Mon Oct 10 22:35:34 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 22:35:35 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 = 2673 !!! 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= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 0.6054216 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): -19.93500 32.22600 ymin,ymax (A): 18.03600 76.83800 zmin,zma (A): 9.929000 52.54100 x,y,z range (A): 52.16100 58.80200 42.61200 scale (grids/A): 0.6054216 object centre (A): 6.145501 47.43700 31.23500 number of atom coordinates read : 2673 total number of charged atoms : 2530 net assigned charge : 2.500017 assigned positive charge : 401.8347 centred at (gu) : 91.05270 89.24401 89.83846 assigned negative charge : -399.3353 centred at (gu) : 91.02824 89.55167 90.03512 start vw surface at 0.1800000 fill in re-entrant regions at 0.1900000 boundary points on vw surface= 6398 nv = 96 ne = 84 npr = 54591 no. pairs analyzed = 54591 no. exposed pairs = 3138 no. arc points = 21856 no. surface atoms = 1063 nbur = 1610 mkacc time = 0.1500000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 275 mr = 3580 m= 0 mr = 29 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 6 time to turn everything in is 0.3700000 number of dielectric boundary points 3064 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2148 ## 238 charges are in solution ## iepsmp to db, and charging done at 0.5200000 number of grid points assigned charge 7980 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.0046836E-08 -7.4673512E-09 midg,1,midg; midg,igrid,midg 1.7035884E-08 -1.0895355E-08 1,midg,midg; igrid,midg,midg 7.1909333E-11 2.8406004E-09 gauss-seidel spectral radius is 0.9858791 estimated iterations to convergence 69 setup time was (sec) 0.7100000 now iterating at: 22:35:36 rms-change max change #iterations 0.1160766 17.44065 at 10iterations 1.0729730E-02 1.666443 at 20iterations 1.3462648E-03 0.2867737 at 30iterations 3.3149714E-04 8.2668304E-02 at 40iterations 9.5446492E-05 2.4311066E-02 at 50iterations finished qdiffx linear iterations at : 22:35:40 total time elapsed so far: 4.310000 # loops : 50 mean,max change (kT/e) : 9.5446492E-05 2.4311066E-02 energy calculations done at 4.310000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.510000 DelPhi exited at 22:35:40 4.511u 0.291s 0:05.63 85.2% 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 Mon Oct 10 2011 at 22:35:40 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 = 2673 !!! 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= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.816265 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): -19.93500 32.22600 ymin,ymax (A): 18.03600 76.83800 zmin,zma (A): 9.929000 52.54100 x,y,z range (A): 52.16100 58.80200 42.61200 scale (grids/A): 1.816265 object centre (A): 6.145501 47.43700 31.23500 number of atom coordinates read : 2673 total number of charged atoms : 2530 net assigned charge : 2.500017 assigned positive charge : 401.8347 centred at (gu) : 93.15746 87.73183 89.51509 assigned negative charge : -399.3353 centred at (gu) : 93.08450 88.65468 90.10519 start vw surface at 0.1500000 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 70059 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21856 grid for indexing accessible points = 1.400000 m= 23511 mr = 49222 m= 3226 mr = 17404 m= 144 mr = 2031 m= 5 mr = 38 m= 0 mr = 0 time to grow re-entrant surface = 0.2300000 no. cavity mid-points inaccessible to solvent = 2173 time to turn everything in is 0.5200000 number of dielectric boundary points 28250 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 162 iepsmp to db, and charging done at 0.6500000 number of grid points assigned charge 19746 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) : 0.6054216 object centre at (A) : 6.145501 47.43700 31.23500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.5303783E-02 7.7801681E-04 