Sun Oct 9 00:51:24 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 00:51:24 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 = 2224 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: 0.6668790 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): -0.2510000 53.13200 ymin,ymax (A): -16.13700 27.51000 zmin,zma (A): 32.76100 84.72400 x,y,z range (A): 53.38300 43.64700 51.96300 scale (grids/A): 0.6668790 object centre (A): 26.44050 5.686500 58.74250 number of atom coordinates read : 2224 total number of charged atoms : 2089 net assigned charge : 11.00002 assigned positive charge : 325.9525 centred at (gu) : 90.23321 89.28169 88.82764 assigned negative charge : -314.9532 centred at (gu) : 90.24848 89.35081 88.87971 start vw surface at 0.1700000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 6824 nv = 96 ne = 84 npr = 43920 no. pairs analyzed = 43920 no. exposed pairs = 3073 no. arc points = 22041 no. surface atoms = 1027 nbur = 1197 mkacc time = 9.9999994E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 471 mr = 3498 m= 2 mr = 56 m= 0 mr = 0 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3100000 number of dielectric boundary points 3743 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2047 ## 168 charges are in solution ## iepsmp to db, and charging done at 0.4200000 number of grid points assigned charge 7831 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 5.4818774E-08 1.8637191E-08 midg,1,midg; midg,igrid,midg 5.3719745E-08 1.7493264E-08 1,midg,midg; igrid,midg,midg 3.4605247E-08 3.1854061E-08 gauss-seidel spectral radius is 0.9883199 estimated iterations to convergence 76 setup time was (sec) 0.5500000 now iterating at: 00:51:25 rms-change max change #iterations 0.1564406 24.72816 at 10iterations 1.6980354E-02 2.376924 at 20iterations 2.0234431E-03 0.3093390 at 30iterations 3.9715524E-04 5.5068016E-02 at 40iterations 1.3272952E-04 2.0812035E-02 at 50iterations finished qdiffx linear iterations at : 00:51:28 total time elapsed so far: 3.140000 # loops : 50 mean,max change (kT/e) : 1.3272952E-04 2.0812035E-02 energy calculations done at 3.140000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.320000 DelPhi exited at 00:51:28 3.323u 0.198s 0:03.83 91.6% 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 00:51:28 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: 255 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2224 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: 2.000637 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): -0.2510000 53.13200 ymin,ymax (A): -16.13700 27.51000 zmin,zma (A): 32.76100 84.72400 x,y,z range (A): 53.38300 43.64700 51.96300 scale (grids/A): 2.000637 object centre (A): 26.44050 5.686500 58.74250 number of atom coordinates read : 2224 total number of charged atoms : 2089 net assigned charge : 11.00002 assigned positive charge : 325.9525 centred at (gu) : 90.69944 87.84473 86.48264 assigned negative charge : -314.9532 centred at (gu) : 90.74564 88.05248 86.63921 start vw surface at 0.1400000 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 72092 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22041 grid for indexing accessible points = 1.400000 m= 27073 mr = 47851 m= 5135 mr = 19136 m= 440 mr = 3191 m= 13 mr = 157 m= 0 mr = 0 time to grow re-entrant surface = 0.2500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5400000 number of dielectric boundary points 34418 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 112 iepsmp to db, and charging done at 0.6600000 number of grid points assigned charge 16516 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) : 0.6668790 object centre at (A) : 26.44050 5.686500 58.74250 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.4073304E-02 4.8918791E-02 midg,1,midg; midg,igrid,midg 3.8519803E-02 4.3621743E-03 1,midg,midg; igrid,midg,midg 5.2236661E-02 5.2306917E-02 gauss-seidel spectral radius is 0.9987329 estimated iterations to convergence 223 setup time was (sec) 0.8300000 now iterating at: 00:51:29 rms-change max change #iterations 4.167160 230.4339 at 10iterations 2.000204 69.10854 at 20iterations 0.9595887 32.21519 at 30iterations 0.4609111 14.47037 at 40iterations 0.2205296 6.577875 at 50iterations 0.1062079 3.495163 at 60iterations 5.1246207E-02 1.562557 at 70iterations 2.4698913E-02 0.8319092 at 80iterations 1.1932268E-02 0.3937769 at 90iterations 5.8120429E-03 0.1816330 at 100iterations 2.8823223E-03 9.7558022E-02 at 110iterations 1.4743909E-03 4.9690247E-02 at 120iterations finished qdiffx linear iterations at : 00:51:36 total time elapsed so far: 7.310000 # loops : 120 mean,max change (kT/e) : 1.4743909E-03 4.9690247E-02 energy calculations done at 7.310000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.490000 DelPhi exited at 00:51:36 7.496u 0.226s 0:08.02 96.1% 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 Sun Oct 9 2011 at 00:51:36 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 = 2224 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: 3.000955 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): -0.2510000 53.13200 ymin,ymax (A): -16.13700 27.51000 zmin,zma (A): 32.76100 84.72400 x,y,z range (A): 53.38300 43.64700 51.96300 scale (grids/A): 3.000955 object centre (A): 26.44050 5.686500 58.74250 number of atom coordinates read : 2224 total number of charged atoms : 2089 net assigned charge : 11.00002 assigned positive charge : 325.9525 centred at (gu) : 91.04899 86.76691 84.72380 assigned negative charge : -314.9532 centred at (gu) : 91.11852 87.07877 84.95868 start vw surface at 0.1500000 fill in re-entrant regions at 0.4600000 boundary points on vw surface= 166401 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22041 grid for indexing accessible points = 1.400000 m= 84521 mr = 116504 m= 33234 mr = 67239 m= 9573 mr = 26108 m= 1825 mr = 6989 m= 142 mr = 1202 m= 3 mr = 55 m= 0 mr = 0 time to grow re-entrant surface = 0.8100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.390000 number of dielectric boundary points 77602 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.530000 number of grid points assigned charge 16712 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) : 2.000637 object centre at (A) : 26.44050 5.686500 58.74250 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.3027307 0.6169231 midg,1,midg; midg,igrid,midg 0.3369515 2.2654200E-02 1,midg,midg; igrid,midg,midg 0.4573151 0.4386117 gauss-seidel spectral radius is 0.9992890 estimated iterations to convergence 296 setup time was (sec) 1.720000 now iterating at: 00:51:38 rms-change max change #iterations 9.803202 431.3605 at 10iterations 5.863933 148.6170 at 20iterations 3.480623 72.72755 at 30iterations 2.061399 43.32930 at 40iterations 1.216615 25.60691 at 50iterations 0.7135464 13.34648 at 60iterations 0.4193738 8.734177 at 70iterations 0.2451210 4.927561 at 80iterations 0.1436553 3.019435 at 90iterations 8.4093265E-02 1.906921 at 100iterations 4.9110923E-02 0.9987364 at 110iterations 2.8661825E-02 0.5299492 at 120iterations 1.6735835E-02 0.3225098 at 130iterations 9.8045925E-03 0.1737499 at 140iterations 5.7557877E-03 0.1073856 at 150iterations 3.4028161E-03 6.7837715E-02 at 160iterations 2.0465755E-03 4.1357040E-02 at 170iterations 1.2693539E-03 2.6153564E-02 at 180iterations finished qdiffx linear iterations at : 00:51:49 total time elapsed so far: 12.30000 # loops : 180 mean,max change (kT/e) : 1.2693539E-03 2.6153564E-02 energy calculations done at 12.30000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.48000 DelPhi exited at 00:51:49 12.478u 0.212s 0:12.97 97.7% 0+0k 0+0io 0pf+0w