Mon Oct 10 11:02:38 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 11:02:38 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 = 5316 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: 0.4807303 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): -28.75000 29.73100 ymin,ymax (A): -42.38000 19.82200 zmin,zma (A): -31.45300 42.60100 x,y,z range (A): 58.48100 62.20200 74.05400 scale (grids/A): 0.4807303 object centre (A): 0.4904995 -11.27900 5.574001 number of atom coordinates read : 5316 total number of charged atoms : 5162 net assigned charge : 13.00003 assigned positive charge : 841.6884 centred at (gu) : 90.75481 89.86514 91.92137 assigned negative charge : -828.6970 centred at (gu) : 90.73476 89.93169 91.98242 start vw surface at 0.1800000 fill in re-entrant regions at 0.1900000 boundary points on vw surface= 7699 nv = 96 ne = 84 npr = 104189 no. pairs analyzed = 104189 no. exposed pairs = 6468 no. arc points = 44550 no. surface atoms = 2166 nbur = 3150 mkacc time = 0.2800000 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 = 1.764000 m= 238 mr = 4091 m= 1 mr = 0 m= 0 mr = 0 time to grow re-entrant surface = 0.3200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5200000 number of dielectric boundary points 3847 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4160 ## 695 charges are in solution ## iepsmp to db, and charging done at 0.6200000 number of grid points assigned charge 10395 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 5.4415018E-11 -5.3050030E-12 midg,1,midg; midg,igrid,midg 9.9950354E-11 -6.0507276E-12 1,midg,midg; igrid,midg,midg 2.4525494E-11 7.4925892E-11 gauss-seidel spectral radius is 0.9779205 estimated iterations to convergence 56 setup time was (sec) 0.7800000 now iterating at: 11:02:39 rms-change max change #iterations 5.3162009E-02 9.231750 at 10iterations 2.8376363E-03 0.4529877 at 20iterations 6.2332192E-04 0.1034918 at 30iterations 3.0375939E-04 5.0959587E-02 at 40iterations 1.5248093E-04 2.5734901E-02 at 50iterations finished qdiffx linear iterations at : 11:02:43 total time elapsed so far: 4.590000 # loops : 50 mean,max change (kT/e) : 1.5248093E-04 2.5734901E-02 energy calculations done at 4.590000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.760000 DelPhi exited at 11:02:44 4.767u 0.410s 0:05.44 95.0% 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 11:02:44 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 = 5316 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: 1.442191 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): -28.75000 29.73100 ymin,ymax (A): -42.38000 19.82200 zmin,zma (A): -31.45300 42.60100 x,y,z range (A): 58.48100 62.20200 74.05400 scale (grids/A): 1.442191 object centre (A): 0.4904995 -11.27900 5.574001 number of atom coordinates read : 5316 total number of charged atoms : 5162 net assigned charge : 13.00003 assigned positive charge : 841.6884 centred at (gu) : 92.26272 89.59373 95.76214 assigned negative charge : -828.6970 centred at (gu) : 92.20419 89.79514 95.94728 start vw surface at 0.1900000 fill in re-entrant regions at 0.3100000 boundary points on vw surface= 89161 reading accessible surface arcs data from file ARCDAT no. of arc points read = 44550 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.652000 m= 24487 mr = 62592 m= 1755 mr = 16258 m= 18 mr = 607 m= 0 mr = 0 time to grow re-entrant surface = 0.3700000 no. cavity mid-points inaccessible to solvent = 859 time to turn everything in is 0.7400000 number of dielectric boundary points 35964 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 714 ## 17 charges are in solution ## iepsmp to db, and charging done at 0.8600000 number of grid points assigned charge 37874 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) : 0.4807303 object centre at (A) : 0.4904995 -11.27900 5.574001 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.3912009E-02 2.4407867E-02 midg,1,midg; midg,igrid,midg 