Sat Oct 8 23:36:54 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 23:36:54 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: 269 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2451 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: 0.6486408 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): 56.38000 99.50300 ymin,ymax (A): 30.75100 85.63500 zmin,zma (A): 25.99700 80.07500 x,y,z range (A): 43.12300 54.88400 54.07800 scale (grids/A): 0.6486408 object centre (A): 77.94150 58.19300 53.03600 number of atom coordinates read : 2451 total number of charged atoms : 2315 net assigned charge : 11.50002 assigned positive charge : 359.5943 centred at (gu) : 89.60910 89.13028 90.72295 assigned negative charge : -348.0950 centred at (gu) : 89.68674 89.20186 90.68705 start vw surface at 9.0000004E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 7131 nv = 96 ne = 84 npr = 48877 no. pairs analyzed = 48877 no. exposed pairs = 3189 no. arc points = 22298 no. surface atoms = 1081 nbur = 1370 mkacc time = 9.0000004E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 436 mr = 3815 m= 2 mr = 77 m= 0 mr = 0 time to grow re-entrant surface = 9.9999994E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.1900000 number of dielectric boundary points 3677 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2171 ## 196 charges are in solution ## iepsmp to db, and charging done at 0.2600000 number of grid points assigned charge 8280 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.4234568E-08 3.0093570E-08 midg,1,midg; midg,igrid,midg 3.6641758E-08 9.8764756E-09 1,midg,midg; igrid,midg,midg 3.4008512E-08 1.0084409E-08 gauss-seidel spectral radius is 0.9876783 estimated iterations to convergence 74 setup time was (sec) 0.3800000 now iterating at: 23:36:55 rms-change max change #iterations 0.1480415 22.30250 at 10iterations 1.4947628E-02 2.259312 at 20iterations 1.6014845E-03 0.2332611 at 30iterations 2.2924831E-04 3.5575867E-02 at 40iterations 5.3802363E-05 9.5806122E-03 at 50iterations finished qdiffx linear iterations at : 23:36:58 total time elapsed so far: 3.230000 # loops : 50 mean,max change (kT/e) : 5.3802363E-05 9.5806122E-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) 3.360000 DelPhi exited at 23:36:58 3.359u 0.173s 0:03.81 92.3% 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 23:36:58 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: 269 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2451 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: 1.945922 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): 56.38000 99.50300 ymin,ymax (A): 30.75100 85.63500 zmin,zma (A): 25.99700 80.07500 x,y,z range (A): 43.12300 54.88400 54.07800 scale (grids/A): 1.945922 object centre (A): 77.94150 58.19300 53.03600 number of atom coordinates read : 2451 total number of charged atoms : 2315 net assigned charge : 11.50002 assigned positive charge : 359.5943 centred at (gu) : 88.82684 87.39046 92.16873 assigned negative charge : -348.0950 centred at (gu) : 89.06001 87.60559 92.06097 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 75689 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22298 grid for indexing accessible points = 1.400000 m= 29291 mr = 51517 m= 5356 mr = 21850 m= 379 mr = 3506 m= 3 mr = 173 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 0.3800000 number of dielectric boundary points 33672 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 125 iepsmp to db, and charging done at 0.4600000 number of grid points assigned charge 18297 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) : 0.6486408 object centre at (A) : 77.94150 58.19300 53.03600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.1593446E-02 5.5740830E-02 midg,1,midg; midg,igrid,midg 3.9688613E-02 5.8502659E-02 1,midg,midg; igrid,midg,midg 2.6871148E-02 8.1963399E-03 gauss-seidel spectral radius is 0.9986845 estimated iterations to convergence 218 setup time was (sec) 0.6100000 now iterating at: 23:36:59 rms-change max change #iterations 4.163683 249.2869 at 10iterations 1.973907 74.45786 at 20iterations 0.9363226 36.13760 at 30iterations 0.4441179 13.91823 at 40iterations 0.2112678 6.688126 at 50iterations 0.1001791 3.422376 at 60iterations 4.7599576E-02 1.502739 at 70iterations 2.2632262E-02 0.7289429 at 80iterations 1.0782492E-02 0.3606541 at 90iterations 5.1569561E-03 0.2024345 at 100iterations 2.4645824E-03 7.1140289E-02 at 110iterations 1.2018747E-03 3.9101779E-02 at 120iterations finished qdiffx linear iterations at : 23:37:06 total time elapsed so far: 7.680000 # loops : 120 mean,max change (kT/e) : 1.2018747E-03 3.9101779E-02 energy calculations done at 7.680000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.810000 DelPhi exited at 23:37:06 7.812u 0.195s 0:08.33 96.0% 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 Sat Oct 8 2011 at 23:37:07 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: 269 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2451 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: 2.918883 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): 56.38000 99.50300 ymin,ymax (A): 30.75100 85.63500 zmin,zma (A): 25.99700 80.07500 x,y,z range (A): 43.12300 54.88400 54.07800 scale (grids/A): 2.918883 object centre (A): 77.94150 58.19300 53.03600 number of atom coordinates read : 2451 total number of charged atoms : 2315 net assigned charge : 11.50002 assigned positive charge : 359.5943 centred at (gu) : 88.24021 86.08557 93.25299 assigned negative charge : -348.0950 centred at (gu) : 88.59001 86.40843 93.09132 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.3200000 boundary points on vw surface= 174202 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22298 grid for indexing accessible points = 1.400000 m= 91080 mr = 124477 m= 36860 mr = 74551 m= 9931 mr = 30124 m= 1623 mr = 7636 m= 146 mr = 1165 m= 4 mr = 96 m= 0 mr = 0 time to grow re-entrant surface = 0.5800000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.9800000 number of dielectric boundary points 75797 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.070000 number of grid points assigned charge 18519 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) : 1.945922 object centre at (A) : 77.94150 58.19300 53.03600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.3118185 0.4575021 midg,1,midg; midg,igrid,midg 0.4080097 0.7667122 1,midg,midg; igrid,midg,midg 0.2302785 8.3699793E-02 gauss-seidel spectral radius is 0.9992777 estimated iterations to convergence 294 setup time was (sec) 1.220000 now iterating at: 23:37:08 rms-change max change #iterations 9.837437 428.2007 at 10iterations 5.819173 144.1349 at 20iterations 3.429862 77.30872 at 30iterations 2.006346 41.65197 at 40iterations 1.172057 23.73414 at 50iterations 0.6840647 14.70584 at 60iterations 0.3999533 7.488766 at 70iterations 0.2320924 4.237391 at 80iterations 0.1348929 2.672023 at 90iterations 7.8337669E-02 1.523085 at 100iterations 4.5462742E-02 0.8716373 at 110iterations 2.6408173E-02 0.4825325 at 120iterations 1.5297675E-02 0.2869835 at 130iterations 8.8762883E-03 0.1558228 at 140iterations 5.1406953E-03 9.3605042E-02 at 150iterations 2.9836553E-03 5.6609154E-02 at 160iterations 1.7347395E-03 3.1785965E-02 at 170iterations 1.0114950E-03 1.9212723E-02 at 180iterations finished qdiffx linear iterations at : 23:37:21 total time elapsed so far: 13.87000 # loops : 180 mean,max change (kT/e) : 1.0114950E-03 1.9212723E-02 energy calculations done at 13.87000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 14.00000 DelPhi exited at 23:37:21 14.001u 0.217s 0:14.49 98.0% 0+0k 0+0io 0pf+0w