Sat Oct 8 17:10:37 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 Sat Oct 8 2011 at 17:10:38 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: 258 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3215 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: 0.5509045 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): 37.84300 93.63300 ymin,ymax (A): 16.51600 81.13700 zmin,zma (A): -22.82700 26.07500 x,y,z range (A): 55.78999 64.62100 48.90200 scale (grids/A): 0.5509045 object centre (A): 65.73800 48.82650 1.624000 number of atom coordinates read : 3215 total number of charged atoms : 3070 net assigned charge : -5.499977 assigned positive charge : 478.9759 centred at (gu) : 90.06726 90.68095 89.92875 assigned negative charge : -484.4771 centred at (gu) : 90.02885 90.66164 89.92050 start vw surface at 0.1900000 fill in re-entrant regions at 0.2000000 boundary points on vw surface= 6423 nv = 96 ne = 84 npr = 65056 no. pairs analyzed = 65056 no. exposed pairs = 3995 no. arc points = 27555 no. surface atoms = 1352 nbur = 1863 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 = 1.568000 m= 274 mr = 3457 m= 1 mr = 13 m= 0 mr = 0 time to grow re-entrant surface = 0.2000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4200000 number of dielectric boundary points 3228 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2796 ## 358 charges are in solution ## iepsmp to db, and charging done at 0.5300000 number of grid points assigned charge 8333 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -4.9633836E-10 -3.3872699E-10 midg,1,midg; midg,igrid,midg -4.9617505E-10 -2.9098243E-10 1,midg,midg; igrid,midg,midg -7.3954171E-10 -8.4823704E-11 gauss-seidel spectral radius is 0.9830269 estimated iterations to convergence 63 setup time was (sec) 0.6800000 now iterating at: 17:10:38 rms-change max change #iterations 8.1421524E-02 12.55199 at 10iterations 5.5680051E-03 0.9359818 at 20iterations 3.9689816E-04 7.8498840E-02 at 30iterations 3.6189082E-05 6.7253113E-03 at 40iterations 5.4441084E-06 1.1410713E-03 at 50iterations finished qdiffx linear iterations at : 17:10:42 total time elapsed so far: 4.030000 # loops : 50 mean,max change (kT/e) : 5.4441084E-06 1.1410713E-03 energy calculations done at 4.030000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.210000 DelPhi exited at 17:10:42 4.214u 0.282s 0:04.76 94.3% 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 Sat Oct 8 2011 at 17:10:42 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: 258 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3215 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: 1.652713 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): 37.84300 93.63300 ymin,ymax (A): 16.51600 81.13700 zmin,zma (A): -22.82700 26.07500 x,y,z range (A): 55.78999 64.62100 48.90200 scale (grids/A): 1.652713 object centre (A): 65.73800 48.82650 1.624000 number of atom coordinates read : 3215 total number of charged atoms : 3070 net assigned charge : -5.499977 assigned positive charge : 478.9759 centred at (gu) : 90.20113 92.04222 89.78543 assigned negative charge : -484.4771 centred at (gu) : 90.08630 91.98455 89.76151 start vw surface at 0.1800000 fill in re-entrant regions at 0.3000000 boundary points on vw surface= 70945 reading accessible surface arcs data from file ARCDAT no. of arc points read = 27555 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 23490 mr = 49464 m= 2750 mr = 16658 m= 116 mr = 1457 m= 0 mr = 9 time to grow re-entrant surface = 0.3100000 no. cavity mid-points inaccessible to solvent = 233 time to turn everything in is 0.6500000 number of dielectric boundary points 29713 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 320 ## 2 charges are in solution ## iepsmp to db, and charging done at 0.7800000 number of grid points assigned charge 23553 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) : 0.5509045 object centre at (A) : 65.73800 48.82650 1.624000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -6.4058737E-03 -4.4485368E-03 