Mon Oct 10 14:40:36 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 Mon Oct 10 2011 at 14:40:36 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: 315 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2862 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 0.6252195 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): 6.319000 58.01800 ymin,ymax (A): -17.64900 39.29100 zmin,zma (A): 39.56000 88.61200 x,y,z range (A): 51.69900 56.94000 49.05200 scale (grids/A): 0.6252195 object centre (A): 32.16850 10.82100 64.08600 number of atom coordinates read : 2862 total number of charged atoms : 2712 net assigned charge : -2.999973 assigned positive charge : 442.3012 centred at (gu) : 89.80387 89.60756 90.94270 assigned negative charge : -445.3020 centred at (gu) : 89.98080 89.72326 90.71475 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1000000 boundary points on vw surface= 7417 nv = 96 ne = 84 npr = 58585 no. pairs analyzed = 58585 no. exposed pairs = 3389 no. arc points = 23872 no. surface atoms = 1145 nbur = 1717 mkacc time = 0.1000000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 391 mr = 4216 m= 2 mr = 36 m= 0 mr = 0 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 30 time to turn everything in is 0.2200000 number of dielectric boundary points 3558 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2405 ## 229 charges are in solution ## iepsmp to db, and charging done at 0.2800000 number of grid points assigned charge 9160 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.9333745E-08 2.0574374E-08 midg,1,midg; midg,igrid,midg 7.7114199E-09 -1.2348490E-08 1,midg,midg; igrid,midg,midg 1.2861597E-08 -1.8260783E-08 gauss-seidel spectral radius is 0.9867696 estimated iterations to convergence 71 setup time was (sec) 0.4000000 now iterating at: 14:40:36 rms-change max change #iterations 0.1432767 20.17328 at 10iterations 1.3534101E-02 1.733687 at 20iterations 1.3098551E-03 0.1671715 at 30iterations 1.7452601E-04 2.6787758E-02 at 40iterations 4.9103444E-05 9.5300674E-03 at 50iterations finished qdiffx linear iterations at : 14:40:40 total time elapsed so far: 3.620000 # loops : 50 mean,max change (kT/e) : 4.9103444E-05 9.5300674E-03 energy calculations done at 3.620000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.740000 DelPhi exited at 14:40:40 3.748u 0.178s 0:04.25 92.0% 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 14:40:40 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: 315 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2862 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 1.875659 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): 6.319000 58.01800 ymin,ymax (A): -17.64900 39.29100 zmin,zma (A): 39.56000 88.61200 x,y,z range (A): 51.69900 56.94000 49.05200 scale (grids/A): 1.875659 object centre (A): 32.16850 10.82100 64.08600 number of atom coordinates read : 2862 total number of charged atoms : 2712 net assigned charge : -2.999973 assigned positive charge : 442.3012 centred at (gu) : 89.41059 88.82186 92.82734 assigned negative charge : -445.3020 centred at (gu) : 89.94184 89.16943 92.14375 start vw surface at 0.1000000 fill in re-entrant regions at 0.1900000 boundary points on vw surface= 81001 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23872 grid for indexing accessible points = 1.400000 m= 29180 mr = 57608 m= 4213 mr = 21679 m= 196 mr = 2593 m= 4 mr = 35 m= 0 mr = 0 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 2765 time to turn everything in is 0.4100000 number of dielectric boundary points 32679 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 162 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.4900000 number of grid points assigned charge 21281 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) : 0.6252195 object centre at (A) : 32.16850 10.82100 64.08600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -5.7071984E-02 2.7915917E-02 midg,1,midg; midg,igrid,midg 0.1087865 -7.9319989E-03 1,midg,midg; igrid,midg,midg -7.8620920E-03 -4.7856990E-02 gauss-seidel spectral radius is 0.9986152 estimated iterations to convergence 213 setup time was (sec) 0.6200000 now iterating at: 14:40:41 rms-change max change #iterations 4.477930 174.1238 at 10iterations 2.081864 70.99223 at 20iterations 0.9755316 29.70114 at 30iterations 0.4549567 15.78564 at 40iterations 0.2129210 6.898520 at 50iterations 9.9272266E-02 3.127626 at 60iterations 4.6274800E-02 1.420835 at 70iterations 2.1669332E-02 0.6988468 at 80iterations 1.0140487E-02 0.3225060 at 90iterations 4.7562243E-03 0.1492825 at 100iterations 2.2311136E-03 7.0571899E-02 at 110iterations 1.0565122E-03 3.7990570E-02 at 120iterations finished qdiffx linear iterations at : 14:40:48 total time elapsed so far: 7.730000 # loops : 120 mean,max change (kT/e) : 1.0565122E-03 3.7990570E-02 energy calculations done at 7.730000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.860000 DelPhi exited at 14:40:49 7.866u 0.191s 0:08.51 94.5% 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 14:40:49 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: 315 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2862 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 2.813488 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): 6.319000 58.01800 ymin,ymax (A): -17.64900 39.29100 zmin,zma (A): 39.56000 88.61200 x,y,z range (A): 51.69900 56.94000 49.05200 scale (grids/A): 2.813488 object centre (A): 32.16850 10.82100 64.08600 number of atom coordinates read : 2862 total number of charged atoms : 2712 net assigned charge : -2.999973 assigned positive charge : 442.3012 centred at (gu) : 89.11576 88.23276 94.24072 assigned negative charge : -445.3020 centred at (gu) : 89.91272 88.75408 93.21553 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.3500000 boundary points on vw surface= 187685 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23872 grid for indexing accessible points = 1.400000 m= 95850 mr = 139581 m= 33729 mr = 79129 m= 7355 mr = 27107 m= 850 mr = 5401 m= 26 mr = 523 m= 0 mr = 2 time to grow re-entrant surface = 0.5800000 no. cavity mid-points inaccessible to solvent = 9084 time to turn everything in is 1.020000 number of dielectric boundary points 73752 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.110000 number of grid points assigned charge 21695 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) : 1.875659 object centre at (A) : 32.16850 10.82100 64.08600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.7373754 0.2477823 midg,1,midg; midg,igrid,midg 1.108618 -0.1776184 1,midg,midg; igrid,midg,midg -0.1124505 -0.4003942 gauss-seidel spectral radius is 0.9992604 estimated iterations to convergence 290 setup time was (sec) 1.250000 now iterating at: 14:40:50 rms-change max change #iterations 10.56120 366.4828 at 10iterations 6.190186 142.4508 at 20iterations 3.615185 72.05592 at 30iterations 2.104365 38.93326 at 40iterations 1.220642 23.54293 at 50iterations 0.7080394 12.66386 at 60iterations 0.4098360 8.456833 at 70iterations 0.2371297 4.014787 at 80iterations 0.1368474 2.334122 at 90iterations 7.8924976E-02 1.372798 at 100iterations 4.5447633E-02 0.8182192 at 110iterations 2.6228594E-02 0.4618950 at 120iterations 1.5104094E-02 0.2658437 at 130iterations 8.7048775E-03 0.1503162 at 140iterations 5.0042402E-03 8.5929871E-02 at 150iterations 2.8836583E-03 4.9820662E-02 at 160iterations 1.6598144E-03 3.1793594E-02 at 170iterations 9.5798139E-04 1.8299103E-02 at 180iterations finished qdiffx linear iterations at : 14:41:02 total time elapsed so far: 12.66000 # loops : 180 mean,max change (kT/e) : 9.5798139E-04 1.8299103E-02 energy calculations done at 12.66000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.78000 DelPhi exited at 14:41:02 12.786u 0.214s 0:13.49 96.2% 0+0k 0+0io 0pf+0w