Sat Oct 8 16:39:23 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 Sat Oct 8 2011 at 16:39:23 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: 342 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4603 !!! WARNING: FAD 994 has a net charge of -2.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1200000 grid size : 179 scale,in grids/A, set to be: 0.5451261 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): 17.13400 79.06300 ymin,ymax (A): 120.8130 186.1190 zmin,zma (A): -1.854000 59.74800 x,y,z range (A): 61.92900 65.30598 61.60200 scale (grids/A): 0.5451261 object centre (A): 48.09850 153.4660 28.94700 number of atom coordinates read : 4603 total number of charged atoms : 4401 net assigned charge : 2.000036 assigned positive charge : 703.8495 centred at (gu) : 91.75462 89.27962 87.21796 assigned negative charge : -701.8529 centred at (gu) : 91.69277 89.20390 87.23811 start vw surface at 0.1900000 fill in re-entrant regions at 0.2000000 boundary points on vw surface= 8788 nv = 96 ne = 84 npr = 92620 no. pairs analyzed = 92620 no. exposed pairs = 5601 no. arc points = 38961 no. surface atoms = 1893 nbur = 2710 mkacc time = 0.2100000 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 = 1.568000 m= 386 mr = 4670 m= 0 mr = 34 time to grow re-entrant surface = 0.2400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4400000 number of dielectric boundary points 4470 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4032 ## 521 charges are in solution ## iepsmp to db, and charging done at 0.5400000 number of grid points assigned charge 11657 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 6.2038119E-10 -4.6009311E-11 midg,1,midg; midg,igrid,midg -7.9198409E-10 7.1681427E-10 1,midg,midg; igrid,midg,midg -3.3245287E-10 1.1238168E-09 gauss-seidel spectral radius is 0.9827729 estimated iterations to convergence 63 setup time was (sec) 0.6500000 now iterating at: 16:39:24 rms-change max change #iterations 9.2588283E-02 13.78242 at 10iterations 6.4459569E-03 0.9347229 at 20iterations 6.9372240E-04 0.1028671 at 30iterations 1.7025357E-04 2.5573730E-02 at 40iterations 5.1297397E-05 7.0343018E-03 at 50iterations finished qdiffx linear iterations at : 16:39:26 total time elapsed so far: 3.060000 # loops : 50 mean,max change (kT/e) : 5.1297397E-05 7.0343018E-03 energy calculations done at 3.060000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.230000 DelPhi exited at 16:39:27 3.234u 0.141s 0:03.80 88.6% 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 16:39:27 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: 342 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4603 !!! WARNING: FAD 994 has a net charge of -2.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1100000 grid size : 179 scale,in grids/A, set to be: 1.635378 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): 17.13400 79.06300 ymin,ymax (A): 120.8130 186.1190 zmin,zma (A): -1.854000 59.74800 x,y,z range (A): 61.92900 65.30598 61.60200 scale (grids/A): 1.635378 object centre (A): 48.09850 153.4660 28.94700 number of atom coordinates read : 4603 total number of charged atoms : 4401 net assigned charge : 2.000036 assigned positive charge : 703.8495 centred at (gu) : 95.26277 87.83762 81.65260 assigned negative charge : -701.8529 centred at (gu) : 95.07809 87.61123 81.71410 start vw surface at 0.2000000 fill in re-entrant regions at 0.3200000 boundary points on vw surface= 98774 reading accessible surface arcs data from file ARCDAT no. of arc points read = 38961 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 31252 mr = 68821 m= 3566 mr = 21630 m= 101 mr = 1893 m= 1 mr = 15 m= 0 mr = 0 time to grow re-entrant surface = 0.3000000 no. cavity mid-points inaccessible to solvent = 85 time to turn everything in is 0.6600000 number of dielectric boundary points 41335 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 452 ## 6 charges are in solution ## iepsmp to db, and charging done at 0.7800000 number of grid points assigned charge 33741 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) : 0.5451261 object centre at (A) : 48.09850 153.4660 28.94700 