Mon Oct 10 09:44:29 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 09:44:29 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: 302 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2819 !!! WARNING: HIT 235 has a net charge of 0.5140 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: 0.5845169 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): -17.42800 33.83400 ymin,ymax (A): -60.77300 -2.575000 zmin,zma (A): -1.007000 59.89800 x,y,z range (A): 51.26200 58.19800 60.90500 scale (grids/A): 0.5845169 object centre (A): 8.203000 -31.67400 29.44550 number of atom coordinates read : 2819 total number of charged atoms : 2668 net assigned charge : 6.014023 assigned positive charge : 416.0799 centred at (gu) : 88.42672 88.35582 88.24960 assigned negative charge : -410.0663 centred at (gu) : 88.46986 88.24527 88.11444 start vw surface at 7.9999998E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 6643 nv = 96 ne = 84 npr = 53954 no. pairs analyzed = 53954 no. exposed pairs = 4256 no. arc points = 31138 no. surface atoms = 1404 nbur = 1415 mkacc time = 9.0000004E-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 = 1.484000 m= 347 mr = 2932 m= 0 mr = 22 time to grow re-entrant surface = 0.1000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2000000 number of dielectric boundary points 4036 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3032 ## 325 charges are in solution ## iepsmp to db, and charging done at 0.2700000 number of grid points assigned charge 8192 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -2.4574371E-09 3.1520360E-09 midg,1,midg; midg,igrid,midg -1.5168454E-09 2.8502229E-09 1,midg,midg; igrid,midg,midg 3.7706274E-09 4.3888446E-10 gauss-seidel spectral radius is 0.9849016 estimated iterations to convergence 67 setup time was (sec) 0.3900000 now iterating at: 09:44:30 rms-change max change #iterations 0.1007639 16.70618 at 10iterations 7.9341466E-03 1.258511 at 20iterations 6.3907186E-04 0.1265621 at 30iterations 6.0535011E-05 8.9216232E-03 at 40iterations 9.8739320E-06 1.2054443E-03 at 50iterations finished qdiffx linear iterations at : 09:44:32 total time elapsed so far: 3.230000 # loops : 50 mean,max change (kT/e) : 9.8739320E-06 1.2054443E-03 energy calculations done at 3.230000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.360000 DelPhi exited at 09:44:33 3.367u 0.176s 0:04.01 88.0% 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 Mon Oct 10 2011 at 09:44:33 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: 302 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2819 !!! WARNING: HIT 235 has a net charge of 0.5140 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: 1.753551 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): -17.42800 33.83400 ymin,ymax (A): -60.77300 -2.575000 zmin,zma (A): -1.007000 59.89800 x,y,z range (A): 51.26200 58.19800 60.90500 scale (grids/A): 1.753551 object centre (A): 8.203000 -31.67400 29.44550 number of atom coordinates read : 2819 total number of charged atoms : 2668 net assigned charge : 6.014023 assigned positive charge : 416.0799 centred at (gu) : 85.27988 85.06660 84.74847 assigned negative charge : -410.0663 centred at (gu) : 85.40920 84.73552 84.34296 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 70112 reading accessible surface arcs data from file ARCDAT no. of arc points read = 31138 grid for indexing accessible points = 1.400000 m= 22071 mr = 42487 m= 3023 mr = 13956 m= 140 mr = 1430 m= 1 mr = 18 m= 0 mr = 0 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3500000 number of dielectric boundary points 37456 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 228 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.4300000 number of grid points assigned charge 20742 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) : 0.5845169 object centre at (A) : 8.203000 -31.67400 29.44550 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -3.0602105E-02 8.9673623E-03 