Mon Oct 10 14:00:12 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 14:00:12 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: 283 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3789 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: 0.5749912 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): -28.75600 27.60700 ymin,ymax (A): 56.01800 117.9320 zmin,zma (A): 2.012000 62.26500 x,y,z range (A): 56.36300 61.91400 60.25300 scale (grids/A): 0.5749912 object centre (A): -0.5745001 86.97500 32.13850 number of atom coordinates read : 3789 total number of charged atoms : 3635 net assigned charge : -8.999967 assigned positive charge : 569.4893 centred at (gu) : 89.63409 90.05365 92.29228 assigned negative charge : -578.4918 centred at (gu) : 89.58720 90.04967 92.28781 start vw surface at 0.1100000 fill in re-entrant regions at 0.1100000 boundary points on vw surface= 8313 nv = 96 ne = 84 npr = 75086 no. pairs analyzed = 75086 no. exposed pairs = 5047 no. arc points = 36161 no. surface atoms = 1658 nbur = 2131 mkacc time = 0.1200000 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 = 1.484000 m= 383 mr = 4280 m= 2 mr = 13 m= 0 mr = 0 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2600000 number of dielectric boundary points 4405 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3507 ## 385 charges are in solution ## iepsmp to db, and charging done at 0.3200000 number of grid points assigned charge 10662 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.0393855E-09 -2.5973046E-09 midg,1,midg; midg,igrid,midg -1.7126609E-09 -1.5609792E-09 1,midg,midg; igrid,midg,midg -3.0213025E-09 -4.7810639E-10 gauss-seidel spectral radius is 0.9844634 estimated iterations to convergence 66 setup time was (sec) 0.4400000 now iterating at: 14:00:13 rms-change max change #iterations 0.1081794 13.87554 at 10iterations 8.4009506E-03 1.333191 at 20iterations 8.0635981E-04 0.1206951 at 30iterations 1.7113927E-04 2.5177002E-02 at 40iterations 5.5161268E-05 8.2674026E-03 at 50iterations finished qdiffx linear iterations at : 14:00:16 total time elapsed so far: 3.280000 # loops : 50 mean,max change (kT/e) : 5.5161268E-05 8.2674026E-03 energy calculations done at 3.280000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.420000 DelPhi exited at 14:00:17 3.419u 0.209s 0:04.63 77.9% 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 14:00:17 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: 283 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3789 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: 1.724973 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): -28.75600 27.60700 ymin,ymax (A): 56.01800 117.9320 zmin,zma (A): 2.012000 62.26500 x,y,z range (A): 56.36300 61.91400 60.25300 scale (grids/A): 1.724973 object centre (A): -0.5745001 86.97500 32.13850 number of atom coordinates read : 3789 total number of charged atoms : 3635 net assigned charge : -8.999967 assigned positive charge : 569.4893 centred at (gu) : 88.90067 90.15975 96.87533 assigned negative charge : -578.4918 centred at (gu) : 88.76128 90.14870 96.86308 start vw surface at 0.1000000 fill in re-entrant regions at 0.1900000 boundary points on vw surface= 91178 reading accessible surface arcs data from file ARCDAT no. of arc points read = 36161 grid for indexing accessible points = 1.400000 m= 29849 mr = 61604 m= 3737 mr = 20389 m= 148 mr = 1752 m= 4 mr = 13 m= 0 mr = 0 time to grow re-entrant surface = 0.2100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4300000 number of dielectric boundary points 41158 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 340 ## 2 charges are in solution ## iepsmp to db, and charging done at 0.5100000 number of grid points assigned charge 28179 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) : 0.5749912 object centre at (A) : -0.5745001 86.97500 32.13850 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.6675171E-02 -3.2146297E-02 