Tue Oct 11 08:39:44 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 08:39:44 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2549 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 0.6660804 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): -54.55600 -1.109000 ymin,ymax (A): -27.12000 24.17900 zmin,zma (A): -2.627000 44.53700 x,y,z range (A): 53.44700 51.29900 47.16400 scale (grids/A): 0.6660804 object centre (A): -27.83250 -1.470500 20.95500 number of atom coordinates read : 2549 total number of charged atoms : 2410 net assigned charge : -2.999991 assigned positive charge : 378.0551 centred at (gu) : 90.11128 90.50165 88.65144 assigned negative charge : -381.0555 centred at (gu) : 90.03355 90.42470 88.48476 start vw surface at 0.1700000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 7858 nv = 96 ne = 84 npr = 51814 no. pairs analyzed = 51814 no. exposed pairs = 3212 no. arc points = 22545 no. surface atoms = 1096 nbur = 1453 mkacc time = 0.1200000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 488 mr = 4477 m= 3 mr = 78 m= 0 mr = 0 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3300000 number of dielectric boundary points 3794 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2058 ## 186 charges are in solution ## iepsmp to db, and charging done at 0.4500000 number of grid points assigned charge 8932 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -6.2193870E-08 2.1467573E-08 midg,1,midg; midg,igrid,midg -2.3453167E-08 9.8477857E-09 1,midg,midg; igrid,midg,midg -2.5590881E-08 9.2031698E-09 gauss-seidel spectral radius is 0.9883177 estimated iterations to convergence 75 setup time was (sec) 0.5700000 now iterating at: 08:39:45 rms-change max change #iterations 0.1696424 26.78412 at 10iterations 1.8481843E-02 2.370224 at 20iterations 2.0548471E-03 0.3339834 at 30iterations 2.4970467E-04 3.5787582E-02 at 40iterations 3.9857809E-05 7.1020126E-03 at 50iterations finished qdiffx linear iterations at : 08:39:48 total time elapsed so far: 3.200000 # loops : 50 mean,max change (kT/e) : 3.9857809E-05 7.1020126E-03 energy calculations done at 3.200000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.380000 DelPhi exited at 08:39:48 3.387u 0.147s 0:04.01 87.7% 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 08:39:48 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2549 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: 1.998241 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): -54.55600 -1.109000 ymin,ymax (A): -27.12000 24.17900 zmin,zma (A): -2.627000 44.53700 x,y,z range (A): 53.44700 51.29900 47.16400 scale (grids/A): 1.998241 object centre (A): -27.83250 -1.470500 20.95500 number of atom coordinates read : 2549 total number of charged atoms : 2410 net assigned charge : -2.999991 assigned positive charge : 378.0551 centred at (gu) : 90.33355 91.50474 85.95381 assigned negative charge : -381.0555 centred at (gu) : 90.10044 91.27381 85.45416 start vw surface at 0.1600000 fill in re-entrant regions at 0.2800000 boundary points on vw surface= 83638 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22545 grid for indexing accessible points = 1.400000 m= 33331 mr = 58601 m= 6210 mr = 25579 m= 452 mr = 4193 m= 6 mr = 211 m= 0 mr = 0 time to grow re-entrant surface = 0.3100000 no. cavity mid-points inaccessible to solvent = 412 time to turn everything in is 0.6300000 number of dielectric boundary points 35053 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 106 iepsmp to db, and charging done at 0.7500000 number of grid points assigned charge 19062 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) : 0.6660804 object centre at (A) : -27.83250 -1.470500 20.95500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.0921273E-02 2.4307735E-02 midg,1,midg; midg,igrid,midg -4.6094216E-02 -3.4770221E-02 1,midg,midg; igrid,midg,midg -1.7126091E-02 -4.1209213E-02 gauss-seidel spectral radius is 0.9987561 estimated iterations to convergence 225 setup time was (sec) 0.9100000 now iterating at: 08:39:49 rms-change max change #iterations 4.589648 223.4754 at 10iterations 2.228807 74.25628 at 20iterations 1.075369 35.81801 at 30iterations 0.5225748 17.33849 at 40iterations 0.2539946 7.608738 at 50iterations 0.1233387 3.606211 at 60iterations 5.9893761E-02 1.691551 at 70iterations 2.9055161E-02 0.8943195 at 80iterations 1.4104571E-02 0.4549599 at 90iterations 6.8468493E-03 0.2357159 at 100iterations 3.3161934E-03 0.1056004 at 110iterations 1.6112993E-03 4.8614502E-02 at 120iterations finished qdiffx linear iterations at : 08:39:56 total time elapsed so far: 7.620000 # loops : 120 mean,max change (kT/e) : 1.6112993E-03 4.8614502E-02 energy calculations done at 7.620000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.810000 DelPhi exited at 08:39:57 7.811u 0.186s 0:08.57 93.2% 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 08:39:57 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2549 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 2.997362 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): -54.55600 -1.109000 ymin,ymax (A): -27.12000 24.17900 zmin,zma (A): -2.627000 44.53700 x,y,z range (A): 53.44700 51.29900 47.16400 scale (grids/A): 2.997362 object centre (A): -27.83250 -1.470500 20.95500 number of atom coordinates read : 2549 total number of charged atoms : 2410 net assigned charge : -2.999991 assigned positive charge : 378.0551 centred at (gu) : 90.50035 92.25714 83.93059 assigned negative charge : -381.0555 centred at (gu) : 90.15064 91.91064 83.18109 start vw surface at 0.1600000 fill in re-entrant regions at 0.5300000 boundary points on vw surface= 192822 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22545 grid for indexing accessible points = 1.400000 m= 104119 mr = 141117 m= 42339 mr = 87026 m= 11569 mr = 35189 m= 2009 mr = 8951 m= 160 mr = 1487 m= 3 mr = 78 m= 0 mr = 0 time to grow re-entrant surface = 0.9900000 no. cavity mid-points inaccessible to solvent = 1375 time to turn everything in is 1.640000 number of dielectric boundary points 79173 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.770000 number of grid points assigned charge 19280 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) : 1.998241 object centre at (A) : -27.83250 -1.470500 20.95500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.4111769 0.1558329 midg,1,midg; midg,igrid,midg -0.6580533 -0.4804904 1,midg,midg; igrid,midg,midg 6.4217627E-02 -0.4658611 gauss-seidel spectral radius is 0.9992918 estimated iterations to convergence 296 setup time was (sec) 1.930000 now iterating at: 08:39:59 rms-change max change #iterations 10.54456 402.9913 at 10iterations 6.218098 139.9661 at 20iterations 3.641514 64.30367 at 30iterations 2.127952 38.13656 at 40iterations 1.243144 23.45615 at 50iterations 0.7230791 12.02740 at 60iterations 0.4223832 7.640516 at 70iterations 0.2454655 4.300593 at 80iterations 0.1433452 2.542034 at 90iterations 8.3147280E-02 1.431511 at 100iterations 4.8470695E-02 0.7972875 at 110iterations 2.8165555E-02 0.4918140 at 120iterations 1.6361177E-02 0.2846684 at 130iterations 9.5406668E-03 0.1668882 at 140iterations 5.5487808E-03 9.3925476E-02 at 150iterations 3.2455502E-03 5.3565979E-02 at 160iterations 1.9009113E-03 3.3165932E-02 at 170iterations 1.1193963E-03 1.7972946E-02 at 180iterations finished qdiffx linear iterations at : 08:40:09 total time elapsed so far: 12.24000 # loops : 180 mean,max change (kT/e) : 1.1193963E-03 1.7972946E-02 energy calculations done at 12.24000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.45000 DelPhi exited at 08:40:10 12.450u 0.176s 0:13.10 96.3% 0+0k 0+0io 0pf+0w