Sat Oct 8 12:48:42 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 Sat Oct 8 2011 at 12:48:42 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: 287 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2344 !!! WARNING: SEP 181 has a net charge of -0.4750 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6054834 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): 30.17600 88.97200 ymin,ymax (A): -5.350000 37.42900 zmin,zma (A): -13.52100 44.46800 x,y,z range (A): 58.79600 42.77900 57.98900 scale (grids/A): 0.6054834 object centre (A): 59.57400 16.03950 15.47350 number of atom coordinates read : 2344 total number of charged atoms : 2207 net assigned charge : -2.474992 assigned positive charge : 319.7807 centred at (gu) : 89.45631 89.19934 87.91804 assigned negative charge : -322.2561 centred at (gu) : 89.64548 89.16219 87.96067 start vw surface at 0.1600000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 5787 nv = 96 ne = 84 npr = 49921 no. pairs analyzed = 49921 no. exposed pairs = 3045 no. arc points = 21373 no. surface atoms = 1041 nbur = 1303 mkacc time = 0.1300000 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 = 1.456000 m= 257 mr = 2884 m= 0 mr = 7 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3300000 number of dielectric boundary points 3153 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2003 ## 147 charges are in solution ## iepsmp to db, and charging done at 0.4500000 number of grid points assigned charge 7055 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 3.7049444E-10 -1.7932265E-09 midg,1,midg; midg,igrid,midg -3.1680072E-09 -6.7019654E-12 1,midg,midg; igrid,midg,midg 5.9981331E-09 -7.2559940E-09 gauss-seidel spectral radius is 0.9858689 estimated iterations to convergence 69 setup time was (sec) 0.6100000 now iterating at: 12:48:43 rms-change max change #iterations 0.1038146 17.23388 at 10iterations 8.8978484E-03 1.520508 at 20iterations 8.2526973E-04 0.1286793 at 30iterations 8.4513689E-05 1.4369965E-02 at 40iterations 1.0691243E-05 1.8482208E-03 at 50iterations finished qdiffx linear iterations at : 12:48:46 total time elapsed so far: 4.000000 # loops : 50 mean,max change (kT/e) : 1.0691243E-05 1.8482208E-03 energy calculations done at 4.000000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.170000 DelPhi exited at 12:48:47 4.176u 0.299s 0:04.74 94.0% 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 12:48:47 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: 287 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2344 !!! WARNING: SEP 181 has a net charge of -0.4750 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.816450 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): 30.17600 88.97200 ymin,ymax (A): -5.350000 37.42900 zmin,zma (A): -13.52100 44.46800 x,y,z range (A): 58.79600 42.77900 57.98900 scale (grids/A): 1.816450 object centre (A): 59.57400 16.03950 15.47350 number of atom coordinates read : 2344 total number of charged atoms : 2207 net assigned charge : -2.474992 assigned positive charge : 319.7807 centred at (gu) : 88.36871 87.59773 83.75370 assigned negative charge : -322.2561 centred at (gu) : 88.93632 87.48666 83.88217 start vw surface at 0.1500000 fill in re-entrant regions at 0.2700000 boundary points on vw surface= 62961 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21373 grid for indexing accessible points = 1.400000 m= 19778 mr = 41474 m= 2628 mr = 13249 m= 81 mr = 1412 m= 2 mr = 17 m= 0 mr = 0 time to grow re-entrant surface = 0.2700000 no. cavity mid-points inaccessible to solvent = 73 time to turn everything in is 0.5700000 number of dielectric boundary points 29298 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 108 iepsmp to db, and charging done at 0.7000000 number of grid points assigned charge 17283 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) : 0.6054834 object centre at (A) : 59.57400 16.03950 15.47350 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 