Mon Oct 10 17:17:56 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 Mon Oct 10 2011 at 17:17:56 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: 315 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2814 !!! WARNING: GLM 75 has a net charge of -0.0940 !!! WARNING: GLM 155 has a net charge of -0.0940 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 0.5457444 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): -47.45500 4.413000 ymin,ymax (A): 1.277000 66.50900 zmin,zma (A): -17.15500 29.42200 x,y,z range (A): 51.86800 65.23200 46.57700 scale (grids/A): 0.5457444 object centre (A): -21.52100 33.89300 6.133500 number of atom coordinates read : 2814 total number of charged atoms : 2642 net assigned charge : 3.812023 assigned positive charge : 416.0364 centred at (gu) : 89.62089 88.83669 90.50452 assigned negative charge : -412.2255 centred at (gu) : 89.51996 88.88361 90.46811 start vw surface at 7.9999998E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 5588 nv = 96 ne = 84 npr = 56212 no. pairs analyzed = 56212 no. exposed pairs = 3707 no. arc points = 27382 no. surface atoms = 1245 nbur = 1569 mkacc time = 9.9999994E-02 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 = 1.568000 m= 203 mr = 2749 m= 1 mr = 12 m= 0 mr = 0 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2000000 number of dielectric boundary points 3031 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2749 ## 416 charges are in solution ## iepsmp to db, and charging done at 0.2600000 number of grid points assigned charge 7184 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 9.8065965E-12 5.1404164E-10 midg,1,midg; midg,igrid,midg 6.9062556E-10 -3.8722803E-11 1,midg,midg; igrid,midg,midg -4.3115439E-10 7.6530571E-10 gauss-seidel spectral radius is 0.9826845 estimated iterations to convergence 63 setup time was (sec) 0.3800000 now iterating at: 17:17:56 rms-change max change #iterations 6.9261268E-02 14.58027 at 10iterations 4.5677968E-03 0.8222568 at 20iterations 3.0360452E-04 5.1002502E-02 at 30iterations 2.1314590E-05 3.5095215E-03 at 40iterations 1.6308560E-06 2.7465820E-04 at 50iterations finished qdiffx linear iterations at : 17:17:59 total time elapsed so far: 3.280000 # loops : 50 mean,max change (kT/e) : 1.6308560E-06 2.7465820E-04 energy calculations done at 3.280000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.410000 DelPhi exited at 17:18:00 3.418u 0.180s 0:04.05 88.6% 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 17:18:00 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: 315 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2814 !!! WARNING: GLM 75 has a net charge of -0.0940 !!! WARNING: GLM 155 has a net charge of -0.0940 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 1.637233 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): -47.45500 4.413000 ymin,ymax (A): 1.277000 66.50900 zmin,zma (A): -17.15500 29.42200 x,y,z range (A): 51.86800 65.23200 46.57700 scale (grids/A): 1.637233 object centre (A): -21.52100 33.89300 6.133500 number of atom coordinates read : 2814 total number of charged atoms : 2642 net assigned charge : 3.812023 assigned positive charge : 416.0364 centred at (gu) : 88.86172 86.50939 91.51252 assigned negative charge : -412.2255 centred at (gu) : 88.55949 86.65022 91.40434 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 61135 reading accessible surface arcs data from file ARCDAT no. of arc points read = 27382 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 18951 mr = 40187 m= 1932 mr = 12878 m= 54 mr = 888 m= 0 mr = 3 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3000000 number of dielectric boundary points 28116 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 322 ## 4 charges are in solution ## iepsmp to db, and charging done at 0.3700000 number of grid points assigned charge 20227 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) : 0.5457444 object centre at (A) : -21.52100 33.89300 6.133500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.6895639E-05 -3.1637150E-04 