Thu Jan 19 11:45:04 PST 2012 #!/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 Thu Jan 19 2012 at 11:45:09 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: 299 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5805 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1100000 grid size : 179 scale,in grids/A, set to be: 0.5060484 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): -0.8010000 69.54800 ymin,ymax (A): 2.855000 69.41200 zmin,zma (A): 18.16600 86.21600 x,y,z range (A): 70.34901 66.55700 68.05000 scale (grids/A): 0.5060484 object centre (A): 34.37350 36.13350 52.19100 number of atom coordinates read : 5805 total number of charged atoms : 5636 net assigned charge : 7.0452690E-05 assigned positive charge : 883.8184 centred at (gu) : 90.30525 89.10320 89.11339 assigned negative charge : -883.8251 centred at (gu) : 90.37038 89.01387 89.14178 start vw surface at 0.1400000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 9665 nv = 96 ne = 84 npr = 112030 no. pairs analyzed = 112030 no. exposed pairs = 7917 no. arc points = 55227 no. surface atoms = 2634 nbur = 3171 mkacc time = 0.2000000 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 = 1.680000 m= 335 mr = 4760 m= 2 mr = 8 m= 0 mr = 0 time to grow re-entrant surface = 0.2200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3700000 number of dielectric boundary points 5234 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 5337 ## 816 charges are in solution ## iepsmp to db, and charging done at 0.4500000 number of grid points assigned charge 12905 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 9.7730192E-11 -5.7339140E-11 midg,1,midg; midg,igrid,midg -3.0081029E-10 1.8457876E-10 1,midg,midg; igrid,midg,midg 1.5876067E-10 -1.8541110E-10 gauss-seidel spectral radius is 0.9801206 estimated iterations to convergence 59 setup time was (sec) 0.5800000 now iterating at: 11:45:13 rms-change max change #iterations 7.0410393E-02 10.23286 at 10iterations 4.4242446E-03 0.5781593 at 20iterations 9.1254304E-04 7.5241089E-02 at 30iterations 3.4934003E-04 2.5018692E-02 at 40iterations 1.3869263E-04 1.0008812E-02 at 50iterations finished qdiffx linear iterations at : 11:45:23 total time elapsed so far: 3.670000 # loops : 50 mean,max change (kT/e) : 1.3869263E-04 1.0008812E-02 energy calculations done at 3.670000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.810000 DelPhi exited at 11:45:24 3.816u 0.206s 0:15.30 26.2% 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 Thu Jan 19 2012 at 11:45:26 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: 299 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5805 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1000000 grid size : 179 scale,in grids/A, set to be: 1.518145 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): -0.8010000 69.54800 ymin,ymax (A): 2.855000 69.41200 zmin,zma (A): 18.16600 86.21600 x,y,z range (A): 70.34901 66.55700 68.05000 scale (grids/A): 1.518145 object centre (A): 34.37350 36.13350 52.19100 number of atom coordinates read : 5805 total number of charged atoms : 5636 net assigned charge : 7.0452690E-05 assigned positive charge : 883.8184 centred at (gu) : 90.91391 87.30791 87.33865 assigned negative charge : -883.8251 centred at (gu) : 91.11082 87.04138 87.42522 start vw surface at 0.1400000 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 109329 reading accessible surface arcs data from file ARCDAT no. of arc points read = 55227 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.568000 m= 31451 mr = 72956 m= 2475 mr = 20528 m= 45 mr = 917 m= 0 mr = 0 time to grow re-entrant surface = 0.2400000 no. cavity mid-points inaccessible to solvent = 398 time to turn everything in is 0.5300000 number of dielectric boundary points 48899 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 774 ## 12 charges are in solution ## iepsmp to db, and charging done at 0.6200000 number of grid points assigned charge 42299 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) : 0.5060484 object centre at (A) : 34.37350 36.13350 52.19100 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -4.2930306E-03 