Tue Oct 11 08:20:52 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 Tue Oct 11 2011 at 08:20:52 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: 270 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2193 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6945393 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): 35.28000 80.20100 ymin,ymax (A): 30.10900 77.33300 zmin,zma (A): 1.519000 52.77600 x,y,z range (A): 44.92100 47.22400 51.25700 scale (grids/A): 0.6945393 object centre (A): 57.74050 53.72100 27.14750 number of atom coordinates read : 2193 total number of charged atoms : 2070 net assigned charge : 2.500008 assigned positive charge : 328.4925 centred at (gu) : 89.52615 89.25839 88.99150 assigned negative charge : -325.9929 centred at (gu) : 89.45486 89.30237 88.80927 start vw surface at 7.9999998E-02 fill in re-entrant regions at 7.9999998E-02 boundary points on vw surface= 7091 nv = 96 ne = 84 npr = 45839 no. pairs analyzed = 45839 no. exposed pairs = 2818 no. arc points = 19737 no. surface atoms = 940 nbur = 1253 mkacc time = 6.9999993E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 441 mr = 3826 m= 4 mr = 60 m= 0 mr = 0 time to grow re-entrant surface = 7.9999998E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.1800000 number of dielectric boundary points 3650 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1779 ## 139 charges are in solution ## iepsmp to db, and charging done at 0.2500000 number of grid points assigned charge 8030 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -6.7943759E-08 6.9628427E-08 midg,1,midg; midg,igrid,midg 3.8419607E-08 -4.5762683E-10 1,midg,midg; igrid,midg,midg -1.2538965E-08 3.9644256E-08 gauss-seidel spectral radius is 0.9892150 estimated iterations to convergence 78 setup time was (sec) 0.3700000 now iterating at: 08:20:52 rms-change max change #iterations 0.1872664 27.27275 at 10iterations 2.2026246E-02 2.906934 at 20iterations 2.6556931E-03 0.3679109 at 30iterations 3.4661242E-04 4.6522141E-02 at 40iterations 5.6346842E-05 8.2111359E-03 at 50iterations finished qdiffx linear iterations at : 08:20:55 total time elapsed so far: 3.220000 # loops : 50 mean,max change (kT/e) : 5.6346842E-05 8.2111359E-03 energy calculations done at 3.220000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.350000 DelPhi exited at 08:20:56 3.355u 0.168s 0:03.89 90.2% 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 Tue Oct 11 2011 at 08:20:56 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: 270 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2193 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.083618 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): 35.28000 80.20100 ymin,ymax (A): 30.10900 77.33300 zmin,zma (A): 1.519000 52.77600 x,y,z range (A): 44.92100 47.22400 51.25700 scale (grids/A): 2.083618 object centre (A): 57.74050 53.72100 27.14750 number of atom coordinates read : 2193 total number of charged atoms : 2070 net assigned charge : 2.500008 assigned positive charge : 328.4925 centred at (gu) : 88.57822 87.77514 86.97401 assigned negative charge : -325.9929 centred at (gu) : 88.36459 87.90716 86.42777 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 76183 reading accessible surface arcs data from file ARCDAT no. of arc points read = 19737 grid for indexing accessible points = 1.400000 m= 28377 mr = 52371 m= 5416 mr = 20770 m= 472 mr = 3360 m= 12 mr = 164 m= 1 mr = 1 m= 0 mr = 0 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3800000 number of dielectric boundary points 33795 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 91 iepsmp to db, and charging done at 0.4500000 number of grid points assigned charge 16436 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) : 0.6945393 object centre at (A) : 57.74050 53.72100 27.14750 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -3.6283467E-02 6.0107179E-02 