Mon Oct 10 14:37:27 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 14:37:27 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: 263 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2831 !!! WARNING: ADP 662 has a net charge of -2.0000 !!! WARNING: MG6 664 has a net charge of 1.4000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 0.5702661 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): -9.833000 52.59400 ymin,ymax (A): -16.13300 34.29700 zmin,zma (A): 77.46200 129.2770 x,y,z range (A): 62.42700 50.43000 51.81501 scale (grids/A): 0.5702661 object centre (A): 21.38050 9.081999 103.3695 number of atom coordinates read : 2831 total number of charged atoms : 2688 net assigned charge : -2.099993 assigned positive charge : 440.3312 centred at (gu) : 92.45597 89.54191 89.46712 assigned negative charge : -442.4323 centred at (gu) : 92.32178 89.62183 89.54377 start vw surface at 0.1200000 fill in re-entrant regions at 0.1300000 boundary points on vw surface= 6028 nv = 96 ne = 84 npr = 55597 no. pairs analyzed = 55597 no. exposed pairs = 3860 no. arc points = 26870 no. surface atoms = 1297 nbur = 1534 mkacc time = 0.1400000 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 = 1.512000 m= 285 mr = 2971 m= 1 mr = 17 m= 0 mr = 0 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3300000 number of dielectric boundary points 3326 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2830 ## 370 charges are in solution ## iepsmp to db, and charging done at 0.4700000 number of grid points assigned charge 7784 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 9.1097579E-10 -1.4126220E-09 midg,1,midg; midg,igrid,midg 9.5050245E-10 -1.4848025E-09 1,midg,midg; igrid,midg,midg -1.4128223E-09 3.0839022E-09 gauss-seidel spectral radius is 0.9841254 estimated iterations to convergence 65 setup time was (sec) 0.6900000 now iterating at: 14:37:28 rms-change max change #iterations 9.0790339E-02 13.47809 at 10iterations 6.7386352E-03 1.044741 at 20iterations 5.1495282E-04 8.6307526E-02 at 30iterations 4.0347313E-05 7.4386597E-03 at 40iterations 4.2950128E-06 7.3623657E-04 at 50iterations finished qdiffx linear iterations at : 14:37:32 total time elapsed so far: 4.900000 # loops : 50 mean,max change (kT/e) : 4.2950128E-06 7.3623657E-04 energy calculations done at 4.900000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 5.070000 DelPhi exited at 14:37:33 5.073u 0.439s 0:06.73 81.7% 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 14:37:33 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: 263 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2831 !!! WARNING: ADP 662 has a net charge of -2.0000 !!! WARNING: MG6 664 has a net charge of 1.4000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 1.710798 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): -9.833000 52.59400 ymin,ymax (A): -16.13300 34.29700 zmin,zma (A): 77.46200 129.2770 x,y,z range (A): 62.42700 50.43000 51.81501 scale (grids/A): 1.710798 object centre (A): 21.38050 9.081999 103.3695 number of atom coordinates read : 2831 total number of charged atoms : 2688 net assigned charge : -2.099993 assigned positive charge : 440.3312 centred at (gu) : 97.36745 88.62463 88.40039 assigned negative charge : -442.4323 centred at (gu) : 96.96490 88.86510 88.63101 start vw surface at 0.1300000 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 66032 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26870 grid for indexing accessible points = 1.400000 m= 21730 mr = 43610 m= 2857 mr = 14556 m= 94 mr = 1542 m= 1 mr = 6 m= 0 mr = 0 time to grow re-entrant surface = 0.2900000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5700000 number of dielectric boundary points 31000 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 265 iepsmp to db, and charging done at 0.7100000 number of grid points assigned charge 20753 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) : 0.5702661 object centre at (A) : 21.38050 9.081999 103.3695 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -7.9971207E-03 -2.0583889E-02 midg,1,midg; midg,igrid,midg -2.2511638E-03 -1.4491579E-02 1,midg,midg; igrid,midg,midg 1.5189352E-02 4.9340729E-02 gauss-seidel spectral radius is 0.9983445 estimated iterations to convergence 195 setup time was (sec) 0.9100000 now iterating at: 14:37:35 rms-change max change #iterations 3.693450 175.9804 at 10iterations 1.592756 61.12297 at 20iterations 0.6938571 24.28421 at 30iterations 0.2993339 10.42968 at 40iterations 0.1301622 4.983301 at 50iterations 5.6325249E-02 2.049782 at 60iterations 2.4376109E-02 0.8203964 at 70iterations 1.0626400E-02 0.3877958 at 80iterations 4.5936434E-03 0.1755948 at 90iterations 1.9937714E-03 6.9070816E-02 at 100iterations 8.6883362E-04 3.2022476E-02 at 110iterations 3.7936278E-04 1.4012337E-02 at 120iterations finished qdiffx linear iterations at : 14:37:46 total time elapsed so far: 12.46000 # loops : 120 mean,max change (kT/e) : 3.7936278E-04 1.4012337E-02 energy calculations done at 12.46000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.62000 DelPhi exited at 14:37:47 12.623u 0.487s 0:13.80 94.9% 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 14:37:47 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: 263 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2831 !!! WARNING: ADP 662 has a net charge of -2.0000 !!! WARNING: MG6 664 has a net charge of 1.4000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.566197 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): -9.833000 52.59400 ymin,ymax (A): -16.13300 34.29700 zmin,zma (A): 77.46200 129.2770 x,y,z range (A): 62.42700 50.43000 51.81501 scale (grids/A): 2.566197 object centre (A): 21.38050 9.081999 103.3695 number of atom coordinates read : 2831 total number of charged atoms : 2688 net assigned charge : -2.099993 assigned positive charge : 440.3312 centred at (gu) : 101.0510 87.93687 87.60035 assigned negative charge : -442.4323 centred at (gu) : 100.4473 88.29771 87.94642 start vw surface at 0.1300000 fill in re-entrant regions at 0.4500000 boundary points on vw surface= 153097 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26870 grid for indexing accessible points = 1.400000 m= 71934 mr = 107043 m= 23248 mr = 55708 m= 4767 mr = 17343 m= 418 mr = 3295 m= 6 mr = 207 m= 0 mr = 0 time to grow re-entrant surface = 0.8500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.400000 number of dielectric boundary points 69874 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 15 iepsmp to db, and charging done at 1.530000 number of grid points assigned charge 21494 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) : 1.710798 object centre at (A) : 21.38050 9.081999 103.3695 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -8.7425336E-02 -0.2944768 midg,1,midg; midg,igrid,midg -3.3231270E-02 -0.1656964 1,midg,midg; igrid,midg,midg 0.3331321 0.5156595 gauss-seidel spectral radius is 0.9991859 estimated iterations to convergence 277 setup time was (sec) 1.740000 now iterating at: 14:37:49 rms-change max change #iterations 9.374054 314.9653 at 10iterations 5.376312 147.3199 at 20iterations 3.067253 73.16869 at 30iterations 1.738341 36.79343 at 40iterations 0.9832760 23.06692 at 50iterations 0.5540704 12.38792 at 60iterations 0.3115162 6.400129 at 70iterations 0.1749938 3.554039 at 80iterations 9.8188683E-02 1.886262 at 90iterations 5.5025134E-02 1.075485 at 100iterations 3.0899322E-02 0.5879498 at 110iterations 1.7277660E-02 0.3830128 at 120iterations 9.6775610E-03 0.1979408 at 130iterations 5.4073283E-03 0.1110554 at 140iterations 3.0323758E-03 6.5883160E-02 at 150iterations 1.6921704E-03 3.3729553E-02 at 160iterations 9.4748329E-04 1.9063167E-02 at 170iterations 5.3150725E-04 1.0906279E-02 at 180iterations finished qdiffx linear iterations at : 14:38:08 total time elapsed so far: 20.00000 # loops : 180 mean,max change (kT/e) : 5.3150725E-04 1.0906279E-02 energy calculations done at 20.00000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 20.17000 DelPhi exited at 14:38:08 20.172u 0.473s 0:21.06 98.0% 0+0k 0+0io 0pf+0w