Sun Oct 9 11:50:33 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 Sun Oct 9 2011 at 11:50:33 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2673 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 0.6444605 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): -5.956000 47.77400 ymin,ymax (A): 9.246000 59.30900 zmin,zma (A): 4.737000 59.97700 x,y,z range (A): 53.73000 50.06300 55.24000 scale (grids/A): 0.6444605 object centre (A): 20.90900 34.27750 32.35700 number of atom coordinates read : 2673 total number of charged atoms : 2599 net assigned charge : 1.000013 assigned positive charge : 396.8511 centred at (gu) : 90.83791 90.08575 91.51471 assigned negative charge : -395.8527 centred at (gu) : 90.85928 90.10004 91.44887 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 7874 nv = 96 ne = 84 npr = 51170 no. pairs analyzed = 51170 no. exposed pairs = 3840 no. arc points = 27338 no. surface atoms = 1277 nbur = 1396 mkacc time = 0.1100000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 453 mr = 3899 m= 0 mr = 63 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2900000 number of dielectric boundary points 4365 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2498 ## 193 charges are in solution ## iepsmp to db, and charging done at 0.3900000 number of grid points assigned charge 9206 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -5.2851981E-09 1.4281692E-08 midg,1,midg; midg,igrid,midg 3.3758889E-09 -3.9540976E-10 1,midg,midg; igrid,midg,midg 3.6714134E-09 -1.6272839E-09 gauss-seidel spectral radius is 0.9875525 estimated iterations to convergence 73 setup time was (sec) 0.5100000 now iterating at: 11:50:33 rms-change max change #iterations 0.1461474 26.20554 at 10iterations 1.4863558E-02 2.195614 at 20iterations 1.4854386E-03 0.2165241 at 30iterations 1.4986207E-04 2.0142555E-02 at 40iterations 1.7021059E-05 2.1018982E-03 at 50iterations finished qdiffx linear iterations at : 11:50:36 total time elapsed so far: 2.910000 # loops : 50 mean,max change (kT/e) : 1.7021059E-05 2.1018982E-03 energy calculations done at 2.910000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.080000 DelPhi exited at 11:50:36 3.083u 0.149s 0:03.49 92.2% 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 Sun Oct 9 2011 at 11:50:36 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2673 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 1.933382 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): -5.956000 47.77400 ymin,ymax (A): 9.246000 59.30900 zmin,zma (A): 4.737000 59.97700 x,y,z range (A): 53.73000 50.06300 55.24000 scale (grids/A): 1.933382 object centre (A): 20.90900 34.27750 32.35700 number of atom coordinates read : 2673 total number of charged atoms : 2599 net assigned charge : 1.000013 assigned positive charge : 396.8511 centred at (gu) : 92.51292 90.25627 94.54372 assigned negative charge : -395.8527 centred at (gu) : 92.57790 90.29987 94.34655 start vw surface at 0.1500000 fill in re-entrant regions at 0.2600000 boundary points on vw surface= 83580 reading accessible surface arcs data from file ARCDAT no. of arc points read = 27338 grid for indexing accessible points = 1.400000 m= 29653 mr = 54844 m= 5271 mr = 20550 m= 366 mr = 3131 m= 8 mr = 137 m= 0 mr = 0 time to grow re-entrant surface = 0.2800000 no. cavity mid-points inaccessible to solvent = 108 time to turn everything in is 0.5700000 number of dielectric boundary points 40216 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 156 iepsmp to db, and charging done at 0.6900000 number of grid points assigned charge 20496 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) : 0.6444605 object centre at (A) : 20.90900 34.27750 32.35700 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -4.8469543E-03 2.7145173E-02 midg,1,midg; midg,igrid,midg -3.7386001E-04 4.1201450E-03 