Sun Oct 9 19:33:00 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 19:33:00 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: 319 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5357 !!! WARNING: HIQ 377 has a net charge of 0.5140 !!! WARNING: LLP 1 has a net charge of 1.7400 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1200000 grid size : 179 scale,in grids/A, set to be: 0.5146368 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): 3.280000 68.36000 ymin,ymax (A): -8.995000 53.41400 zmin,zma (A): -1.984000 67.19100 x,y,z range (A): 65.08000 62.40900 69.17500 scale (grids/A): 0.5146368 object centre (A): 35.82000 22.20950 32.60350 number of atom coordinates read : 5357 total number of charged atoms : 5180 net assigned charge : 5.754030 assigned positive charge : 823.0204 centred at (gu) : 88.19435 89.33797 88.90474 assigned negative charge : -817.2724 centred at (gu) : 88.12670 89.36131 88.81254 start vw surface at 0.1800000 fill in re-entrant regions at 0.1900000 boundary points on vw surface= 9111 nv = 96 ne = 84 npr = 108809 no. pairs analyzed = 108809 no. exposed pairs = 6180 no. arc points = 42227 no. surface atoms = 2102 nbur = 3255 mkacc time = 0.2400000 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 = 1.680000 m= 324 mr = 5117 m= 1 mr = 9 m= 0 mr = 0 time to grow re-entrant surface = 0.2600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4600000 number of dielectric boundary points 4310 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4227 ## 568 charges are in solution ## iepsmp to db, and charging done at 0.5600000 number of grid points assigned charge 12149 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -2.9828420E-10 3.1860189E-10 midg,1,midg; midg,igrid,midg 2.2199681E-10 2.0332709E-11 1,midg,midg; igrid,midg,midg -2.2026878E-10 2.1282116E-10 gauss-seidel spectral radius is 0.9807249 estimated iterations to convergence 59 setup time was (sec) 0.6900000 now iterating at: 19:33:01 rms-change max change #iterations 8.2851954E-02 13.48529 at 10iterations 1.1416338E-02 1.780033 at 20iterations 4.9573439E-03 0.8352661 at 30iterations 2.3810773E-03 0.4051971 at 40iterations 1.1490913E-03 0.1954498 at 50iterations finished qdiffx linear iterations at : 19:33:04 total time elapsed so far: 3.430000 # loops : 50 mean,max change (kT/e) : 1.1490913E-03 0.1954498 energy calculations done at 3.430000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.600000 DelPhi exited at 19:33:04 3.605u 0.268s 0:04.19 92.1% 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 19:33:04 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: 319 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5357 !!! WARNING: HIQ 377 has a net charge of 0.5140 !!! WARNING: LLP 1 has a net charge of 1.7400 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1400000 grid size : 179 scale,in grids/A, set to be: 1.543910 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): 3.280000 68.36000 ymin,ymax (A): -8.995000 53.41400 zmin,zma (A): -1.984000 67.19100 x,y,z range (A): 65.08000 62.40900 69.17500 scale (grids/A): 1.543910 object centre (A): 35.82000 22.20950 32.60350 number of atom coordinates read : 5357 total number of charged atoms : 5180 net assigned charge : 5.754030 assigned positive charge : 823.0204 centred at (gu) : 84.58143 88.01244 86.71253 assigned negative charge : -817.2724 centred at (gu) : 84.37992 88.08348 86.43761 start vw surface at 0.2000000 fill in re-entrant regions at 0.3200000 boundary points on vw surface= 104045 reading accessible surface arcs data from file ARCDAT no. of arc points read = 42227 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.568000 m= 32645 mr = 75146 m= 3069 mr = 22888 m= 55 mr = 1487 m= 0 mr = 5 time to grow re-entrant surface = 0.3300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.7000000 number of dielectric boundary points 40288 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 575 ## 5 charges are in solution ## iepsmp to db, and charging done at 0.8300000 number of grid points assigned charge 39071 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) : 0.5146368 object centre at (A) : 35.82000 22.20950 