midg,1,midg; midg,igrid,midg 2.4064889E-02 3.2542691E-02 1,midg,midg; igrid,midg,midg 1.9652829E-02 8.4668929E-03 gauss-seidel spectral radius is 0.9984452 estimated iterations to convergence 201 setup time was (sec) 0.5700000 now iterating at: 09:44:34 rms-change max change #iterations 3.776355 162.9217 at 10iterations 1.682951 65.94307 at 20iterations 0.7451128 35.02658 at 30iterations 0.3325373 11.67127 at 40iterations 0.1478407 5.048948 at 50iterations 6.5693162E-02 2.391243 at 60iterations 2.9188598E-02 1.163895 at 70iterations 1.3018228E-02 0.4772720 at 80iterations 5.7785478E-03 0.2220545 at 90iterations 2.5643683E-03 9.9674225E-02 at 100iterations 1.1475170E-03 3.8078785E-02 at 110iterations 5.1017210E-04 1.8829346E-02 at 120iterations finished qdiffx linear iterations at : 09:44:41 total time elapsed so far: 7.650000 # loops : 120 mean,max change (kT/e) : 5.1017210E-04 1.8829346E-02 energy calculations done at 7.650000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.770000 DelPhi exited at 09:44:41 7.774u 0.206s 0:08.34 95.5% 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 09:44:41 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: 302 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2819 !!! WARNING: HIT 235 has a net charge of 0.5140 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: 2.630326 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): -17.42800 33.83400 ymin,ymax (A): -60.77300 -2.575000 zmin,zma (A): -1.007000 59.89800 x,y,z range (A): 51.26200 58.19800 60.90500 scale (grids/A): 2.630326 object centre (A): 8.203000 -31.67400 29.44550 number of atom coordinates read : 2819 total number of charged atoms : 2668 net assigned charge : 6.014023 assigned positive charge : 416.0799 centred at (gu) : 82.91975 82.59981 82.12259 assigned negative charge : -410.0663 centred at (gu) : 83.11366 82.10319 81.51433 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.2900000 boundary points on vw surface= 162068 reading accessible surface arcs data from file ARCDAT no. of arc points read = 31138 grid for indexing accessible points = 1.400000 m= 72013 mr = 105002 m= 23568 mr = 53455 m= 4868 mr = 16773 m= 494 mr = 3034 m= 29 mr = 221 m= 0 mr = 0 time to grow re-entrant surface = 0.4700000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.8600000 number of dielectric boundary points 84555 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 9 iepsmp to db, and charging done at 0.9500000 number of grid points assigned charge 21331 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) : 1.753551 object centre at (A) : 8.203000 -31.67400 29.44550 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.2636582 2.1521447E-02 midg,1,midg; midg,igrid,midg 0.5018229 0.4135538 1,midg,midg; igrid,midg,midg 0.1852235 8.7141812E-02 gauss-seidel spectral radius is 0.9992377 estimated iterations to convergence 286 setup time was (sec) 1.100000 now iterating at: 09:44:43 rms-change max change #iterations 9.594648 291.0892 at 10iterations 5.719429 142.5913 at 20iterations 3.352086 92.97812 at 30iterations 1.953579 52.84065 at 40iterations 1.131088 29.70747 at 50iterations 0.6544779 15.85317 at 60iterations 0.3767462 9.592963 at 70iterations 0.2167025 4.657894 at 80iterations 0.1241237 2.861750 at 90iterations 7.1270958E-02 1.720947 at 100iterations 4.0740270E-02 0.9864130 at 110iterations 2.3250522E-02 0.4982811 at 120iterations 1.3288920E-02 0.2714863 at 130iterations 7.5798952E-03 0.1655197 at 140iterations 4.3272334E-03 8.8828087E-02 at 150iterations 2.4657296E-03 5.4802895E-02 at 160iterations 1.4057598E-03 2.7618408E-02 at 170iterations 8.0338737E-04 1.8069267E-02 at 180iterations finished qdiffx linear iterations at : 09:44:54 total time elapsed so far: 12.51000 # loops : 180 mean,max change (kT/e) : 8.0338737E-04 1.8069267E-02 energy calculations done at 12.51000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.65000 DelPhi exited at 09:44:55 12.648u 0.216s 0:13.14 97.7% 0+0k 0+0io 0pf+0w