Mon Oct 10 17:02:49 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 Mon Oct 10 2011 at 17:02:49 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: 303 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2780 !!! WARNING: HIT 107 has a net charge of 0.5140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.5830140 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): -30.14000 30.92200 ymin,ymax (A): -22.31200 24.69800 zmin,zma (A): -7.671000 41.91600 x,y,z range (A): 61.06200 47.01000 49.58700 scale (grids/A): 0.5830140 object centre (A): 0.3909998 1.193000 17.12250 number of atom coordinates read : 2780 total number of charged atoms : 2640 net assigned charge : -0.9859756 assigned positive charge : 418.5793 centred at (gu) : 90.31339 90.23101 88.99040 assigned negative charge : -419.5662 centred at (gu) : 90.34533 90.08104 88.87502 start vw surface at 9.0000004E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 6221 nv = 96 ne = 84 npr = 55632 no. pairs analyzed = 55632 no. exposed pairs = 3730 no. arc points = 26067 no. surface atoms = 1263 nbur = 1517 mkacc time = 9.9999994E-02 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 = 1.484000 m= 256 mr = 3094 m= 0 mr = 18 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2000000 number of dielectric boundary points 3365 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2628 ## 271 charges are in solution ## iepsmp to db, and charging done at 0.2600000 number of grid points assigned charge 7880 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -3.6791292E-09 1.8888136E-09 midg,1,midg; midg,igrid,midg -3.5144327E-09 3.3470609E-09 1,midg,midg; igrid,midg,midg 4.8083459E-10 -1.0181578E-09 gauss-seidel spectral radius is 0.9848017 estimated iterations to convergence 67 setup time was (sec) 0.3800000 now iterating at: 17:02:49 rms-change max change #iterations 9.8401390E-02 13.24168 at 10iterations 7.7449558E-03 1.199157 at 20iterations 6.3551229E-04 0.1026831 at 30iterations 6.4865599E-05 9.9792480E-03 at 40iterations 1.1635474E-05 1.9454956E-03 at 50iterations finished qdiffx linear iterations at : 17:02:52 total time elapsed so far: 3.250000 # loops : 50 mean,max change (kT/e) : 1.1635474E-05 1.9454956E-03 energy calculations done at 3.250000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.380000 DelPhi exited at 17:02:53 3.385u 0.178s 0:03.94 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 Mon Oct 10 2011 at 17:02:53 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: 303 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2780 !!! WARNING: HIT 107 has a net charge of 0.5140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.749042 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): -30.14000 30.92200 ymin,ymax (A): -22.31200 24.69800 zmin,zma (A): -7.671000 41.91600 x,y,z range (A): 61.06200 47.01000 49.58700 scale (grids/A): 1.749042 object centre (A): 0.3909998 1.193000 17.12250 number of atom coordinates read : 2780 total number of charged atoms : 2640 net assigned charge : -0.9859756 assigned positive charge : 418.5793 centred at (gu) : 90.93970 90.69218 86.97055 assigned negative charge : -419.5662 centred at (gu) : 91.03563 90.24290 86.62460 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 68303 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26067 grid for indexing accessible points = 1.400000 m= 21119 mr = 45370 m= 2198 mr = 14152 m= 65 mr = 1013 m= 0 mr = 5 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 149 time to turn everything in is 0.3300000 number of dielectric boundary points 31145 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 247 ## 2 charges are in solution ## iepsmp to db, and charging done at 0.4000000 number of grid points assigned charge 20532 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) : 0.5830140 object centre at (A) : 0.3909998 1.193000 17.12250 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -8.0087669E-03 3.5102849E-03 midg,1,midg; midg,igrid,midg -1.9355590E-02 1.4230912E-02 1,midg,midg; igrid,midg,midg 2.3188762E-02 -3.3181178E-04 gauss-seidel spectral radius is 0.9984104 estimated iterations to convergence 199 setup time was (sec) 0.5400000 now iterating at: 17:02:54 rms-change max change #iterations 3.719667 157.4697 at 10iterations 1.640955 55.73940 at 20iterations 0.7222261 27.12190 at 30iterations 0.3191749 11.61105 at 40iterations 0.1404256 4.996227 at 50iterations 6.1970558E-02 2.441966 at 60iterations 2.7342735E-02 1.057892 at 70iterations 1.2054703E-02 0.3976364 at 80iterations 5.3361543E-03 0.1756897 at 90iterations 2.3558841E-03 7.6853752E-02 at 100iterations 1.0400582E-03 3.4458160E-02 at 110iterations 4.6216699E-04 1.6864777E-02 at 120iterations finished qdiffx linear iterations at : 17:03:01 total time elapsed so far: 7.550000 # loops : 120 mean,max change (kT/e) : 4.6216699E-04 1.6864777E-02 energy calculations done at 7.550000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.690000 DelPhi exited at 17:03:02 7.690u 0.213s 0:09.05 87.2% 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 17:03:02 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: 303 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2780 !!! WARNING: HIT 107 has a net charge of 0.5140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.623563 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): -30.14000 30.92200 ymin,ymax (A): -22.31200 24.69800 zmin,zma (A): -7.671000 41.91600 x,y,z range (A): 61.06200 47.01000 49.58700 scale (grids/A): 2.623563 object centre (A): 0.3909998 1.193000 17.12250 number of atom coordinates read : 2780 total number of charged atoms : 2640 net assigned charge : -0.9859756 assigned positive charge : 418.5793 centred at (gu) : 91.40936 91.03822 85.45567 assigned negative charge : -419.5662 centred at (gu) : 91.55335 90.36437 84.93695 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.2800000 boundary points on vw surface= 158438 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26067 grid for indexing accessible points = 1.400000 m= 71881 mr = 111187 m= 20971 mr = 55919 m= 3453 mr = 15388 m= 268 mr = 2128 m= 4 mr = 103 m= 0 mr = 0 time to grow re-entrant surface = 0.4600000 no. cavity mid-points inaccessible to solvent = 510 time to turn everything in is 0.8100000 number of dielectric boundary points 70290 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 6 iepsmp to db, and charging done at 0.9000000 number of grid points assigned charge 21112 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) : 1.749042 object centre at (A) : 0.3909998 1.193000 17.12250 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -6.7022748E-02 5.3252231E-02 midg,1,midg; midg,igrid,midg -0.2185949 0.2076718 1,midg,midg; igrid,midg,midg 0.8310786 6.6788130E-02 gauss-seidel spectral radius is 0.9992139 estimated iterations to convergence 282 setup time was (sec) 1.040000 now iterating at: 17:03:03 rms-change max change #iterations 9.404865 282.5824 at 10iterations 5.443618 133.4235 at 20iterations 3.128110 77.55396 at 30iterations 1.788505 39.52028 at 40iterations 1.022579 26.96711 at 50iterations 0.5813527 11.98759 at 60iterations 0.3309587 7.048790 at 70iterations 0.1882625 4.060884 at 80iterations 0.1066419 2.263206 at 90iterations 6.0371548E-02 1.217942 at 100iterations 3.4256931E-02 0.7430172 at 110iterations 1.9357936E-02 0.3780308 at 120iterations 1.0950889E-02 0.2180824 at 130iterations 6.1739543E-03 0.1291885 at 140iterations 3.4889858E-03 6.5962791E-02 at 150iterations 1.9754223E-03 4.0248871E-02 at 160iterations 1.1154830E-03 2.2278786E-02 at 170iterations 6.3174032E-04 1.2994766E-02 at 180iterations finished qdiffx linear iterations at : 17:03:14 total time elapsed so far: 12.02000 # loops : 180 mean,max change (kT/e) : 6.3174032E-04 1.2994766E-02 energy calculations done at 12.02000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.15000 DelPhi exited at 17:03:15 12.157u 0.209s 0:13.22 93.4% 0+0k 0+0io 0pf+0w