : 89.59837 90.40239 91.46938 start vw surface at 0.1300000 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 7307 nv = 96 ne = 84 npr = 44470 no. pairs analyzed = 44470 no. exposed pairs = 2786 no. arc points = 20069 no. surface atoms = 941 nbur = 1230 mkacc time = 0.1100000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 418 mr = 3933 m= 4 mr = 69 m= 0 mr = 0 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 33 time to turn everything in is 0.3200000 number of dielectric boundary points 3727 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1762 ## 133 charges are in solution ## iepsmp to db, and charging done at 0.5300000 number of grid points assigned charge 8041 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.9180210E-08 -1.3896235E-07 midg,1,midg; midg,igrid,midg -7.9036294E-10 -7.0459173E-08 1,midg,midg; igrid,midg,midg 8.6626804E-09 -6.7785095E-08 gauss-seidel spectral radius is 0.9893451 estimated iterations to convergence 79 setup time was (sec) 0.8200000 now iterating at: 11:34:24 rms-change max change #iterations 0.1995643 31.85044 at 10iterations 2.4035491E-02 3.053455 at 20iterations 2.8276760E-03 0.4042816 at 30iterations 3.4528386E-04 4.8548222E-02 at 40iterations 4.0591731E-05 5.5236816E-03 at 50iterations finished qdiffx linear iterations at : 11:34:31 total time elapsed so far: 8.040000 # loops : 50 mean,max change (kT/e) : 4.0591731E-05 5.5236816E-03 energy calculations done at 8.040000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.220000 DelPhi exited at 11:34:31 8.223u 0.707s 0:09.21 96.8% 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 Mon Oct 10 2011 at 11:34:31 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 = 2171 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: 2.096255 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): 5.265000 54.88300 ymin,ymax (A): -8.535000 36.48200 zmin,zma (A): 17.38800 68.33600 x,y,z range (A): 49.61800 45.01700 50.94800 scale (grids/A): 2.096255 object centre (A): 30.07400 13.97350 42.86200 number of atom coordinates read : 2171 total number of charged atoms : 2031 net assigned charge : -4.999979 assigned positive charge : 325.6908 centred at (gu) : 88.50768 90.97909 93.90021 assigned negative charge : -330.6909 centred at (gu) : 88.79523 91.20718 94.40813 start vw surface at 0.1300000 fill in re-entrant regions at 0.3000000 boundary points on vw surface= 77059 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20069 grid for indexing accessible points = 1.400000 m= 29013 mr = 52258 m= 5392 mr = 21506 m= 441 mr = 3538 m= 6 mr = 229 m= 0 mr = 0 time to grow re-entrant surface = 0.3900000 no. cavity mid-points inaccessible to solvent = 375 time to turn everything in is 0.7800000 number of dielectric boundary points 34380 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 60 iepsmp to db, and charging done at 1.000000 number of grid points assigned charge 16106 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) : 0.6987517 object centre at (A) : 30.07400 13.97350 42.86200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.4201506E-02 -0.1160350 midg,1,midg; midg,igrid,midg -7.1196677E-03 -2.8267477E-02 1,midg,midg; igrid,midg,midg 1.5709452E-02 -2.4536908E-02 gauss-seidel spectral radius is 0.9988259 estimated iterations to convergence 231 setup time was (sec) 1.340000 now iterating at: 11:34:33 rms-change max change #iterations 4.645448 162.3251 at 10iterations 2.293340 73.90482 at 20iterations 1.131591 33.30509 at 30iterations 0.5585713 16.87351 at 40iterations 0.2754287 8.100267 at 50iterations 0.1360858 4.224461 at 60iterations 6.7211546E-02 2.054861 at 70iterations 3.3265006E-02 1.008553 at 80iterations 1.6448895E-02 0.5034485 at 90iterations 8.0976766E-03 0.2476792 at 100iterations 4.0199733E-03 0.1211910 at 110iterations 1.9840898E-03 5.8956146E-02 at 120iterations finished qdiffx linear iterations at : 11:34:50 total time elapsed so far: 17.46000 # loops : 120 mean,max change (kT/e) : 1.9840898E-03 5.8956146E-02 energy calculations done at 17.46000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 17.63000 DelPhi exited at 11:34:50 17.639u 0.842s 0:18.83 98.0% 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 Mon Oct 10 2011 at 11:34:50 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 = 2171 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: 3.144383 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): 5.265000 54.88300 ymin,ymax (A): -8.535000 36.48200 zmin,zma (A): 17.38800 68.33600 x,y,z range (A): 49.61800 45.01700 50.94800 scale (grids/A): 3.144383 object centre (A): 30.07400 13.97350 42.86200 number of atom coordinates read : 2171 total number of charged atoms : 2031 net assigned charge : -4.999979 assigned positive charge : 325.6908 centred at (gu) : 87.76155 91.46863 95.85043 assigned negative charge : -330.6909 centred at (gu) : 88.19282 91.81069 96.61211 start vw surface at 0.1000000 fill in re-entrant regions at 0.8800000 boundary points on vw surface= 177732 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20069 grid for indexing accessible points = 1.400000 m= 91280 mr = 126439 m= 36097 mr = 74758 m= 9844 mr = 29219 m= 1931 mr = 7554 m= 175 mr = 1460 m= 4 mr = 92 m= 0 mr = 0 time to grow re-entrant surface = 1.250000 no. cavity mid-points inaccessible to solvent = 1277 time to turn everything in is 2.320000 number of dielectric boundary points 77541 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.870000 number of grid points assigned charge 16248 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) : 2.096255 object centre at (A) : 30.07400 13.97350 42.86200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1686012 -1.297112 midg,1,midg; midg,igrid,midg -8.3160810E-02 -0.2020058 1,midg,midg; igrid,midg,midg 8.3210148E-02 -0.2099850 gauss-seidel spectral radius is 0.9992989 estimated iterations to convergence 298 setup time was (sec) 3.240000 now iterating at: 11:34:54 rms-change max change #iterations 10.31904 388.1873 at 10iterations 6.043945 127.4839 at 20iterations 3.541347 75.44066 at 30iterations 2.065439 43.11278 at 40iterations 1.207734 28.20178 at 50iterations 0.7040322 13.84817 at 60iterations 0.4107650 7.169209 at 70iterations 0.2394214 4.556355 at 80iterations 0.1395008 2.427320 at 90iterations 8.1287280E-02 1.290718 at 100iterations 4.7260344E-02 0.8165588 at 110iterations 2.7555790E-02 0.4903946 at 120iterations 1.6084738E-02 0.2938957 at 130iterations 9.3581714E-03 0.1975079 at 140iterations 5.4463921E-03 9.1245651E-02 at 150iterations 3.1720668E-03 5.8705330E-02 at 160iterations 1.8482892E-03 3.2157898E-02 at 170iterations 1.0780217E-03 1.9523621E-02 at 180iterations finished qdiffx linear iterations at : 11:35:24 total time elapsed so far: 33.27000 # loops : 180 mean,max change (kT/e) : 1.0780217E-03 1.9523621E-02 energy calculations done at 33.27000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 33.45000 DelPhi exited at 11:35:25 33.456u 0.887s 0:34.62 99.1% 0+0k 0+0io 0pf+0w