Mon Oct 10 16:01:08 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 16:01:08 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 = 5125 !!! WARNING: ASP 610 has a net charge of -2.0000 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: 0.5153594 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): -20.06300 49.01500 ymin,ymax (A): 10.04300 72.89799 zmin,zma (A): 33.71600 95.68200 x,y,z range (A): 69.07800 62.85500 61.96600 scale (grids/A): 0.5153594 object centre (A): 14.47600 41.47050 64.69900 number of atom coordinates read : 5125 total number of charged atoms : 4964 net assigned charge : 1.500020 assigned positive charge : 771.0981 centred at (gu) : 90.13110 90.99763 90.33845 assigned negative charge : -769.6031 centred at (gu) : 90.12834 90.95493 90.33567 start vw surface at 0.1300000 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 8441 nv = 96 ne = 84 npr = 106060 no. pairs analyzed = 106060 no. exposed pairs = 6148 no. arc points = 40985 no. surface atoms = 2071 nbur = 3054 mkacc time = 0.1800000 writing accessible surface arcs data to file ARCDAT initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.652000 m= 322 mr = 4611 m= 0 mr = 10 time to grow re-entrant surface = 0.2000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3400000 number of dielectric boundary points 4142 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4061 ## 556 charges are in solution ## iepsmp to db, and charging done at 0.4000000 number of grid points assigned charge 11441 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.3821968E-11 3.7093658E-11 midg,1,midg; midg,igrid,midg -9.3721864E-11 2.2102706E-10 1,midg,midg; igrid,midg,midg 1.4600524E-11 3.5119071E-11 gauss-seidel spectral radius is 0.9807569 estimated iterations to convergence 60 setup time was (sec) 0.5200000 now iterating at: 16:01:09 rms-change max change #iterations 7.3662303E-02 11.38275 at 10iterations 5.0655166E-03 0.7672501 at 20iterations 1.0592401E-03 0.1654778 at 30iterations 4.2207571E-04 5.6934357E-02 at 40iterations 1.8310185E-04 2.5297165E-02 at 50iterations finished qdiffx linear iterations at : 16:01:12 total time elapsed so far: 3.400000 # loops : 50 mean,max change (kT/e) : 1.8310185E-04 2.5297165E-02 energy calculations done at 3.400000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.530000 DelPhi exited at 16:01:12 3.531u 0.180s 0:04.34 85.4% 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 16:01:13 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 = 5125 !!! WARNING: ASP 610 has a net charge of -2.0000 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: 1.546078 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): -20.06300 49.01500 ymin,ymax (A): 10.04300 72.89799 zmin,zma (A): 33.71600 95.68200 x,y,z range (A): 69.07800 62.85500 61.96600 scale (grids/A): 1.546078 object centre (A): 14.47600 41.47050 64.69900 number of atom coordinates read : 5125 total number of charged atoms : 4964 net assigned charge : 1.500020 assigned positive charge : 771.0981 centred at (gu) : 90.39167 92.99110 91.01366 assigned negative charge : -769.6031 centred at (gu) : 90.38448 92.86439 91.00642 start vw surface at 0.1200000 fill in re-entrant regions at 0.2100000 boundary points on vw surface= 96291 reading accessible surface arcs data from file ARCDAT no. of arc points read = 40985 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.540000 m= 28430 mr = 68401 m= 2588 mr = 19236 m= 48 mr = 1201 m= 0 mr = 0 time to grow re-entrant surface = 0.2100000 no. cavity mid-points inaccessible to solvent = 630 time to turn everything in is 0.4500000 number of dielectric boundary points 38519 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 520 ## 6 charges are in solution ## iepsmp to db, and charging done at 0.5300000 number of grid points assigned charge 37462 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) : 0.5153594 object centre at (A) : 14.47600 41.47050 64.69900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 6.6992678E-03 