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.3414696E-03 9.6686324E-03 midg,1,midg; midg,igrid,midg 1.6443992E-02 3.2003738E-02 1,midg,midg; igrid,midg,midg -1.9707955E-02 -1.5015918E-02 gauss-seidel spectral radius is 0.9983465 estimated iterations to convergence 195 setup time was (sec) 0.9400000 now iterating at: 16:39:28 rms-change max change #iterations 4.353445 202.7613 at 10iterations 1.878465 83.15045 at 20iterations 0.8135301 29.64230 at 30iterations 0.3525671 12.14841 at 40iterations 0.1530297 4.514172 at 50iterations 6.6464417E-02 2.052216 at 60iterations 2.9017234E-02 0.8656902 at 70iterations 1.2640155E-02 0.3998156 at 80iterations 5.5196821E-03 0.1566000 at 90iterations 2.4259321E-03 6.8672180E-02 at 100iterations 1.0860822E-03 3.4721375E-02 at 110iterations 4.9804669E-04 1.4812469E-02 at 120iterations finished qdiffx linear iterations at : 16:39:34 total time elapsed so far: 6.980000 # loops : 120 mean,max change (kT/e) : 4.9804669E-04 1.4812469E-02 energy calculations done at 6.980000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.160000 DelPhi exited at 16:39:35 7.159u 0.144s 0:07.60 95.9% 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 Sat Oct 8 2011 at 16:39:35 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: 342 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4603 !!! WARNING: FAD 994 has a net charge of -2.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1100000 grid size : 179 scale,in grids/A, set to be: 2.453068 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): 17.13400 79.06300 ymin,ymax (A): 120.8130 186.1190 zmin,zma (A): -1.854000 59.74800 x,y,z range (A): 61.92900 65.30598 61.60200 scale (grids/A): 2.453068 object centre (A): 48.09850 153.4660 28.94700 number of atom coordinates read : 4603 total number of charged atoms : 4401 net assigned charge : 2.000036 assigned positive charge : 703.8495 centred at (gu) : 97.89365 86.75629 77.47855 assigned negative charge : -701.8529 centred at (gu) : 97.61704 86.41679 77.57114 start vw surface at 0.2000000 fill in re-entrant regions at 0.5400000 boundary points on vw surface= 229638 reading accessible surface arcs data from file ARCDAT no. of arc points read = 38961 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 107984 mr = 168092 m= 31418 mr = 85958 m= 5596 mr = 23628 m= 440 mr = 3791 m= 12 mr = 232 m= 0 mr = 0 time to grow re-entrant surface = 0.9400001 no. cavity mid-points inaccessible to solvent = 278 time to turn everything in is 1.590000 number of dielectric boundary points 93387 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 34 iepsmp to db, and charging done at 1.730000 number of grid points assigned charge 35162 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) : 1.635378 object centre at (A) : 48.09850 153.4660 28.94700 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.7583270E-03 0.2261920 midg,1,midg; midg,igrid,midg 0.2845743 0.4912108 1,midg,midg; igrid,midg,midg -0.3595922 -0.2238623 gauss-seidel spectral radius is 0.9992194 estimated iterations to convergence 283 setup time was (sec) 1.890000 now iterating at: 16:39:37 rms-change max change #iterations 11.25277 448.2037 at 10iterations 6.536956 147.5861 at 20iterations 3.778799 85.25275 at 30iterations 2.172321 51.73966 at 40iterations 1.243848 23.81661 at 50iterations 0.7087984 13.01304 at 60iterations 0.4052451 6.870297 at 70iterations 0.2300234 4.042862 at 80iterations 0.1306366 2.248342 at 90iterations 7.4226178E-02 1.258004 at 100iterations 4.2136930E-02 0.6929388 at 110iterations 2.3928221E-02 0.4109607 at 120iterations 1.3556032E-02 0.2477264 at 130iterations 7.6680942E-03 0.1218224 at 140iterations 4.3490296E-03 7.5546265E-02 at 150iterations 2.4612672E-03 4.6248913E-02 at 160iterations 1.3978095E-03 2.3422241E-02 at 170iterations 7.9418498E-04 1.2603760E-02 at 180iterations finished qdiffx linear iterations at : 16:39:46 total time elapsed so far: 11.58000 # loops : 180 mean,max change (kT/e) : 7.9418498E-04 1.2603760E-02 energy calculations done at 11.58000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.74000 DelPhi exited at 16:39:47 11.743u 0.174s 0:12.20 97.6% 0+0k 0+0io 0pf+0w