Tue Oct 11 08:20:25 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 08:20:25 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 = 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: 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 : 2.500009 assigned positive charge : 326.0924 centred at (gu) : 89.51273 89.30074 88.97253 assigned negative charge : -323.5929 centred at (gu) : 89.44853 89.34455 88.79568 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 -6.4968269E-08 6.7325836E-08 midg,1,midg; midg,igrid,midg 3.7854484E-08 -3.2407307E-10 1,midg,midg; igrid,midg,midg -9.3444816E-09 3.6914908E-08 gauss-seidel spectral radius is 0.9892150 estimated iterations to convergence 78 setup time was (sec) 0.3800000 now iterating at: 08:20:25 rms-change max change #iterations 0.1821933 24.11980 at 10iterations 2.1497983E-02 2.828564 at 20iterations 2.6065344E-03 0.3720801 at 30iterations 3.4858679E-04 4.7571182E-02 at 40iterations 5.9913982E-05 9.2563629E-03 at 50iterations finished qdiffx linear iterations at : 08:20:28 total time elapsed so far: 3.250000 # loops : 50 mean,max change (kT/e) : 5.9913982E-05 9.2563629E-03 energy calculations done at 3.250000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.380000 DelPhi exited at 08:20:29 3.384u 0.171s 0:03.87 91.7% 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 08:20:29 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 = 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 : 2.500009 assigned positive charge : 326.0924 centred at (gu) : 88.53795 87.90216 86.91708 assigned negative charge : -323.5929 centred at (gu) : 88.34563 88.03368 86.38703 start vw surface at 7.0000000E-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 = 0.1800000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3700000 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 -3.5887316E-02 5.9275370E-02 midg,1,midg; midg,igrid,midg -3.6059212E-02 -2.5693284E-02 1,midg,midg; igrid,midg,midg -1.2876208E-02 1.6505942E-02 gauss-seidel spectral radius is 0.9988125 estimated iterations to convergence 230 setup time was (sec) 0.5900000 now iterating at: 08:20:29 rms-change max change #iterations 4.576457 187.1101 at 10iterations 2.244025 76.76144 at 20iterations 1.110486 33.30759 at 30iterations 0.5483237 16.40176 at 40iterations 0.2706083 8.262028 at 50iterations 0.1331666 3.893784 at 60iterations 6.5674797E-02 2.067608 at 70iterations 3.2448024E-02 1.003758 at 80iterations 1.5990844E-02 0.4856205 at 90iterations 7.9145636E-03 0.2642870 at 100iterations 3.9072232E-03 0.1231041 at 110iterations 1.9256674E-03 5.4987192E-02 at 120iterations finished qdiffx linear iterations at : 08:20:36 total time elapsed so far: 7.580000 # loops : 120 mean,max change (kT/e) : 1.9256674E-03 5.4987192E-02 energy calculations done at 7.580000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.720000 DelPhi exited at 08:20:37 7.720u 0.200s 0:08.57 92.4% 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 Tue Oct 11 2011 at 08:20:37 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 = 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: 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 : 2.500009 assigned positive charge : 326.0924 centred at (gu) : 87.80685 86.85308 85.37556 assigned negative charge : -323.5929 centred at (gu) : 87.51841 87.05054 84.58056 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 = 0.5700000 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 -0.4811547 0.3819974 midg,1,midg; midg,igrid,midg -0.4657480 -0.2404744 1,midg,midg; igrid,midg,midg -0.1675319 0.1195996 gauss-seidel spectral radius is 0.9993069 estimated iterations to convergence 300 setup time was (sec) 1.390000 now iterating at: 08:20:39 rms-change max change #iterations 10.35397 356.2040 at 10iterations 6.114128 125.0934 at 20iterations 3.621345 74.76576 at 30iterations 2.131300 45.05476 at 40iterations 1.255738 23.15243 at 50iterations 0.7366686 13.10164 at 60iterations 0.4324106 7.690084 at 70iterations 0.2537698 4.562695 at 80iterations 0.1486810 2.632942 at 90iterations 8.7118335E-02 1.503387 at 100iterations 5.1102277E-02 0.8635254 at 110iterations 2.9806860E-02 0.4921687 at 120iterations 1.7464783E-02 0.3104985 at 130iterations 1.0230088E-02 0.1917526 at 140iterations 5.9969127E-03 0.1070957 at 150iterations 3.5071468E-03 5.9020996E-02 at 160iterations 2.0552445E-03 3.6523819E-02 at 170iterations 1.2115351E-03 2.0250082E-02 at 180iterations finished qdiffx linear iterations at : 08:20:50 total time elapsed so far: 12.78000 # loops : 180 mean,max change (kT/e) : 1.2115351E-03 2.0250082E-02 energy calculations done at 12.78000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.91000 DelPhi exited at 08:20:52 12.912u 0.213s 0:14.31 91.6% 0+0k 0+0io 0pf+0w