midg,1,midg; midg,igrid,midg -8.2512554E-03 -1.9221392E-03 1,midg,midg; igrid,midg,midg -2.8057495E-02 -1.9396463E-02 gauss-seidel spectral radius is 0.9984785 estimated iterations to convergence 203 setup time was (sec) 0.6400000 now iterating at: 14:00:18 rms-change max change #iterations 4.401223 165.2941 at 10iterations 1.960158 66.77586 at 20iterations 0.8797040 28.15158 at 30iterations 0.3945198 11.73736 at 40iterations 0.1767749 5.959940 at 50iterations 7.9346083E-02 2.499993 at 60iterations 3.5641618E-02 1.159273 at 70iterations 1.6050819E-02 0.4955692 at 80iterations 7.2553158E-03 0.2269783 at 90iterations 3.2664475E-03 0.1018944 at 100iterations 1.4813901E-03 4.6875000E-02 at 110iterations 6.8136648E-04 2.0771027E-02 at 120iterations finished qdiffx linear iterations at : 14:00:25 total time elapsed so far: 7.770000 # loops : 120 mean,max change (kT/e) : 6.8136648E-04 2.0771027E-02 energy calculations done at 7.770000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.900000 DelPhi exited at 14:00:27 7.905u 0.210s 0:09.56 84.8% 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 14:00:28 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: 283 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3789 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: 2.587460 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): -28.75600 27.60700 ymin,ymax (A): 56.01800 117.9320 zmin,zma (A): 2.012000 62.26500 x,y,z range (A): 56.36300 61.91400 60.25300 scale (grids/A): 2.587460 object centre (A): -0.5745001 86.97500 32.13850 number of atom coordinates read : 3789 total number of charged atoms : 3635 net assigned charge : -8.999967 assigned positive charge : 569.4893 centred at (gu) : 88.35098 90.23945 100.3126 assigned negative charge : -578.4918 centred at (gu) : 88.14185 90.22291 100.2942 start vw surface at 0.1100000 fill in re-entrant regions at 0.3700000 boundary points on vw surface= 211278 reading accessible surface arcs data from file ARCDAT no. of arc points read = 36161 grid for indexing accessible points = 1.400000 m= 100688 mr = 150447 m= 31333 mr = 79276 m= 6013 mr = 23240 m= 554 mr = 3790 m= 17 mr = 196 m= 0 mr = 0 time to grow re-entrant surface = 0.6300001 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.100000 number of dielectric boundary points 92934 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 10 iepsmp to db, and charging done at 1.210000 number of grid points assigned charge 29069 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) : 1.724973 object centre at (A) : -0.5745001 86.97500 32.13850 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.2423372 -0.5392665 midg,1,midg; midg,igrid,midg -9.2002802E-02 0.1965556 1,midg,midg; igrid,midg,midg -0.4164375 -0.2211419 gauss-seidel spectral radius is 0.9992599 estimated iterations to convergence 290 setup time was (sec) 1.340000 now iterating at: 14:00:30 rms-change max change #iterations 11.07356 305.6554 at 10iterations 6.565244 158.6126 at 20iterations 3.861990 85.70470 at 30iterations 2.265003 49.34948 at 40iterations 1.320568 27.10305 at 50iterations 0.7675565 15.29873 at 60iterations 0.4451504 8.447815 at 70iterations 0.2578123 4.691933 at 80iterations 0.1492917 2.503513 at 90iterations 8.6142324E-02 1.688902 at 100iterations 4.9656674E-02 0.8735108 at 110iterations 2.8638471E-02 0.4885254 at 120iterations 1.6530143E-02 0.2777977 at 130iterations 9.5308768E-03 0.1604758 at 140iterations 5.5093374E-03 0.1136389 at 150iterations 3.1849416E-03 6.4552546E-02 at 160iterations 1.8471829E-03 3.1082153E-02 at 170iterations 1.0771785E-03 1.9854069E-02 at 180iterations finished qdiffx linear iterations at : 14:00:42 total time elapsed so far: 12.96000 # loops : 180 mean,max change (kT/e) : 1.0771785E-03 1.9854069E-02 energy calculations done at 12.96000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.09000 DelPhi exited at 14:00:43 13.095u 0.221s 0:15.01 88.6% 0+0k 0+0io 0pf+0w