Tue Oct 11 06:03:43 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 Tue Oct 11 2011 at 06:03:43 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: 255 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2277 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 0.7332345 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): 25.60600 72.09600 ymin,ymax (A): -18.51400 30.03800 zmin,zma (A): 4.296000 46.29000 x,y,z range (A): 46.49000 48.55200 41.99400 scale (grids/A): 0.7332345 object centre (A): 48.85100 5.762000 25.29300 number of atom coordinates read : 2277 total number of charged atoms : 1957 net assigned charge : 6.500009 assigned positive charge : 316.7440 centred at (gu) : 89.28242 90.37112 90.21065 assigned negative charge : -310.2442 centred at (gu) : 89.41929 90.31396 90.29389 start vw surface at 0.1600000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 7684 nv = 96 ne = 84 npr = 41618 no. pairs analyzed = 41618 no. exposed pairs = 2555 no. arc points = 17401 no. surface atoms = 869 nbur = 1408 mkacc time = 8.9999989E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 609 mr = 4539 m= 6 mr = 145 m= 0 mr = 0 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2800000 number of dielectric boundary points 3615 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1544 ## 154 charges are in solution ## iepsmp to db, and charging done at 0.3900000 number of grid points assigned charge 8262 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.6220076E-07 2.6870035E-08 midg,1,midg; midg,igrid,midg 4.5740826E-08 1.5712571E-07 1,midg,midg; igrid,midg,midg 2.4468056E-07 -1.7444805E-08 gauss-seidel spectral radius is 0.9902993 estimated iterations to convergence 83 setup time was (sec) 0.5000000 now iterating at: 06:03:44 rms-change max change #iterations 0.2303361 33.15973 at 10iterations 3.0768311E-02 3.821619 at 20iterations 4.3676221E-03 0.5849934 at 30iterations 7.4500073E-04 0.1053638 at 40iterations 1.9744463E-04 2.3094177E-02 at 50iterations finished qdiffx linear iterations at : 06:03:47 total time elapsed so far: 3.130000 # loops : 50 mean,max change (kT/e) : 1.9744463E-04 2.3094177E-02 energy calculations done at 3.130000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.320000 DelPhi exited at 06:03:47 3.321u 0.266s 0:03.97 90.1% 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 Oct 11 2011 at 06:03:47 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: 255 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2277 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: 2.199703 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): 25.60600 72.09600 ymin,ymax (A): -18.51400 30.03800 zmin,zma (A): 4.296000 46.29000 x,y,z range (A): 46.49000 48.55200 41.99400 scale (grids/A): 2.199703 object centre (A): 48.85100 5.762000 25.29300 number of atom coordinates read : 2277 total number of charged atoms : 1957 net assigned charge : 6.500009 assigned positive charge : 316.7440 centred at (gu) : 87.84712 91.11349 90.63226 assigned negative charge : -310.2442 centred at (gu) : 88.25806 90.94177 90.88154 start vw surface at 0.1400000 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 81680 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17401 grid for indexing accessible points = 1.400000 m= 34721 mr = 58706 m= 7515 mr = 26899 m= 831 mr = 5292 m= 26 mr = 434 m= 0 mr = 4 time to grow re-entrant surface = 0.3300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.6300000 number of dielectric boundary points 33438 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 63 iepsmp to db, and charging done at 0.7400000 number of grid points assigned charge 15557 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) : 0.7332345 object centre at (A) : 48.85100 5.762000 25.29300 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.6842788E-02 3.2580230E-02 midg,1,midg; midg,igrid,midg 5.4663215E-02 3.2702614E-02 1,midg,midg; igrid,midg,midg 5.0033014E-02 -6.0619738E-02 gauss-seidel spectral radius is 0.9989015 estimated iterations to convergence 239 setup time was (sec) 0.9400000 now iterating at: 06:03:49 rms-change max change #iterations 4.875735 210.9532 at 10iterations 2.462674 78.32671 at 20iterations 1.254344 39.83456 at 30iterations 0.6335816 17.21889 at 40iterations 0.3210380 9.726507 at 50iterations 0.1634663 4.914459 at 60iterations 8.2889967E-02 2.362401 at 70iterations 4.2105190E-02 1.156715 at 80iterations 2.1442922E-02 0.5601454 at 90iterations 1.0982661E-02 0.3163452 at 100iterations 5.6198193E-03 0.1609650 at 110iterations 2.9257741E-03 8.3009720E-02 at 120iterations finished qdiffx linear iterations at : 06:03:55 total time elapsed so far: 7.600000 # loops : 120 mean,max change (kT/e) : 2.9257741E-03 8.3009720E-02 energy calculations done at 7.600000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.800000 DelPhi exited at 06:03:56 7.806u 0.215s 0:08.58 93.3% 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 Oct 11 2011 at 06:03:56 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: 255 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2277 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 3.299555 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): 25.60600 72.09600 ymin,ymax (A): -18.51400 30.03800 zmin,zma (A): 4.296000 46.29000 x,y,z range (A): 46.49000 48.55200 41.99400 scale (grids/A): 3.299555 object centre (A): 48.85100 5.762000 25.29300 number of atom coordinates read : 2277 total number of charged atoms : 1957 net assigned charge : 6.500009 assigned positive charge : 316.7440 centred at (gu) : 86.77073 91.67017 90.94827 assigned negative charge : -310.2442 centred at (gu) : 87.38707 91.41264 91.32248 start vw surface at 0.1600000 fill in re-entrant regions at 0.8900000 boundary points on vw surface= 187799 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17401 grid for indexing accessible points = 1.400000 m= 105662 mr = 140568 m= 46121 mr = 88972 m= 14546 mr = 38645 m= 3333 mr = 11623 m= 439 mr = 2479 m= 23 mr = 283 m= 0 mr = 11 time to grow re-entrant surface = 1.010000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 2.020000 number of dielectric boundary points 75342 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.160000 number of grid points assigned charge 15656 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) : 2.199703 object centre at (A) : 48.85100 5.762000 25.29300 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1127009 0.2719842 midg,1,midg; midg,igrid,midg 0.4064704 0.1809594 1,midg,midg; igrid,midg,midg 0.4874353 -0.7090363 gauss-seidel spectral radius is 0.9993147 estimated iterations to convergence 301 setup time was (sec) 2.350000 now iterating at: 06:03:59 rms-change max change #iterations 10.70685 364.9594 at 10iterations 6.373859 114.7829 at 20iterations 3.790944 91.00600 at 30iterations 2.256003 41.63048 at 40iterations 1.338678 23.94989 at 50iterations 0.7915725 14.02336 at 60iterations 0.4692784 8.204178 at 70iterations 0.2771870 5.730558 at 80iterations 0.1636404 2.769233 at 90iterations 9.6737251E-02 1.623611 at 100iterations 5.7188161E-02 0.8708134 at 110iterations 3.3985201E-02 0.5874197 at 120iterations 2.0317089E-02 0.3914108 at 130iterations 1.2289486E-02 0.2175951 at 140iterations 7.6478128E-03 0.1249657 at 150iterations 4.9416381E-03 8.8226318E-02 at 160iterations 3.3574575E-03 6.5536499E-02 at 170iterations 2.4387538E-03 4.2190552E-02 at 180iterations finished qdiffx linear iterations at : 06:04:09 total time elapsed so far: 12.92000 # loops : 180 mean,max change (kT/e) : 2.4387538E-03 4.2190552E-02 energy calculations done at 12.92000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.10000 DelPhi exited at 06:04:10 13.107u 0.242s 0:13.87 96.1% 0+0k 0+0io 0pf+0w