Mon Oct 10 22:45:10 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 Mon Oct 10 2011 at 22:45:10 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 = 2746 !!! WARNING: ASP 298 has a net charge of -2.0000 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: 0.6355327 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): -8.335999 47.68000 ymin,ymax (A): -15.45100 31.46800 zmin,zma (A): -11.82000 41.53400 x,y,z range (A): 56.01600 46.91900 53.35400 scale (grids/A): 0.6355327 object centre (A): 19.67200 8.008501 14.85700 number of atom coordinates read : 2746 total number of charged atoms : 2603 net assigned charge : 5.500013 assigned positive charge : 415.6904 centred at (gu) : 89.47446 89.89175 89.08326 assigned negative charge : -410.1913 centred at (gu) : 89.75986 89.89635 89.13882 start vw surface at 0.1400000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 7434 nv = 96 ne = 84 npr = 54939 no. pairs analyzed = 54939 no. exposed pairs = 3271 no. arc points = 22574 no. surface atoms = 1109 nbur = 1637 mkacc time = 0.1800000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 364 mr = 4259 m= 0 mr = 41 time to grow re-entrant surface = 0.2200000 no. cavity mid-points inaccessible to solvent = 46 time to turn everything in is 0.3900000 number of dielectric boundary points 3498 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2191 ## 205 charges are in solution ## iepsmp to db, and charging done at 0.5000000 number of grid points assigned charge 8941 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.5649785E-08 6.6748485E-10 midg,1,midg; midg,igrid,midg 7.5030808E-09 6.1942220E-09 1,midg,midg; igrid,midg,midg 4.1490804E-08 -2.2490726E-08 gauss-seidel spectral radius is 0.9871845 estimated iterations to convergence 72 setup time was (sec) 0.6800000 now iterating at: 22:45:11 rms-change max change #iterations 0.1474548 23.43781 at 10iterations 1.5476068E-02 2.540581 at 20iterations 2.0521563E-03 0.3557663 at 30iterations 4.7501407E-04 0.1022568 at 40iterations 1.3956311E-04 3.0780792E-02 at 50iterations finished qdiffx linear iterations at : 22:45:15 total time elapsed so far: 4.210000 # loops : 50 mean,max change (kT/e) : 1.3956311E-04 3.0780792E-02 energy calculations done at 4.210000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.450000 DelPhi exited at 22:45:15 4.453u 0.456s 0:05.46 89.7% 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 Mon Oct 10 2011 at 22:45:16 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 = 2746 !!! WARNING: ASP 298 has a net charge of -2.0000 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: 1.906598 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): -8.335999 47.68000 ymin,ymax (A): -15.45100 31.46800 zmin,zma (A): -11.82000 41.53400 x,y,z range (A): 56.01600 46.91900 53.35400 scale (grids/A): 1.906598 object centre (A): 19.67200 8.008501 14.85700 number of atom coordinates read : 2746 total number of charged atoms : 2603 net assigned charge : 5.500013 assigned positive charge : 415.6904 centred at (gu) : 88.42262 89.67476 87.24921 assigned negative charge : -410.1913 centred at (gu) : 89.27934 89.68892 87.41630 start vw surface at 0.1600000 fill in re-entrant regions at 0.3300000 boundary points on vw surface= 80429 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22574 grid for indexing accessible points = 1.400000 m= 29294 mr = 56965 m= 4610 mr = 22241 m= 271 mr = 3022 m= 0 mr = 108 time to grow re-entrant surface = 0.4100000 no. cavity mid-points inaccessible to solvent = 1014 time to turn everything in is 0.8000000 number of dielectric boundary points 32268 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 131 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.9300000 number of grid points assigned charge 20458 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) : 0.6355327 object centre at (A) : 19.67200 8.008501 14.85700 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -8.9543322E-03 -2.4374058E-04 midg,1,midg; midg,igrid,midg 1.7144920E-02 1.3503177E-02 1,midg,midg; igrid,midg,midg 7.1670040E-02 -2.5251474E-02 gauss-seidel spectral radius is 0.9986488 estimated iterations to convergence 216 setup time was (sec) 1.130000 now iterating at: 22:45:17 rms-change max change #iterations 4.436397 196.6180 at 10iterations 2.077635 65.39645 at 20iterations 0.9808806 29.03011 at 30iterations 0.4624674 14.68062 at 40iterations 0.2174102 7.425400 at 50iterations 0.1025902 3.045300 at 60iterations 4.8443407E-02 1.544453 at 70iterations 2.2802310E-02 0.6983271 at 80iterations 1.0953119E-02 0.3239441 at 90iterations 5.2947830E-03 0.2069492 at 100iterations 2.6250514E-03 9.7937584E-02 at 110iterations 1.3577567E-03 5.2558899E-02 at 120iterations finished qdiffx linear iterations at : 22:45:26 total time elapsed so far: 10.14000 # loops : 120 mean,max change (kT/e) : 1.3577567E-03 5.2558899E-02 energy calculations done at 10.14000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.37000 DelPhi exited at 22:45:27 10.371u 0.474s 0:11.47 94.5% 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 Mon Oct 10 2011 at 22:45:27 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 = 2746 !!! WARNING: ASP 298 has a net charge of -2.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 2.859897 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): -8.335999 47.68000 ymin,ymax (A): -15.45100 31.46800 zmin,zma (A): -11.82000 41.53400 x,y,z range (A): 56.01600 46.91900 53.35400 scale (grids/A): 2.859897 object centre (A): 19.67200 8.008501 14.85700 number of atom coordinates read : 2746 total number of charged atoms : 2603 net assigned charge : 5.500013 assigned positive charge : 415.6904 centred at (gu) : 87.63386 89.51186 85.87370 assigned negative charge : -410.1913 centred at (gu) : 88.91890 89.53330 86.12437 start vw surface at 0.1600000 fill in re-entrant regions at 0.6900000 boundary points on vw surface= 186112 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22574 grid for indexing accessible points = 1.400000 m= 94963 mr = 137701 m= 34435 mr = 79072 m= 8563 mr = 28299 m= 1264 mr = 6686 m= 76 mr = 879 m= 0 mr = 39 time to grow re-entrant surface = 1.270000 no. cavity mid-points inaccessible to solvent = 3514 time to turn everything in is 2.100000 number of dielectric boundary points 72737 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 2.340000 number of grid points assigned charge 20824 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) : 1.906598 object centre at (A) : 19.67200 8.008501 14.85700 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1677667 -7.2650619E-02 midg,1,midg; midg,igrid,midg 0.2429396 0.1420429 1,midg,midg; igrid,midg,midg 0.7444544 -0.2936959 gauss-seidel spectral radius is 0.9992570 estimated iterations to convergence 290 setup time was (sec) 2.540000 now iterating at: 22:45:30 rms-change max change #iterations 10.24931 375.6390 at 10iterations 5.925715 141.7560 at 20iterations 3.423261 62.18121 at 30iterations 1.973922 40.68801 at 40iterations 1.135594 24.15081 at 50iterations 0.6531661 11.56903 at 60iterations 0.3741015 7.161819 at 70iterations 0.2161127 3.753500 at 80iterations 0.1238266 2.325087 at 90iterations 7.1219802E-02 1.441280 at 100iterations 4.0921845E-02 0.7271080 at 110iterations 2.3570964E-02 0.4308262 at 120iterations 1.3645612E-02 0.2573433 at 130iterations 7.9462240E-03 0.1552505 at 140iterations 4.6914583E-03 8.9340210E-02 at 150iterations 2.8291324E-03 6.3697815E-02 at 160iterations 1.7684418E-03 4.2453766E-02 at 170iterations 1.1629360E-03 2.8633118E-02 at 180iterations finished qdiffx linear iterations at : 22:45:45 total time elapsed so far: 17.56000 # loops : 180 mean,max change (kT/e) : 1.1629360E-03 2.8633118E-02 energy calculations done at 17.56000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 17.78000 DelPhi exited at 22:45:46 17.786u 0.510s 0:18.63 98.1% 0+0k 0+0io 0pf+0w