Tue Oct 11 04:45:34 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 Tue Oct 11 2011 at 04:45:34 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: 254 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2755 !!! WARNING: TYS 1 has a net charge of -0.3380 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1000000 grid size : 179 scale,in grids/A, set to be: 0.6465204 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): -11.90300 36.32700 ymin,ymax (A): -25.88500 22.49300 zmin,zma (A): -9.678000 45.38600 x,y,z range (A): 48.23000 48.37800 55.06400 scale (grids/A): 0.6465204 object centre (A): 12.21200 -1.696000 17.85400 number of atom coordinates read : 2755 total number of charged atoms : 2603 net assigned charge : 3.162012 assigned positive charge : 414.7707 centred at (gu) : 90.29682 90.56929 91.84948 assigned negative charge : -411.6093 centred at (gu) : 90.04517 90.38355 91.78949 start vw surface at 0.1900000 fill in re-entrant regions at 0.2000000 boundary points on vw surface= 7594 nv = 96 ne = 84 npr = 56645 no. pairs analyzed = 56645 no. exposed pairs = 3344 no. arc points = 23592 no. surface atoms = 1123 nbur = 1632 mkacc time = 0.1300000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 393 mr = 4256 m= 4 mr = 40 m= 0 mr = 0 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 43 time to turn everything in is 0.3500000 number of dielectric boundary points 3695 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2309 ## 228 charges are in solution ## iepsmp to db, and charging done at 0.4500000 number of grid points assigned charge 9182 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -2.4468982E-09 2.0626096E-08 midg,1,midg; midg,igrid,midg -2.0077547E-08 3.6033690E-08 1,midg,midg; igrid,midg,midg -3.0836567E-08 4.3836639E-08 gauss-seidel spectral radius is 0.9876120 estimated iterations to convergence 73 setup time was (sec) 0.5600000 now iterating at: 04:45:35 rms-change max change #iterations 0.1559681 19.84611 at 10iterations 1.6044073E-02 2.449783 at 20iterations 1.6635589E-03 0.2072945 at 30iterations 1.7076817E-04 3.2898903E-02 at 40iterations 1.8719014E-05 2.2530556E-03 at 50iterations finished qdiffx linear iterations at : 04:45:37 total time elapsed so far: 2.990000 # loops : 50 mean,max change (kT/e) : 1.8719014E-05 2.2530556E-03 energy calculations done at 2.990000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.210000 DelPhi exited at 04:45:38 3.214u 0.149s 0:04.05 82.7% 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 Tue Oct 11 2011 at 04:45:38 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: 254 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2755 !!! WARNING: TYS 1 has a net charge of -0.3380 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: 1.939561 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): -11.90300 36.32700 ymin,ymax (A): -25.88500 22.49300 zmin,zma (A): -9.678000 45.38600 x,y,z range (A): 48.23000 48.37800 55.06400 scale (grids/A): 1.939561 object centre (A): 12.21200 -1.696000 17.85400 number of atom coordinates read : 2755 total number of charged atoms : 2603 net assigned charge : 3.162012 assigned positive charge : 414.7707 centred at (gu) : 90.88996 91.70748 95.54781 assigned negative charge : -411.6093 centred at (gu) : 90.13509 91.15031 95.36824 start vw surface at 0.1800000 fill in re-entrant regions at 0.2900000 boundary points on vw surface= 81992 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23592 grid for indexing accessible points = 1.400000 m= 29922 mr = 57829 m= 4557 mr = 22100 m= 273 mr = 2806 m= 2 mr = 84 m= 0 mr = 0 time to grow re-entrant surface = 0.2500000 no. cavity mid-points inaccessible to solvent = 1733 time to turn everything in is 0.5900000 number of dielectric boundary points 33927 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 145 iepsmp to db, and charging done at 0.7100000 number of grid points assigned charge 20491 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) : 0.6465204 object centre at (A) : 12.21200 -1.696000 