midg,1,midg; midg,igrid,midg -3.2362439E-02 -2.5736360E-02 1,midg,midg; igrid,midg,midg -1.4494685E-02 1.7047757E-02 gauss-seidel spectral radius is 0.9988125 estimated iterations to convergence 230 setup time was (sec) 0.5900000 now iterating at: 08:20:56 rms-change max change #iterations 4.621831 187.1101 at 10iterations 2.267237 77.02264 at 20iterations 1.122184 32.55161 at 30iterations 0.5538207 16.74667 at 40iterations 0.2733580 8.500227 at 50iterations 0.1345660 3.964526 at 60iterations 6.6307336E-02 2.048070 at 70iterations 3.2780871E-02 1.001708 at 80iterations 1.6150070E-02 0.4910526 at 90iterations 7.9886494E-03 0.2555742 at 100iterations 3.9426782E-03 0.1227074 at 110iterations 1.9418728E-03 5.4266214E-02 at 120iterations finished qdiffx linear iterations at : 08:21:04 total time elapsed so far: 7.670000 # loops : 120 mean,max change (kT/e) : 1.9418728E-03 5.4266214E-02 energy calculations done at 7.670000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.800000 DelPhi exited at 08:21:04 7.801u 0.201s 0:08.58 93.2% 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 Tue Oct 11 2011 at 08:21:04 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: 270 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2193 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 3.125427 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): 35.28000 80.20100 ymin,ymax (A): 30.10900 77.33300 zmin,zma (A): 1.519000 52.77600 x,y,z range (A): 44.92100 47.22400 51.25700 scale (grids/A): 3.125427 object centre (A): 57.74050 53.72100 27.14750 number of atom coordinates read : 2193 total number of charged atoms : 2070 net assigned charge : 2.500008 assigned positive charge : 328.4925 centred at (gu) : 87.86729 86.66257 85.46096 assigned negative charge : -325.9929 centred at (gu) : 87.54686 86.86076 84.64168 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.4800000 boundary points on vw surface= 176218 reading accessible surface arcs data from file ARCDAT no. of arc points read = 19737 grid for indexing accessible points = 1.400000 m= 88684 mr = 126926 m= 35496 mr = 72222 m= 10021 mr = 28356 m= 1838 mr = 7362 m= 178 mr = 1193 m= 6 mr = 80 m= 0 mr = 0 time to grow re-entrant surface = 0.5800000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.150000 number of dielectric boundary points 76302 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.240000 number of grid points assigned charge 16560 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) : 2.083618 object centre at (A) : 57.74050 53.72100 27.14750 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.4836406 0.3874929 midg,1,midg; midg,igrid,midg -0.4178016 -0.2409098 1,midg,midg; igrid,midg,midg -0.1798426 0.1243155 gauss-seidel spectral radius is 0.9993069 estimated iterations to convergence 300 setup time was (sec) 1.390000 now iterating at: 08:21:06 rms-change max change #iterations 10.44670 356.2042 at 10iterations 6.167610 125.0960 at 20iterations 3.652411 77.78809 at 30iterations 2.149740 45.50780 at 40iterations 1.266229 23.51171 at 50iterations 0.7430230 13.43958 at 60iterations 0.4359716 7.719532 at 70iterations 0.2558750 4.664769 at 80iterations 0.1499030 2.595702 at 90iterations 8.7792888E-02 1.565372 at 100iterations 5.1500417E-02 0.8538189 at 110iterations 3.0042641E-02 0.4888865 at 120iterations 1.7594844E-02 0.3075867 at 130iterations 1.0304252E-02 0.1883609 at 140iterations 6.0374290E-03 0.1085129 at 150iterations 3.5305808E-03 5.9612274E-02 at 160iterations 2.0660814E-03 3.6939621E-02 at 170iterations 1.2152342E-03 1.9730449E-02 at 180iterations finished qdiffx linear iterations at : 08:21:17 total time elapsed so far: 12.77000 # loops : 180 mean,max change (kT/e) : 1.2152342E-03 1.9730449E-02 energy calculations done at 12.77000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.90000 DelPhi exited at 08:21:18 12.901u 0.204s 0:13.39 97.8% 0+0k 0+0io 0pf+0w