1,midg,midg; igrid,midg,midg -1.8137367E-02 -1.9168369E-03 gauss-seidel spectral radius is 0.9987144 estimated iterations to convergence 221 setup time was (sec) 0.8300000 now iterating at: 11:50:37 rms-change max change #iterations 4.438574 184.6443 at 10iterations 2.120376 72.46758 at 20iterations 1.012581 34.17884 at 30iterations 0.4836279 16.02794 at 40iterations 0.2322981 7.615597 at 50iterations 0.1112159 3.179704 at 60iterations 5.3116985E-02 1.506845 at 70iterations 2.5496986E-02 0.7641144 at 80iterations 1.2160545E-02 0.3896275 at 90iterations 5.8367997E-03 0.1984506 at 100iterations 2.7893386E-03 8.7326050E-02 at 110iterations 1.3377604E-03 4.3533325E-02 at 120iterations finished qdiffx linear iterations at : 11:50:43 total time elapsed so far: 6.820000 # loops : 120 mean,max change (kT/e) : 1.3377604E-03 4.3533325E-02 energy calculations done at 6.820000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 6.990000 DelPhi exited at 11:50:44 6.997u 0.175s 0:07.43 96.3% 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 Sun Oct 9 2011 at 11:50:44 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 = 2673 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 2.900072 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): -5.956000 47.77400 ymin,ymax (A): 9.246000 59.30900 zmin,zma (A): 4.737000 59.97700 x,y,z range (A): 53.73000 50.06300 55.24000 scale (grids/A): 2.900072 object centre (A): 20.90900 34.27750 32.35700 number of atom coordinates read : 2673 total number of charged atoms : 2599 net assigned charge : 1.000013 assigned positive charge : 396.8511 centred at (gu) : 93.76912 90.38425 96.81539 assigned negative charge : -395.8527 centred at (gu) : 93.86667 90.44975 96.51978 start vw surface at 0.1500000 fill in re-entrant regions at 0.4700000 boundary points on vw surface= 193326 reading accessible surface arcs data from file ARCDAT no. of arc points read = 27338 grid for indexing accessible points = 1.400000 m= 93988 mr = 134314 m= 35608 mr = 73755 m= 9752 mr = 27538 m= 1607 mr = 7096 m= 135 mr = 1020 m= 8 mr = 67 m= 0 mr = 0 time to grow re-entrant surface = 0.8600000 no. cavity mid-points inaccessible to solvent = 354 time to turn everything in is 1.440000 number of dielectric boundary points 90634 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.570000 number of grid points assigned charge 20792 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) : 1.933382 object centre at (A) : 20.90900 34.27750 32.35700 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.9289450E-02 0.3173918 midg,1,midg; midg,igrid,midg 3.9867342E-02 6.3956901E-02 1,midg,midg; igrid,midg,midg -0.2269169 0.2774476 gauss-seidel spectral radius is 0.9993085 estimated iterations to convergence 300 setup time was (sec) 1.730000 now iterating at: 11:50:46 rms-change max change #iterations 10.61397 394.9729 at 10iterations 6.429156 165.8859 at 20iterations 3.869084 77.59216 at 30iterations 2.315041 48.63214 at 40iterations 1.375679 27.42465 at 50iterations 0.8194528 16.51740 at 60iterations 0.4845878 9.851715 at 70iterations 0.2867478 5.437120 at 80iterations 0.1688329 3.214649 at 90iterations 9.9753499E-02 1.924179 at 100iterations 5.8709688E-02 1.112008 at 110iterations 3.4446564E-02 0.5857573 at 120iterations 2.0262240E-02 0.3635988 at 130iterations 1.1898298E-02 0.2424842 at 140iterations 6.9826525E-03 0.1396633 at 150iterations 4.1014175E-03 7.4898243E-02 at 160iterations 2.4107795E-03 4.3698311E-02 at 170iterations 1.4216352E-03 2.5228500E-02 at 180iterations finished qdiffx linear iterations at : 11:50:55 total time elapsed so far: 11.18000 # loops : 180 mean,max change (kT/e) : 1.4216352E-03 2.5228500E-02 energy calculations done at 11.18000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.35000 DelPhi exited at 11:50:56 11.350u 0.165s 0:11.81 97.4% 0+0k 0+0io 0pf+0w