9.6433293E-03 7.2953445E-03 midg,1,midg; midg,igrid,midg -8.3583901E-03 -2.7967764E-03 1,midg,midg; igrid,midg,midg 2.1170504E-02 -2.9924054E-02 gauss-seidel spectral radius is 0.9984788 estimated iterations to convergence 203 setup time was (sec) 0.8700000 now iterating at: 12:48:48 rms-change max change #iterations 3.473809 180.7094 at 10iterations 1.549824 60.21454 at 20iterations 0.6979142 26.82932 at 30iterations 0.3127109 11.37572 at 40iterations 0.1404491 4.947399 at 50iterations 6.3216045E-02 2.277069 at 60iterations 2.8339684E-02 1.008384 at 70iterations 1.2709116E-02 0.4438114 at 80iterations 5.7090623E-03 0.1920571 at 90iterations 2.5698859E-03 8.2731247E-02 at 100iterations 1.1620761E-03 3.9566040E-02 at 110iterations 5.2623404E-04 1.9676387E-02 at 120iterations finished qdiffx linear iterations at : 12:48:56 total time elapsed so far: 9.370000 # loops : 120 mean,max change (kT/e) : 5.2623404E-04 1.9676387E-02 energy calculations done at 9.370000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.540000 DelPhi exited at 12:48:57 9.545u 0.351s 0:10.19 97.0% 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 12:48:57 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: 287 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2344 !!! WARNING: SEP 181 has a net charge of -0.4750 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.724675 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): 30.17600 88.97200 ymin,ymax (A): -5.350000 37.42900 zmin,zma (A): -13.52100 44.46800 x,y,z range (A): 58.79600 42.77900 57.98900 scale (grids/A): 2.724675 object centre (A): 59.57400 16.03950 15.47350 number of atom coordinates read : 2344 total number of charged atoms : 2207 net assigned charge : -2.474992 assigned positive charge : 319.7807 centred at (gu) : 87.55295 86.39663 80.63043 assigned negative charge : -322.2561 centred at (gu) : 88.40449 86.23000 80.82328 start vw surface at 0.1500000 fill in re-entrant regions at 0.4900000 boundary points on vw surface= 146092 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21373 grid for indexing accessible points = 1.400000 m= 65859 mr = 101529 m= 21145 mr = 51252 m= 4391 mr = 15859 m= 387 mr = 3010 m= 14 mr = 200 m= 0 mr = 4 time to grow re-entrant surface = 0.8100000 no. cavity mid-points inaccessible to solvent = 267 time to turn everything in is 1.410000 number of dielectric boundary points 66034 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 17654 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) : 1.816450 object centre at (A) : 59.57400 16.03950 15.47350 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.2402159E-02 8.6095348E-02 midg,1,midg; midg,igrid,midg -7.4372627E-02 -1.8412704E-02 1,midg,midg; igrid,midg,midg 0.3699863 -0.3401186 gauss-seidel spectral radius is 0.9992129 estimated iterations to convergence 281 setup time was (sec) 1.750000 now iterating at: 12:48:59 rms-change max change #iterations 8.342112 264.1743 at 10iterations 4.799172 174.1021 at 20iterations 2.735853 63.55041 at 30iterations 1.551850 41.30325 at 40iterations 0.8784571 21.55298 at 50iterations 0.4986609 11.10759 at 60iterations 0.2824427 5.704813 at 70iterations 0.1592145 3.403404 at 80iterations 9.0176418E-02 1.796532 at 90iterations 5.0860588E-02 1.012402 at 100iterations 2.8680647E-02 0.5345795 at 110iterations 1.6179206E-02 0.3205895 at 120iterations 9.1582621E-03 0.1766585 at 130iterations 5.1672608E-03 0.1023149 at 140iterations 2.9191768E-03 5.9650421E-02 at 150iterations 1.6506409E-03 3.3723831E-02 at 160iterations 9.3490945E-04 1.8859863E-02 at 170iterations 5.3280353E-04 1.0809898E-02 at 180iterations finished qdiffx linear iterations at : 12:49:13 total time elapsed so far: 15.64000 # loops : 180 mean,max change (kT/e) : 5.3280353E-04 1.0809898E-02 energy calculations done at 15.64000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.83000 DelPhi exited at 12:49:13 15.828u 0.342s 0:16.44 98.2% 0+0k 0+0io 0pf+0w