Sat Oct 8 22:14:41 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 22:14:42 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 = 2242 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 0.6506561 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): -14.77600 27.69600 ymin,ymax (A): -11.92900 42.12100 zmin,zma (A): -4.6999931E-02 54.66700 x,y,z range (A): 42.47200 54.05000 54.71400 scale (grids/A): 0.6506561 object centre (A): 6.460001 15.09600 27.31000 number of atom coordinates read : 2242 total number of charged atoms : 2108 net assigned charge : 11.50002 assigned positive charge : 325.3997 centred at (gu) : 88.48085 91.25571 89.25318 assigned negative charge : -313.9003 centred at (gu) : 88.55121 91.28048 89.26303 start vw surface at 0.1400000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 6562 nv = 96 ne = 84 npr = 44300 no. pairs analyzed = 44300 no. exposed pairs = 3069 no. arc points = 21416 no. surface atoms = 1027 nbur = 1215 mkacc time = 8.9999989E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 423 mr = 3399 m= 1 mr = 49 m= 0 mr = 0 time to grow re-entrant surface = 9.9999979E-02 no. cavity mid-points inaccessible to solvent = 7 time to turn everything in is 0.2600000 number of dielectric boundary points 3538 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2036 ## 194 charges are in solution ## iepsmp to db, and charging done at 0.3700000 number of grid points assigned charge 7640 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.7542850E-08 1.8216207E-08 midg,1,midg; midg,igrid,midg 1.9755717E-08 2.4902642E-08 1,midg,midg; igrid,midg,midg 4.2733401E-08 1.0093485E-08 gauss-seidel spectral radius is 0.9877369 estimated iterations to convergence 74 setup time was (sec) 0.4900000 now iterating at: 22:14:42 rms-change max change #iterations 0.1396151 24.62729 at 10iterations 1.4289999E-02 2.203491 at 20iterations 1.4978566E-03 0.2185469 at 30iterations 1.7920896E-04 3.1393051E-02 at 40iterations 2.9439265E-05 4.3983459E-03 at 50iterations finished qdiffx linear iterations at : 22:14:45 total time elapsed so far: 2.990000 # loops : 50 mean,max change (kT/e) : 2.9439265E-05 4.3983459E-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) 3.170000 DelPhi exited at 22:14:45 3.172u 0.180s 0:03.62 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 Sat Oct 8 2011 at 22:14:45 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 = 2242 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 1.951968 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): -14.77600 27.69600 ymin,ymax (A): -11.92900 42.12100 zmin,zma (A): -4.6999931E-02 54.66700 x,y,z range (A): 42.47200 54.05000 54.71400 scale (grids/A): 1.951968 object centre (A): 6.460001 15.09600 27.31000 number of atom coordinates read : 2242 total number of charged atoms : 2108 net assigned charge : 11.50002 assigned positive charge : 325.3997 centred at (gu) : 85.44244 93.76685 87.75928 assigned negative charge : -313.9003 centred at (gu) : 85.65366 93.84176 87.78936 start vw surface at 0.1500000 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 69788 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21416 grid for indexing accessible points = 1.400000 m= 26294 mr = 46444 m= 4795 mr = 18891 m= 348 mr = 2891 m= 5 mr = 125 m= 0 mr = 0 time to grow re-entrant surface = 0.2400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5300000 number of dielectric boundary points 32879 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 155 iepsmp to db, and charging done at 0.6500000 number of grid points assigned charge 16646 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) : 0.6506561 object centre at (A) : 6.460001 15.09600 27.31000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 6.2952116E-02 5.0337851E-02 midg,1,midg; midg,igrid,midg 