3.0909025E-03 4.9308757E-03 1,midg,midg; igrid,midg,midg -1.8429334E-03 2.5350433E-03 gauss-seidel spectral radius is 0.9978784 estimated iterations to convergence 173 setup time was (sec) 1.040000 now iterating at: 11:02:45 rms-change max change #iterations 3.565503 147.7914 at 10iterations 1.379762 45.31580 at 20iterations 0.5381274 19.73566 at 30iterations 0.2090051 6.950011 at 40iterations 8.1710152E-02 2.595236 at 50iterations 3.1784646E-02 1.072529 at 60iterations 1.2446541E-02 0.4493065 at 70iterations 4.9932357E-03 0.1687469 at 80iterations 2.1385087E-03 7.3659897E-02 at 90iterations 1.0796654E-03 4.1713715E-02 at 100iterations 6.8889547E-04 2.6649475E-02 at 110iterations 5.0278206E-04 1.7436981E-02 at 120iterations finished qdiffx linear iterations at : 11:02:55 total time elapsed so far: 10.61000 # loops : 120 mean,max change (kT/e) : 5.0278206E-04 1.7436981E-02 energy calculations done at 10.61000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.77000 DelPhi exited at 11:02:55 10.775u 0.470s 0:11.59 96.9% 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 11:02:55 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 = 5316 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: 2.163286 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): -28.75000 29.73100 ymin,ymax (A): -42.38000 19.82200 zmin,zma (A): -31.45300 42.60100 x,y,z range (A): 58.48100 62.20200 74.05400 scale (grids/A): 2.163286 object centre (A): 0.4904995 -11.27900 5.574001 number of atom coordinates read : 5316 total number of charged atoms : 5162 net assigned charge : 13.00003 assigned positive charge : 841.6884 centred at (gu) : 93.39354 89.39001 98.64284 assigned negative charge : -828.6970 centred at (gu) : 93.30636 89.69270 98.92101 start vw surface at 0.1800000 fill in re-entrant regions at 0.5400000 boundary points on vw surface= 208907 reading accessible surface arcs data from file ARCDAT no. of arc points read = 44550 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.652000 m= 91070 mr = 154247 m= 20253 mr = 71345 m= 2076 mr = 14202 m= 55 mr = 1126 m= 0 mr = 8 time to grow re-entrant surface = 1.100000 no. cavity mid-points inaccessible to solvent = 2836 time to turn everything in is 1.760000 number of dielectric boundary points 81433 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 144 iepsmp to db, and charging done at 1.960000 number of grid points assigned charge 41077 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) : 1.442191 object centre at (A) : 0.4904995 -11.27900 5.574001 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2183809 0.6708364 midg,1,midg; midg,igrid,midg 6.0177498E-02 0.1120796 1,midg,midg; igrid,midg,midg -2.1205787E-02 2.1360585E-02 gauss-seidel spectral radius is 0.9990902 estimated iterations to convergence 262 setup time was (sec) 2.150000 now iterating at: 11:02:58 rms-change max change #iterations 9.988402 320.0449 at 10iterations 5.538934 143.1150 at 20iterations 3.055849 62.25843 at 30iterations 1.680374 37.62154 at 40iterations 0.9211108 17.01395 at 50iterations 0.5023840 10.93288 at 60iterations 0.2737778 5.373638 at 70iterations 0.1494155 2.817322 at 80iterations 8.1183873E-02 1.531790 at 90iterations 4.4114299E-02 0.9473267 at 100iterations 2.3910249E-02 0.4479523 at 110iterations 1.3000784E-02 0.2977371 at 120iterations 7.0474995E-03 0.1312485 at 130iterations 3.8236023E-03 7.5592041E-02 at 140iterations 2.0765264E-03 4.0979385E-02 at 150iterations 1.1349493E-03 2.2493362E-02 at 160iterations 6.2477699E-04 1.4245987E-02 at 170iterations 3.5300921E-04 7.2555542E-03 at 180iterations finished qdiffx linear iterations at : 11:03:14 total time elapsed so far: 18.25000 # loops : 180 mean,max change (kT/e) : 3.5300921E-04 7.2555542E-03 energy calculations done at 18.25000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 18.42000 DelPhi exited at 11:03:15 18.423u 0.507s 0:19.20 98.5% 0+0k 0+0io 0pf+0w