Mon Oct 10 09:07:06 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 09:07:06 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 = 1964 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: 0.6396206 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): -6.201000 34.76800 ymin,ymax (A): -3.390000 48.46200 zmin,zma (A): -24.46000 31.19800 x,y,z range (A): 40.96900 51.85200 55.65800 scale (grids/A): 0.6396206 object centre (A): 14.28350 22.53600 3.369000 number of atom coordinates read : 1964 total number of charged atoms : 1832 net assigned charge : 3.000004 assigned positive charge : 287.8260 centred at (gu) : 90.82660 92.62913 90.13991 assigned negative charge : -284.8263 centred at (gu) : 90.93182 92.75550 90.08549 start vw surface at 7.9999998E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 5604 nv = 96 ne = 84 npr = 39648 no. pairs analyzed = 39648 no. exposed pairs = 2483 no. arc points = 17544 no. surface atoms = 838 nbur = 1126 mkacc time = 6.0000002E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 327 mr = 3148 m= 0 mr = 51 time to grow re-entrant surface = 6.0000002E-02 no. cavity mid-points inaccessible to solvent = 12 time to turn everything in is 0.1600000 number of dielectric boundary points 2732 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1745 ## 171 charges are in solution ## iepsmp to db, and charging done at 0.2300000 number of grid points assigned charge 6528 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 9.7250881E-11 9.5043644E-09 midg,1,midg; midg,igrid,midg 8.6861576E-09 -1.1125976E-08 1,midg,midg; igrid,midg,midg 1.1245849E-08 -5.1412212E-09 gauss-seidel spectral radius is 0.9872826 estimated iterations to convergence 72 setup time was (sec) 0.3600000 now iterating at: 09:07:06 rms-change max change #iterations 0.1222925 18.69576 at 10iterations 1.2095237E-02 1.782890 at 20iterations 1.1763086E-03 0.1946068 at 30iterations 1.1659237E-04 1.7436981E-02 at 40iterations 1.1389959E-05 1.5716553E-03 at 50iterations finished qdiffx linear iterations at : 09:07:09 total time elapsed so far: 3.230000 # loops : 50 mean,max change (kT/e) : 1.1389959E-05 1.5716553E-03 energy calculations done at 3.230000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.350000 DelPhi exited at 09:07:10 3.355u 0.181s 0:03.81 92.6% 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 09:07:10 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 = 1964 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: 1.918862 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): -6.201000 34.76800 ymin,ymax (A): -3.390000 48.46200 zmin,zma (A): -24.46000 31.19800 x,y,z range (A): 40.96900 51.85200 55.65800 scale (grids/A): 1.918862 object centre (A): 14.28350 22.53600 3.369000 number of atom coordinates read : 1964 total number of charged atoms : 1832 net assigned charge : 3.000004 assigned positive charge : 287.8260 centred at (gu) : 92.47978 97.88746 90.42004 assigned negative charge : -284.8263 centred at (gu) : 92.79568 98.26662 90.25652 start vw surface at 7.0000000E-02 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 59567 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17544 grid for indexing accessible points = 1.400000 m= 22976 mr = 41117 m= 3920 mr = 17699 m= 202 mr = 2655 m= 3 mr = 85 m= 0 mr = 0 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 1942 time to turn everything in is 0.3100000 number of dielectric boundary points 25112 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 127 iepsmp to db, and charging done at 0.3900000 number of grid points assigned charge 14418 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) : 0.6396206 object centre at (A) : 14.28350 22.53600 3.369000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.3571584E-02 1.4339400E-02 midg,1,midg; midg,igrid,midg 3.0365985E-02 -7.5601935E-03 1,midg,midg; igrid,midg,midg 7.0520276E-03 -4.7164112E-03 gauss-seidel spectral radius is 0.9985795 estimated iterations to convergence 210 setup time was (sec) 0.5300000 now iterating at: 09:07:10 rms-change max change #iterations 3.619050 187.0453 at 10iterations 1.671243 62.27296 at 20iterations 0.7707723 28.51798 at 30iterations 0.3568791 13.34714 at 40iterations 0.1637794 5.472290 at 50iterations 7.5808458E-02 2.826614 at 60iterations 3.4785900E-02 1.172579 at 70iterations 1.6084714E-02 0.5585747 at 80iterations 7.3701981E-03 0.2881603 at 90iterations 3.4161571E-03 0.1171188 at 100iterations 1.5758079E-03 5.2999020E-02 at 110iterations 7.2491466E-04 2.9549599E-02 at 120iterations finished qdiffx linear iterations at : 09:07:17 total time elapsed so far: 7.660000 # loops : 120 mean,max change (kT/e) : 7.2491466E-04 2.9549599E-02 energy calculations done at 7.660000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.790000 DelPhi exited at 09:07:18 7.790u 0.209s 0:08.28 96.4% 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 09:07:18 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 = 1964 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.878293 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): -6.201000 34.76800 ymin,ymax (A): -3.390000 48.46200 zmin,zma (A): -24.46000 31.19800 x,y,z range (A): 40.96900 51.85200 55.65800 scale (grids/A): 2.878293 object centre (A): 14.28350 22.53600 3.369000 number of atom coordinates read : 1964 total number of charged atoms : 1832 net assigned charge : 3.000004 assigned positive charge : 287.8260 centred at (gu) : 93.71976 101.8310 90.62990 assigned negative charge : -284.8263 centred at (gu) : 94.19360 102.4000 90.38486 start vw surface at 5.9999999E-02 fill in re-entrant regions at 0.2600000 boundary points on vw surface= 137548 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17544 grid for indexing accessible points = 1.400000 m= 72423 mr = 99314 m= 28433 mr = 60500 m= 7237 mr = 23743 m= 953 mr = 5733 m= 60 mr = 693 m= 0 mr = 23 time to grow re-entrant surface = 0.4400000 no. cavity mid-points inaccessible to solvent = 6426 time to turn everything in is 0.7700000 number of dielectric boundary points 56648 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 0.8600000 number of grid points assigned charge 14656 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) : 1.918862 object centre at (A) : 14.28350 22.53600 3.369000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.007729 3.2288007E-02 midg,1,midg; midg,igrid,midg 0.3329442 -0.1198699 1,midg,midg; igrid,midg,midg 3.8565408E-02 -3.1566139E-02 gauss-seidel spectral radius is 0.9992308 estimated iterations to convergence 285 setup time was (sec) 1.000000 now iterating at: 09:07:19 rms-change max change #iterations 8.476869 430.5015 at 10iterations 4.868231 148.2426 at 20iterations 2.768567 76.78979 at 30iterations 1.575052 35.93238 at 40iterations 0.8984753 19.86907 at 50iterations 0.5108614 11.21307 at 60iterations 0.2901915 5.659331 at 70iterations 0.1651687 4.601448 at 80iterations 9.3634829E-02 1.827049 at 90iterations 5.3094801E-02 1.117285 at 100iterations 3.0074526E-02 0.6244583 at 110iterations 1.7143605E-02 0.3366318 at 120iterations 9.6952599E-03 0.1893703 at 130iterations 5.5088350E-03 0.1082420 at 140iterations 3.1172256E-03 6.7786694E-02 at 150iterations 1.7681174E-03 3.3082247E-02 at 160iterations 1.0043874E-03 2.1238327E-02 at 170iterations 5.6944246E-04 1.1507034E-02 at 180iterations finished qdiffx linear iterations at : 09:07:30 total time elapsed so far: 11.97000 # loops : 180 mean,max change (kT/e) : 5.6944246E-04 1.1507034E-02 energy calculations done at 11.97000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.11000 DelPhi exited at 09:07:31 12.114u 0.214s 0:12.65 97.3% 0+0k 0+0io 0pf+0w