midg,1,midg; midg,igrid,midg -8.7480843E-03 1.7651320E-02 1,midg,midg; igrid,midg,midg -1.5439761E-02 -2.7351151E-03 gauss-seidel spectral radius is 0.9982554 estimated iterations to convergence 190 setup time was (sec) 0.9500000 now iterating at: 17:10:44 rms-change max change #iterations 3.555762 162.9866 at 10iterations 1.498986 59.57737 at 20iterations 0.6395893 21.07285 at 30iterations 0.2715618 8.891424 at 40iterations 0.1151794 4.582718 at 50iterations 4.8973389E-02 1.823137 at 60iterations 2.0823726E-02 0.7226143 at 70iterations 8.8336123E-03 0.2994614 at 80iterations 3.7684457E-03 0.1468697 at 90iterations 1.6039110E-03 6.1382294E-02 at 100iterations 6.8286882E-04 2.2312164E-02 at 110iterations 2.9418286E-04 1.0042191E-02 at 120iterations finished qdiffx linear iterations at : 17:10:52 total time elapsed so far: 9.340000 # loops : 120 mean,max change (kT/e) : 2.9418286E-04 1.0042191E-02 energy calculations done at 9.340000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.520000 DelPhi exited at 17:10:52 9.524u 0.302s 0:10.11 97.1% 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 Sat Oct 8 2011 at 17:10:53 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: 258 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3215 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: 2.479070 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): 37.84300 93.63300 ymin,ymax (A): 16.51600 81.13700 zmin,zma (A): -22.82700 26.07500 x,y,z range (A): 55.78999 64.62100 48.90200 scale (grids/A): 2.479070 object centre (A): 65.73800 48.82650 1.624000 number of atom coordinates read : 3215 total number of charged atoms : 3070 net assigned charge : -5.499977 assigned positive charge : 478.9759 centred at (gu) : 90.30152 93.06298 89.67776 assigned negative charge : -484.4771 centred at (gu) : 90.12932 92.97652 89.64192 start vw surface at 0.1800000 fill in re-entrant regions at 0.5400000 boundary points on vw surface= 164416 reading accessible surface arcs data from file ARCDAT no. of arc points read = 27555 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 79824 mr = 120111 m= 24501 mr = 64316 m= 4522 mr = 18913 m= 373 mr = 3077 m= 7 mr = 177 m= 0 mr = 0 time to grow re-entrant surface = 0.9600000 no. cavity mid-points inaccessible to solvent = 839 time to turn everything in is 1.600000 number of dielectric boundary points 67049 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 10 iepsmp to db, and charging done at 1.750000 number of grid points assigned charge 24543 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) : 1.652713 object centre at (A) : 65.73800 48.82650 1.624000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -8.5074328E-02 -3.8837958E-02 midg,1,midg; midg,igrid,midg -0.2041794 0.5545058 1,midg,midg; igrid,midg,midg -0.2278857 -1.7411163E-02 gauss-seidel spectral radius is 0.9991642 estimated iterations to convergence 273 setup time was (sec) 1.930000 now iterating at: 17:10:55 rms-change max change #iterations 9.090778 287.1253 at 10iterations 5.135870 109.6599 at 20iterations 2.879114 59.54148 at 30iterations 1.613738 34.93643 at 40iterations 0.9014212 18.40645 at 50iterations 0.5002992 10.00246 at 60iterations 0.2794675 5.678276 at 70iterations 0.1550425 3.107487 at 80iterations 8.6136557E-02 1.655617 at 90iterations 4.7854230E-02 0.9427643 at 100iterations 2.6594451E-02 0.5101900 at 110iterations 1.4715461E-02 0.2825062 at 120iterations 8.1979344E-03 0.1661806 at 130iterations 4.5430958E-03 8.4198542E-02 at 140iterations 2.5198327E-03 4.8365831E-02 at 150iterations 1.4012352E-03 2.8177261E-02 at 160iterations 7.7851996E-04 1.5398026E-02 at 170iterations 4.3292771E-04 8.2063675E-03 at 180iterations finished qdiffx linear iterations at : 17:11:09 total time elapsed so far: 15.72000 # loops : 180 mean,max change (kT/e) : 4.3292771E-04 8.2063675E-03 energy calculations done at 15.72000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.91000 DelPhi exited at 17:11:09 15.911u 0.301s 0:16.51 98.1% 0+0k 0+0io 0pf+0w