32.60350 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.4295530E-02 2.9255975E-02 midg,1,midg; midg,igrid,midg 1.5378167E-02 5.9060687E-03 1,midg,midg; igrid,midg,midg -1.0280566E-02 6.0927332E-04 gauss-seidel spectral radius is 0.9981851 estimated iterations to convergence 186 setup time was (sec) 1.010000 now iterating at: 19:33:06 rms-change max change #iterations 4.201469 149.1497 at 10iterations 1.751968 54.31401 at 20iterations 0.7325110 21.66293 at 30iterations 0.3076161 8.410461 at 40iterations 0.1293560 4.221924 at 50iterations 5.5993326E-02 1.854238 at 60iterations 2.5601817E-02 0.8445435 at 70iterations 1.3273940E-02 0.4450378 at 80iterations 8.1578111E-03 0.2777252 at 90iterations 5.6343526E-03 0.1804047 at 100iterations 4.1386178E-03 0.1322174 at 110iterations 3.1020336E-03 9.8499298E-02 at 120iterations finished qdiffx linear iterations at : 19:33:13 total time elapsed so far: 7.850000 # loops : 120 mean,max change (kT/e) : 3.1020336E-03 9.8499298E-02 energy calculations done at 7.850000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.010000 DelPhi exited at 19:33:13 8.016u 0.301s 0:08.70 95.5% 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 19:33:13 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: 319 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5357 !!! WARNING: HIQ 377 has a net charge of 0.5140 !!! WARNING: LLP 1 has a net charge of 1.7400 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1200000 grid size : 179 scale,in grids/A, set to be: 2.315866 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): 3.280000 68.36000 ymin,ymax (A): -8.995000 53.41400 zmin,zma (A): -1.984000 67.19100 x,y,z range (A): 65.08000 62.40900 69.17500 scale (grids/A): 2.315866 object centre (A): 35.82000 22.20950 32.60350 number of atom coordinates read : 5357 total number of charged atoms : 5180 net assigned charge : 5.754030 assigned positive charge : 823.0204 centred at (gu) : 81.87191 87.01826 85.06836 assigned negative charge : -817.2724 centred at (gu) : 81.56984 87.12529 84.65614 start vw surface at 0.1800000 fill in re-entrant regions at 0.5400000 boundary points on vw surface= 242566 reading accessible surface arcs data from file ARCDAT no. of arc points read = 42227 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.540000 m= 115990 mr = 183800 m= 31629 mr = 93536 m= 4565 mr = 23718 m= 258 mr = 2949 m= 2 mr = 111 m= 0 mr = 0 time to grow re-entrant surface = 1.040000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.710000 number of dielectric boundary points 90896 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 67 iepsmp to db, and charging done at 1.860000 number of grid points assigned charge 41322 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) : 1.543910 object centre at (A) : 35.82000 22.20950 32.60350 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.3423326 0.8528661 midg,1,midg; midg,igrid,midg 0.2258330 4.3984834E-02 1,midg,midg; igrid,midg,midg -0.2860928 -1.8572865E-02 gauss-seidel spectral radius is 0.9991832 estimated iterations to convergence 276 setup time was (sec) 2.050000 now iterating at: 19:33:15 rms-change max change #iterations 11.11110 299.3062 at 10iterations 6.384795 121.9355 at 20iterations 3.625172 83.44509 at 30iterations 2.053490 37.68938 at 40iterations 1.160281 20.11993 at 50iterations 0.6540903 11.07366 at 60iterations 0.3682145 7.021294 at 70iterations 0.2072252 3.535749 at 80iterations 0.1167210 1.960345 at 90iterations 6.5933637E-02 1.195335 at 100iterations 3.7625331E-02 0.6264229 at 110iterations 2.1842625E-02 0.3717632 at 120iterations 1.3179050E-02 0.2606392 at 130iterations 8.4283389E-03 0.1866302 at 140iterations 5.8070603E-03 0.1154633 at 150iterations 4.3111527E-03 8.7825775E-02 at 160iterations 3.3791969E-03 6.7981720E-02 at 170iterations 2.7355347E-03 5.2684784E-02 at 180iterations finished qdiffx linear iterations at : 19:33:27 total time elapsed so far: 13.47000 # loops : 180 mean,max change (kT/e) : 2.7355347E-03 5.2684784E-02 energy calculations done at 13.47000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.63000 DelPhi exited at 19:33:27 13.634u 0.291s 0:14.28 97.4% 0+0k 0+0io 0pf+0w