4.5636065E-02 2.7401945E-02 1,midg,midg; igrid,midg,midg 3.2585498E-02 -1.9652380E-03 gauss-seidel spectral radius is 0.9986719 estimated iterations to convergence 217 setup time was (sec) 0.8100000 now iterating at: 22:14:46 rms-change max change #iterations 3.933340 180.7790 at 10iterations 1.855009 66.31844 at 20iterations 0.8777722 28.76795 at 30iterations 0.4123766 12.77694 at 40iterations 0.1954298 6.953991 at 50iterations 9.2286587E-02 2.905826 at 60iterations 4.3714952E-02 1.376863 at 70iterations 2.0550566E-02 0.7275629 at 80iterations 9.7574731E-03 0.3152542 at 90iterations 4.6183108E-03 0.1402025 at 100iterations 2.1959401E-03 7.0005417E-02 at 110iterations 1.0517178E-03 3.6453247E-02 at 120iterations finished qdiffx linear iterations at : 22:14:53 total time elapsed so far: 7.560000 # loops : 120 mean,max change (kT/e) : 1.0517178E-03 3.6453247E-02 energy calculations done at 7.560000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.730000 DelPhi exited at 22:14:53 7.729u 0.234s 0:08.24 96.4% 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 Sat Oct 8 2011 at 22:14:54 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 = 2242 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 2.927953 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): -14.77600 27.69600 ymin,ymax (A): -11.92900 42.12100 zmin,zma (A): -4.6999931E-02 54.66700 x,y,z range (A): 42.47200 54.05000 54.71400 scale (grids/A): 2.927953 object centre (A): 6.460001 15.09600 27.31000 number of atom coordinates read : 2242 total number of charged atoms : 2108 net assigned charge : 11.50002 assigned positive charge : 325.3997 centred at (gu) : 83.16375 95.65016 86.63869 assigned negative charge : -313.9003 centred at (gu) : 83.48050 95.76275 86.68404 start vw surface at 0.1500000 fill in re-entrant regions at 0.4300000 boundary points on vw surface= 160972 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21416 grid for indexing accessible points = 1.400000 m= 82311 mr = 112946 m= 32509 mr = 65922 m= 8672 mr = 25631 m= 1504 mr = 6253 m= 133 mr = 1006 m= 0 mr = 55 time to grow re-entrant surface = 0.7600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.310000 number of dielectric boundary points 74288 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.440000 number of grid points assigned charge 16864 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) : 1.951968 object centre at (A) : 6.460001 15.09600 27.31000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.6161778 0.5573397 midg,1,midg; midg,igrid,midg 0.5515763 0.3252971 1,midg,midg; igrid,midg,midg 0.3172717 -1.2226112E-02 gauss-seidel spectral radius is 0.9992771 estimated iterations to convergence 293 setup time was (sec) 1.620000 now iterating at: 22:14:55 rms-change max change #iterations 9.357599 471.1507 at 10iterations 5.545790 145.9193 at 20iterations 3.272813 83.55392 at 30iterations 1.915678 44.36628 at 40iterations 1.118936 27.00880 at 50iterations 0.6546822 16.11652 at 60iterations 0.3810689 9.265977 at 70iterations 0.2211511 4.648987 at 80iterations 0.1285533 2.731826 at 90iterations 7.4768990E-02 1.937263 at 100iterations 4.3322928E-02 0.8848848 at 110iterations 2.5097538E-02 0.5146465 at 120iterations 1.4553979E-02 0.2831326 at 130iterations 8.4550735E-03 0.1564095 at 140iterations 4.9092066E-03 0.1002741 at 150iterations 2.8636951E-03 5.4687142E-02 at 160iterations 1.6846379E-03 3.2293320E-02 at 170iterations 1.0007918E-03 1.9378662E-02 at 180iterations finished qdiffx linear iterations at : 22:15:06 total time elapsed so far: 12.65000 # loops : 180 mean,max change (kT/e) : 1.0007918E-03 1.9378662E-02 energy calculations done at 12.65000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.82000 DelPhi exited at 22:15:07 12.826u 0.242s 0:13.34 97.9% 0+0k 0+0io 0pf+0w