midg,1,midg; midg,igrid,midg -1.4752473E-02 -5.7683185E-02 1,midg,midg; igrid,midg,midg 1.5836144E-03 -1.6244290E-03 gauss-seidel spectral radius is 0.9985040 estimated iterations to convergence 205 setup time was (sec) 0.8400000 now iterating at: 22:35:41 rms-change max change #iterations 3.917672 184.7798 at 10iterations 1.765141 68.81747 at 20iterations 0.7982196 32.07516 at 30iterations 0.3624059 12.12515 at 40iterations 0.1630977 6.358643 at 50iterations 7.3980384E-02 2.352300 at 60iterations 3.3741545E-02 1.086017 at 70iterations 1.5335960E-02 0.4962926 at 80iterations 7.0199990E-03 0.2410812 at 90iterations 3.3130425E-03 0.1118145 at 100iterations 1.6008443E-03 5.9040070E-02 at 110iterations 8.1544812E-04 3.4507751E-02 at 120iterations finished qdiffx linear iterations at : 22:35:50 total time elapsed so far: 9.280000 # loops : 120 mean,max change (kT/e) : 8.1544812E-04 3.4507751E-02 energy calculations done at 9.280000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.470000 DelPhi exited at 22:35:51 9.471u 0.269s 0:10.29 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 22:35:51 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 = 2673 !!! 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= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 2.724397 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): -19.93500 32.22600 ymin,ymax (A): 18.03600 76.83800 zmin,zma (A): 9.929000 52.54100 x,y,z range (A): 52.16100 58.80200 42.61200 scale (grids/A): 2.724397 object centre (A): 6.145501 47.43700 31.23500 number of atom coordinates read : 2673 total number of charged atoms : 2530 net assigned charge : 2.500017 assigned positive charge : 401.8347 centred at (gu) : 94.73627 86.59745 89.27242 assigned negative charge : -399.3353 centred at (gu) : 94.62657 87.98192 90.15764 start vw surface at 0.1700000 fill in re-entrant regions at 0.5200000 boundary points on vw surface= 162540 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21856 grid for indexing accessible points = 1.400000 m= 78915 mr = 119333 m= 25839 mr = 64869 m= 5602 mr = 20831 m= 626 mr = 4280 m= 27 mr = 426 m= 0 mr = 1 time to grow re-entrant surface = 0.7400000 no. cavity mid-points inaccessible to solvent = 7407 time to turn everything in is 1.380000 number of dielectric boundary points 63809 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3 iepsmp to db, and charging done at 1.530000 number of grid points assigned charge 20235 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) : 1.816265 object centre at (A) : 6.145501 47.43700 31.23500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2729213 4.6598915E-02 midg,1,midg; midg,igrid,midg -0.6447012 -0.6771200 1,midg,midg; igrid,midg,midg -2.2711042E-02 -5.2743096E-02 gauss-seidel spectral radius is 0.9992176 estimated iterations to convergence 282 setup time was (sec) 1.720000 now iterating at: 22:35:53 rms-change max change #iterations 9.319082 302.5710 at 10iterations 5.337412 135.9315 at 20iterations 3.032520 63.51801 at 30iterations 1.720645 35.25845 at 40iterations 0.9760994 20.21833 at 50iterations 0.5535836 10.13566 at 60iterations 0.3129767 5.910907 at 70iterations 0.1773723 3.344067 at 80iterations 0.1005080 1.876862 at 90iterations 5.6815293E-02 1.094204 at 100iterations 3.2194685E-02 0.6448994 at 110iterations 1.8306330E-02 0.3591042 at 120iterations 1.0430036E-02 0.2164307 at 130iterations 5.9914389E-03 0.1214294 at 140iterations 3.5020993E-03 8.2762718E-02 at 150iterations 2.0956404E-03 4.7458649E-02 at 160iterations 1.3041837E-03 3.4713745E-02 at 170iterations 8.5369649E-04 2.2270203E-02 at 180iterations finished qdiffx linear iterations at : 22:36:06 total time elapsed so far: 15.15000 # loops : 180 mean,max change (kT/e) : 8.5369649E-04 2.2270203E-02 energy calculations done at 15.15000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.33000 DelPhi exited at 22:36:07 15.334u 0.290s 0:15.90 98.2% 0+0k 0+0io 0pf+0w