1.3878524E-02 midg,1,midg; midg,igrid,midg -6.9940616E-03 1.0074335E-04 1,midg,midg; igrid,midg,midg -2.7299099E-02 -3.5127562E-03 gauss-seidel spectral radius is 0.9981710 estimated iterations to convergence 186 setup time was (sec) 0.6700000 now iterating at: 16:01:14 rms-change max change #iterations 4.034320 164.0603 at 10iterations 1.666259 54.23493 at 20iterations 0.6956664 20.52122 at 30iterations 0.2894966 8.939001 at 40iterations 0.1207414 3.800636 at 50iterations 5.0601054E-02 1.535111 at 60iterations 2.1180298E-02 0.6278038 at 70iterations 8.9794192E-03 0.2879639 at 80iterations 3.9831502E-03 0.1172733 at 90iterations 1.9021673E-03 5.9764862E-02 at 100iterations 1.0497400E-03 3.4248352E-02 at 110iterations 6.7310786E-04 1.8764496E-02 at 120iterations finished qdiffx linear iterations at : 16:01:21 total time elapsed so far: 7.720000 # loops : 120 mean,max change (kT/e) : 6.7310786E-04 1.8764496E-02 energy calculations done at 7.720000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.850000 DelPhi exited at 16:01:22 7.855u 0.210s 0:08.55 94.2% 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 Mon Oct 10 2011 at 16:01:22 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5125 !!! WARNING: ASP 610 has a net charge of -2.0000 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: 2.319117 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): -20.06300 49.01500 ymin,ymax (A): 10.04300 72.89799 zmin,zma (A): 33.71600 95.68200 x,y,z range (A): 69.07800 62.85500 61.96600 scale (grids/A): 2.319117 object centre (A): 14.47600 41.47050 64.69900 number of atom coordinates read : 5125 total number of charged atoms : 4964 net assigned charge : 1.500020 assigned positive charge : 771.0981 centred at (gu) : 90.58703 94.48630 91.51989 assigned negative charge : -769.6031 centred at (gu) : 90.57664 94.29657 91.50951 start vw surface at 0.1400000 fill in re-entrant regions at 0.4100000 boundary points on vw surface= 224761 reading accessible surface arcs data from file ARCDAT no. of arc points read = 40985 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.540000 m= 101918 mr = 167831 m= 26416 mr = 80235 m= 3823 mr = 19595 m= 201 mr = 2477 m= 1 mr = 58 m= 0 mr = 0 time to grow re-entrant surface = 0.6500000 no. cavity mid-points inaccessible to solvent = 2071 time to turn everything in is 1.160000 number of dielectric boundary points 86924 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 56 iepsmp to db, and charging done at 1.270000 number of grid points assigned charge 39610 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) : 1.546078 object centre at (A) : 14.47600 41.47050 64.69900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 9.2977598E-02 0.2264842 midg,1,midg; midg,igrid,midg -0.1370593 -1.6253727E-02 1,midg,midg; igrid,midg,midg -0.6235991 8.8334959E-03 gauss-seidel spectral radius is 0.9991788 estimated iterations to convergence 276 setup time was (sec) 1.420000 now iterating at: 16:01:24 rms-change max change #iterations 10.85025 367.0389 at 10iterations 6.264947 160.5707 at 20iterations 3.595509 77.70477 at 30iterations 2.049736 39.21331 at 40iterations 1.167010 25.01836 at 50iterations 0.6611457 13.15482 at 60iterations 0.3732712 6.786366 at 70iterations 0.2106167 3.786985 at 80iterations 0.1183559 2.180501 at 90iterations 6.6738531E-02 1.415029 at 100iterations 3.7413087E-02 0.7458754 at 110iterations 2.1042138E-02 0.3988943 at 120iterations 1.1823509E-02 0.2133541 at 130iterations 6.6653187E-03 0.1134567 at 140iterations 3.7936415E-03 6.8218231E-02 at 150iterations 2.1961597E-03 4.0324211E-02 at 160iterations 1.3069081E-03 2.2979736E-02 at 170iterations 8.1587798E-04 1.4440536E-02 at 180iterations finished qdiffx linear iterations at : 16:01:35 total time elapsed so far: 13.00000 # loops : 180 mean,max change (kT/e) : 8.1587798E-04 1.4440536E-02 energy calculations done at 13.00000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.13000 DelPhi exited at 16:01:36 13.133u 0.197s 0:13.63 97.7% 0+0k 0+0io 0pf+0w