1.5439446E-02 midg,1,midg; midg,igrid,midg -1.7630020E-03 8.0033531E-03 1,midg,midg; igrid,midg,midg -1.3313898E-03 -1.2810019E-02 gauss-seidel spectral radius is 0.9981908 estimated iterations to convergence 187 setup time was (sec) 0.7700000 now iterating at: 11:45:31 rms-change max change #iterations 4.266623 182.4786 at 10iterations 1.782604 55.36808 at 20iterations 0.7475778 22.60796 at 30iterations 0.3137858 9.708884 at 40iterations 0.1315351 4.204555 at 50iterations 5.5431403E-02 1.773111 at 60iterations 2.3334527E-02 0.6853676 at 70iterations 9.8654628E-03 0.3386774 at 80iterations 4.2248378E-03 0.1331539 at 90iterations 1.8592869E-03 6.5768242E-02 at 100iterations 8.8064058E-04 2.5241852E-02 at 110iterations 4.6165555E-04 1.1930466E-02 at 120iterations finished qdiffx linear iterations at : 11:45:55 total time elapsed so far: 8.350000 # loops : 120 mean,max change (kT/e) : 4.6165555E-04 1.1930466E-02 energy calculations done at 8.350000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.480000 DelPhi exited at 11:45:56 8.479u 0.215s 0:30.35 28.5% 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 Thu Jan 19 2012 at 11:45:58 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: 299 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5805 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1000000 grid size : 179 scale,in grids/A, set to be: 2.277218 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): -0.8010000 69.54800 ymin,ymax (A): 2.855000 69.41200 zmin,zma (A): 18.16600 86.21600 x,y,z range (A): 70.34901 66.55700 68.05000 scale (grids/A): 2.277218 object centre (A): 34.37350 36.13350 52.19100 number of atom coordinates read : 5805 total number of charged atoms : 5636 net assigned charge : 7.0452690E-05 assigned positive charge : 883.8184 centred at (gu) : 91.37048 85.96139 86.00755 assigned negative charge : -883.8251 centred at (gu) : 91.66601 85.56181 86.13763 start vw surface at 0.1500000 fill in re-entrant regions at 0.4400000 boundary points on vw surface= 254527 reading accessible surface arcs data from file ARCDAT no. of arc points read = 55227 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.540000 m= 112270 mr = 179932 m= 28121 mr = 86309 m= 3316 mr = 20069 m= 111 mr = 1706 m= 1 mr = 24 m= 0 mr = 0 time to grow re-entrant surface = 0.7400000 no. cavity mid-points inaccessible to solvent = 1358 time to turn everything in is 1.280000 number of dielectric boundary points 110306 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 94 iepsmp to db, and charging done at 1.400000 number of grid points assigned charge 44984 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) : 1.518145 object centre at (A) : 34.37350 36.13350 52.19100 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.0918860E-02 0.2581612 midg,1,midg; midg,igrid,midg -3.6907170E-02 0.1757820 1,midg,midg; igrid,midg,midg -0.1494045 -0.1220663 gauss-seidel spectral radius is 0.9992238 estimated iterations to convergence 283 setup time was (sec) 1.550000 now iterating at: 11:46:06 rms-change max change #iterations 11.73895 318.8971 at 10iterations 6.946203 176.9191 at 20iterations 4.044145 86.31212 at 30iterations 2.356172 49.05013 at 40iterations 1.365614 25.87031 at 50iterations 0.7892424 15.66521 at 60iterations 0.4558819 7.783028 at 70iterations 0.2617499 5.614075 at 80iterations 0.1499306 2.769917 at 90iterations 8.5867941E-02 1.707062 at 100iterations 4.9246680E-02 0.8519506 at 110iterations 2.8126780E-02 0.5803127 at 120iterations 1.6083455E-02 0.2949429 at 130iterations 9.1902949E-03 0.1549587 at 140iterations 5.2433023E-03 0.1057081 at 150iterations 2.9899520E-03 5.6011200E-02 at 160iterations 1.7076706E-03 3.4194946E-02 at 170iterations 9.7512221E-04 1.8367290E-02 at 180iterations finished qdiffx linear iterations at : 11:46:44 total time elapsed so far: 14.36000 # loops : 180 mean,max change (kT/e) : 9.7512221E-04 1.8367290E-02 energy calculations done at 14.36000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 14.48000 DelPhi exited at 11:46:45 14.485u 0.247s 0:47.92 30.7% 0+0k 0+0io 0pf+0w