17.85400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -3.5532329E-02 7.1881101E-03 midg,1,midg; midg,igrid,midg -1.4159158E-02 2.5757525E-02 1,midg,midg; igrid,midg,midg -6.3799596E-03 5.3957921E-02 gauss-seidel spectral radius is 0.9986949 estimated iterations to convergence 219 setup time was (sec) 0.8600000 now iterating at: 04:45:39 rms-change max change #iterations 4.532320 203.6509 at 10iterations 2.167001 75.56355 at 20iterations 1.036518 34.81924 at 30iterations 0.4942282 14.87788 at 40iterations 0.2359342 7.158585 at 50iterations 0.1127419 3.942383 at 60iterations 5.3841535E-02 1.606917 at 70iterations 2.5626654E-02 0.7853584 at 80iterations 1.2248820E-02 0.3862534 at 90iterations 5.8404072E-03 0.1664267 at 100iterations 2.7915353E-03 8.3925247E-02 at 110iterations 1.3325507E-03 3.8269043E-02 at 120iterations finished qdiffx linear iterations at : 04:45:45 total time elapsed so far: 6.860000 # loops : 120 mean,max change (kT/e) : 1.3325507E-03 3.8269043E-02 energy calculations done at 6.860000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.040000 DelPhi exited at 04:45:46 7.044u 0.158s 0:07.77 92.5% 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 Tue Oct 11 2011 at 04:45:46 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: 254 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2755 !!! WARNING: TYS 1 has a net charge of -0.3380 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: 2.909342 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): -11.90300 36.32700 ymin,ymax (A): -25.88500 22.49300 zmin,zma (A): -9.678000 45.38600 x,y,z range (A): 48.23000 48.37800 55.06400 scale (grids/A): 2.909342 object centre (A): 12.21200 -1.696000 17.85400 number of atom coordinates read : 2755 total number of charged atoms : 2603 net assigned charge : 3.162012 assigned positive charge : 414.7707 centred at (gu) : 91.33482 92.56085 98.32158 assigned negative charge : -411.6093 centred at (gu) : 90.20264 91.72535 98.05231 start vw surface at 0.1700000 fill in re-entrant regions at 0.5000000 boundary points on vw surface= 189672 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23592 grid for indexing accessible points = 1.400000 m= 96901 mr = 139760 m= 34499 mr = 79727 m= 7967 mr = 27673 m= 1089 mr = 5868 m= 69 mr = 683 m= 2 mr = 26 m= 0 mr = 0 time to grow re-entrant surface = 0.8200000 no. cavity mid-points inaccessible to solvent = 5790 time to turn everything in is 1.430000 number of dielectric boundary points 76462 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.560000 number of grid points assigned charge 20812 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) : 1.939561 object centre at (A) : 12.21200 -1.696000 17.85400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.5377024 0.3435282 midg,1,midg; midg,igrid,midg -0.1584318 0.2984627 1,midg,midg; igrid,midg,midg -3.4949783E-02 0.4100293 gauss-seidel spectral radius is 0.9992720 estimated iterations to convergence 292 setup time was (sec) 1.710000 now iterating at: 04:45:48 rms-change max change #iterations 10.56328 516.5076 at 10iterations 6.183824 142.8960 at 20iterations 3.612804 72.37220 at 30iterations 2.105257 42.48718 at 40iterations 1.228352 22.12199 at 50iterations 0.7130582 12.27177 at 60iterations 0.4138913 7.685062 at 70iterations 0.2400689 4.439036 at 80iterations 0.1392799 2.842661 at 90iterations 8.0629811E-02 1.467575 at 100iterations 4.6686687E-02 0.9373589 at 110iterations 2.7024275E-02 0.4624748 at 120iterations 1.5667459E-02 0.2631269 at 130iterations 9.0801492E-03 0.1480846 at 140iterations 5.2645984E-03 0.1113572 at 150iterations 3.0663302E-03 5.2415848E-02 at 160iterations 1.7891706E-03 3.4582138E-02 at 170iterations 1.0501283E-03 1.9397736E-02 at 180iterations finished qdiffx linear iterations at : 04:45:57 total time elapsed so far: 11.13000 # loops : 180 mean,max change (kT/e) : 1.0501283E-03 1.9397736E-02 energy calculations done at 11.13000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.32000 DelPhi exited at 04:45:58 11.322u 0.170s 0:11.99 95.8% 0+0k 0+0io 0pf+0w