Mon Oct 10 09:09:43 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 09:09:43 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 = 1962 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: 0.6325403 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): -35.04000 9.719001 ymin,ymax (A): -0.5870000 40.95700 zmin,zma (A): -0.9170000 55.36400 x,y,z range (A): 44.75900 41.54400 56.28100 scale (grids/A): 0.6325403 object centre (A): -12.66050 20.18500 27.22350 number of atom coordinates read : 1962 total number of charged atoms : 1819 net assigned charge : 3.000004 assigned positive charge : 286.2651 centred at (gu) : 90.62342 90.04582 90.53206 assigned negative charge : -283.2653 centred at (gu) : 90.53478 90.20045 90.52892 start vw surface at 0.1700000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 5286 nv = 96 ne = 84 npr = 40489 no. pairs analyzed = 40489 no. exposed pairs = 2459 no. arc points = 17140 no. surface atoms = 835 nbur = 1127 mkacc time = 8.9999989E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 304 mr = 2924 m= 1 mr = 32 m= 0 mr = 0 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2800000 number of dielectric boundary points 2635 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1677 ## 174 charges are in solution ## iepsmp to db, and charging done at 0.3900000 number of grid points assigned charge 6255 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.9294043E-09 4.1451207E-09 midg,1,midg; midg,igrid,midg 1.3888132E-08 -7.4922371E-09 1,midg,midg; igrid,midg,midg -2.3450848E-09 1.0960690E-08 gauss-seidel spectral radius is 0.9869965 estimated iterations to convergence 72 setup time was (sec) 0.5200000 now iterating at: 09:09:44 rms-change max change #iterations 0.1146908 18.76781 at 10iterations 1.1074934E-02 1.658028 at 20iterations 1.0554831E-03 0.1902847 at 30iterations 1.0022182E-04 1.6734362E-02 at 40iterations 9.5362730E-06 1.4839172E-03 at 50iterations finished qdiffx linear iterations at : 09:09:46 total time elapsed so far: 3.070000 # loops : 50 mean,max change (kT/e) : 9.5362730E-06 1.4839172E-03 energy calculations done at 3.070000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.240000 DelPhi exited at 09:09:47 3.245u 0.175s 0:03.69 92.4% 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 09:09:47 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1962 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: 1.897621 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): -35.04000 9.719001 ymin,ymax (A): -0.5870000 40.95700 zmin,zma (A): -0.9170000 55.36400 x,y,z range (A): 44.75900 41.54400 56.28100 scale (grids/A): 1.897621 object centre (A): -12.66050 20.18500 27.22350 number of atom coordinates read : 1962 total number of charged atoms : 1819 net assigned charge : 3.000004 assigned positive charge : 286.2651 centred at (gu) : 91.87043 90.13764 91.59610 assigned negative charge : -283.2653 centred at (gu) : 91.60459 90.60151 91.58686 start vw surface at 0.1300000 fill in re-entrant regions at 0.2000000 boundary points on vw surface= 56849 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17140 grid for indexing accessible points = 1.400000 m= 21227 mr = 39111 m= 3375 mr = 16092 m= 188 mr = 2164 m= 2 mr = 58 m= 0 mr = 0 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4200000 number of dielectric boundary points 24216 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 129 iepsmp to db, and charging done at 0.5400000 number of grid points assigned charge 14286 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) : 0.6325403 object centre at (A) : -12.66050 20.18500 27.22350 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.3533318E-02 3.3885218E-02 midg,1,midg; midg,igrid,midg 5.4192566E-03 -9.8823346E-03 1,midg,midg; igrid,midg,midg -4.2921505E-03 -1.3658243E-03 gauss-seidel spectral radius is 0.9985487 estimated iterations to convergence 208 setup time was (sec) 0.7000000 now iterating at: 09:09:48 rms-change max change #iterations 3.517394 167.2186 at 10iterations 1.613533 65.77698 at 20iterations 0.7383625 25.97414 at 30iterations 0.3376806 11.82906 at 40iterations 0.1543264 5.380630 at 50iterations 7.0678353E-02 2.563072 at 60iterations 3.2224707E-02 1.281757 at 70iterations 1.4768919E-02 0.5697384 at 80iterations 6.7190393E-03 0.2366829 at 90iterations 3.0809222E-03 0.1073475 at 100iterations 1.4059532E-03 5.4170609E-02 at 110iterations 6.4484187E-04 2.3539543E-02 at 120iterations finished qdiffx linear iterations at : 09:09:54 total time elapsed so far: 7.010000 # loops : 120 mean,max change (kT/e) : 6.4484187E-04 2.3539543E-02 energy calculations done at 7.010000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.190000 DelPhi exited at 09:09:54 7.188u 0.212s 0:07.68 96.2% 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 09:09:54 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1962 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: 2.846431 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): -35.04000 9.719001 ymin,ymax (A): -0.5870000 40.95700 zmin,zma (A): -0.9170000 55.36400 x,y,z range (A): 44.75900 41.54400 56.28100 scale (grids/A): 2.846431 object centre (A): -12.66050 20.18500 27.22350 number of atom coordinates read : 1962 total number of charged atoms : 1819 net assigned charge : 3.000004 assigned positive charge : 286.2651 centred at (gu) : 92.80558 90.20646 92.39421 assigned negative charge : -283.2653 centred at (gu) : 92.40696 90.90233 92.38036 start vw surface at 0.1300000 fill in re-entrant regions at 0.3600000 boundary points on vw surface= 131515 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17140 grid for indexing accessible points = 1.400000 m= 68171 mr = 94760 m= 25422 mr = 56434 m= 6075 mr = 20967 m= 853 mr = 4624 m= 57 mr = 602 m= 4 mr = 28 m= 0 mr = 2 time to grow re-entrant surface = 0.5800000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.040000 number of dielectric boundary points 54680 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.160000 number of grid points assigned charge 14543 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) : 1.897621 object centre at (A) : -12.66050 20.18500 27.22350 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 5.0816316E-02 0.1907557 midg,1,midg; midg,igrid,midg -2.6874898E-03 -0.1376632 1,midg,midg; igrid,midg,midg -7.4117981E-02 -6.6915303E-02 gauss-seidel spectral radius is 0.9992187 estimated iterations to convergence 282 setup time was (sec) 1.330000 now iterating at: 09:09:56 rms-change max change #iterations 8.252089 393.1484 at 10iterations 4.700609 97.55138 at 20iterations 2.663954 63.24239 at 30iterations 1.509633 44.14378 at 40iterations 0.8528821 20.81067 at 50iterations 0.4824652 9.923385 at 60iterations 0.2723328 5.670727 at 70iterations 0.1537818 3.295748 at 80iterations 8.6969815E-02 1.753708 at 90iterations 4.9108304E-02 0.9626455 at 100iterations 2.7840728E-02 0.5947456 at 110iterations 1.5671609E-02 0.3640203 at 120iterations 8.8677024E-03 0.1793213 at 130iterations 4.9958280E-03 9.8519325E-02 at 140iterations 2.8264329E-03 5.4008007E-02 at 150iterations 1.5953071E-03 3.1850815E-02 at 160iterations 9.0006622E-04 1.8250346E-02 at 170iterations 5.0870539E-04 1.1047363E-02 at 180iterations finished qdiffx linear iterations at : 09:10:06 total time elapsed so far: 11.36000 # loops : 180 mean,max change (kT/e) : 5.0870539E-04 1.1047363E-02 energy calculations done at 11.36000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.56000 DelPhi exited at 09:10:07 11.560u 0.229s 0:12.06 97.6% 0+0k 0+0io 0pf+0w