midg,1,midg; midg,igrid,midg 2.6812173E-02 6.9889938E-03 1,midg,midg; igrid,midg,midg -1.0439769E-02 9.2359222E-03 gauss-seidel spectral radius is 0.9981815 estimated iterations to convergence 186 setup time was (sec) 0.5000000 now iterating at: 17:18:01 rms-change max change #iterations 3.211787 151.2764 at 10iterations 1.331347 61.97960 at 20iterations 0.5518142 32.74789 at 30iterations 0.2289563 8.804688 at 40iterations 9.5346816E-02 3.511926 at 50iterations 3.9536279E-02 1.512993 at 60iterations 1.6483927E-02 0.5558739 at 70iterations 6.8873847E-03 0.2662468 at 80iterations 2.8606446E-03 0.1084270 at 90iterations 1.1876245E-03 4.8111916E-02 at 100iterations 4.9610785E-04 1.7656326E-02 at 110iterations 2.0566316E-04 8.1701279E-03 at 120iterations finished qdiffx linear iterations at : 17:18:08 total time elapsed so far: 7.470000 # loops : 120 mean,max change (kT/e) : 2.0566316E-04 8.1701279E-03 energy calculations done at 7.470000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.600000 DelPhi exited at 17:18:08 7.599u 0.212s 0:08.09 96.4% 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 Mon Oct 10 2011 at 17:18:08 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: 315 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2814 !!! WARNING: GLM 75 has a net charge of -0.0940 !!! WARNING: GLM 155 has a net charge of -0.0940 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 2.455850 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): -47.45500 4.413000 ymin,ymax (A): 1.277000 66.50900 zmin,zma (A): -17.15500 29.42200 x,y,z range (A): 51.86800 65.23200 46.57700 scale (grids/A): 2.455850 object centre (A): -21.52100 33.89300 6.133500 number of atom coordinates read : 2814 total number of charged atoms : 2642 net assigned charge : 3.812023 assigned positive charge : 416.0364 centred at (gu) : 88.29242 84.76390 92.26854 assigned negative charge : -412.2255 centred at (gu) : 87.83929 84.97535 92.10649 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.2600000 boundary points on vw surface= 141580 reading accessible surface arcs data from file ARCDAT no. of arc points read = 27382 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 65185 mr = 98326 m= 18596 mr = 51102 m= 2871 mr = 13669 m= 167 mr = 1756 m= 3 mr = 61 m= 0 mr = 0 time to grow re-entrant surface = 0.4100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.7300000 number of dielectric boundary points 63488 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 22 iepsmp to db, and charging done at 0.8200000 number of grid points assigned charge 21114 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) : 1.637233 object centre at (A) : -21.52100 33.89300 6.133500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.7824476E-03 -1.3722872E-02 midg,1,midg; midg,igrid,midg 0.4498881 0.2354740 1,midg,midg; igrid,midg,midg -0.1224636 0.1380090 gauss-seidel spectral radius is 0.9991379 estimated iterations to convergence 269 setup time was (sec) 0.9700000 now iterating at: 17:18:09 rms-change max change #iterations 8.401708 392.0729 at 10iterations 4.747382 121.3171 at 20iterations 2.656480 63.40196 at 30iterations 1.478199 37.88329 at 40iterations 0.8206019 20.47637 at 50iterations 0.4527760 9.792321 at 60iterations 0.2502882 5.399887 at 70iterations 0.1378363 3.184505 at 80iterations 7.6047599E-02 1.645702 at 90iterations 4.1764501E-02 0.9939175 at 100iterations 2.2958152E-02 0.5687389 at 110iterations 1.2572340E-02 0.3124886 at 120iterations 6.9297901E-03 0.1403599 at 130iterations 3.7972494E-03 7.7888489E-02 at 140iterations 2.0883072E-03 4.9890518E-02 at 150iterations 1.1485635E-03 2.5226817E-02 at 160iterations 6.2826276E-04 1.2836456E-02 at 170iterations 3.4507748E-04 7.7171326E-03 at 180iterations finished qdiffx linear iterations at : 17:18:20 total time elapsed so far: 12.14000 # loops : 180 mean,max change (kT/e) : 3.4507748E-04 7.7171326E-03 energy calculations done at 12.14000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.27000 DelPhi exited at 17:18:21 12.271u 0.205s 0:12.77 97.6% 0+0k 0+0io 0pf+0w