Tue Oct 11 04:23:36 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 Tue Oct 11 2011 at 04:23:36 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: 242 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2703 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: 0.6743957 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): -10.95200 36.70900 ymin,ymax (A): 6.902000 55.97200 zmin,zma (A): -7.547000 45.24100 x,y,z range (A): 47.66100 49.07000 52.78800 scale (grids/A): 0.6743957 object centre (A): 12.87850 31.43700 18.84700 number of atom coordinates read : 2703 total number of charged atoms : 2550 net assigned charge : 6.500017 assigned positive charge : 408.0409 centred at (gu) : 89.99860 90.48630 91.34926 assigned negative charge : -401.5414 centred at (gu) : 89.73154 90.30112 91.40655 start vw surface at 7.9999998E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 8392 nv = 96 ne = 84 npr = 54976 no. pairs analyzed = 54976 no. exposed pairs = 3195 no. arc points = 22918 no. surface atoms = 1074 nbur = 1629 mkacc time = 9.0000004E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 523 mr = 4874 m= 1 mr = 82 m= 0 mr = 0 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 9 time to turn everything in is 0.2000000 number of dielectric boundary points 3960 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2147 ## 190 charges are in solution ## iepsmp to db, and charging done at 0.2600000 number of grid points assigned charge 9580 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 3.1302292E-08 9.2953387E-09 midg,1,midg; midg,igrid,midg -2.7944184E-08 8.5676682E-08 1,midg,midg; igrid,midg,midg -5.6244211E-08 1.0041526E-07 gauss-seidel spectral radius is 0.9886106 estimated iterations to convergence 76 setup time was (sec) 0.3800000 now iterating at: 04:23:36 rms-change max change #iterations 0.1857198 23.40068 at 10iterations 2.1084312E-02 2.763273 at 20iterations 2.3780214E-03 0.3024940 at 30iterations 2.8158550E-04 4.0916443E-02 at 40iterations 3.9586383E-05 5.0430298E-03 at 50iterations finished qdiffx linear iterations at : 04:23:39 total time elapsed so far: 3.220000 # loops : 50 mean,max change (kT/e) : 3.9586383E-05 5.0430298E-03 energy calculations done at 3.220000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.350000 DelPhi exited at 04:23:40 3.356u 0.180s 0:03.98 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 Tue Oct 11 2011 at 04:23:40 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: 242 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2703 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: 2.023187 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): -10.95200 36.70900 ymin,ymax (A): 6.902000 55.97200 zmin,zma (A): -7.547000 45.24100 x,y,z range (A): 47.66100 49.07000 52.78800 scale (grids/A): 2.023187 object centre (A): 12.87850 31.43700 18.84700 number of atom coordinates read : 2703 total number of charged atoms : 2550 net assigned charge : 6.500017 assigned positive charge : 408.0409 centred at (gu) : 89.99516 91.45827 94.04739 assigned negative charge : -401.5414 centred at (gu) : 89.19421 90.90294 94.21938 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1900000 boundary points on vw surface= 89439 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22918 grid for indexing accessible points = 1.400000 m= 36069 mr = 63804 m= 6800 mr = 27738 m= 542 mr = 4624 m= 9 mr = 236 m= 0 mr = 0 time to grow re-entrant surface = 0.2200000 no. cavity mid-points inaccessible to solvent = 342 time to turn everything in is 0.4400000 number of dielectric boundary points 36457 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 126 iepsmp to db, and charging done at 0.5200000 number of grid points assigned charge 20178 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) : 0.6743957 object centre at (A) : 12.87850 31.43700 18.84700 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.8072571E-02 1.1548654E-02 midg,1,midg; midg,igrid,midg -9.7978488E-03 5.8419794E-02 1,midg,midg; igrid,midg,midg -1.3742033E-02 7.4086018E-02 gauss-seidel spectral radius is 0.9987943 estimated iterations to convergence 228 setup time was (sec) 0.6500000 now iterating at: 04:23:41 rms-change max change #iterations 4.864255 234.0707 at 10iterations 2.392740 77.98062 at 20iterations 1.171022 38.22935 at 30iterations 0.5761015 18.13454 at 40iterations 0.2830109 8.308081 at 50iterations 0.1395623 3.865810 at 60iterations 6.8274692E-02 1.826061 at 70iterations 3.3657957E-02 0.9182243 at 80iterations 1.6522998E-02 0.4654236 at 90iterations 8.1212651E-03 0.2414541 at 100iterations 3.9857146E-03 0.1112919 at 110iterations 1.9673605E-03 5.5740356E-02 at 120iterations finished qdiffx linear iterations at : 04:23:48 total time elapsed so far: 7.710000 # loops : 120 mean,max change (kT/e) : 1.9673605E-03 5.5740356E-02 energy calculations done at 7.710000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.850000 DelPhi exited at 04:23:48 7.848u 0.201s 0:08.36 96.1% 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 Tue Oct 11 2011 at 04:23:48 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: 242 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2703 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: 3.034781 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): -10.95200 36.70900 ymin,ymax (A): 6.902000 55.97200 zmin,zma (A): -7.547000 45.24100 x,y,z range (A): 47.66100 49.07000 52.78800 scale (grids/A): 3.034781 object centre (A): 12.87850 31.43700 18.84700 number of atom coordinates read : 2703 total number of charged atoms : 2550 net assigned charge : 6.500017 assigned positive charge : 408.0409 centred at (gu) : 89.99257 92.18738 96.07100 assigned negative charge : -401.5414 centred at (gu) : 88.79131 91.35443 96.32909 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.3900000 boundary points on vw surface= 206011 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22918 grid for indexing accessible points = 1.400000 m= 112733 mr = 153249 m= 45981 mr = 94557 m= 12818 mr = 38122 m= 2338 mr = 10139 m= 197 mr = 1666 m= 6 mr = 88 m= 0 mr = 0 time to grow re-entrant surface = 0.6899999 no. cavity mid-points inaccessible to solvent = 1088 time to turn everything in is 1.170000 number of dielectric boundary points 82263 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.270000 number of grid points assigned charge 20396 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) : 2.023187 object centre at (A) : 12.87850 31.43700 18.84700 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1567632 0.3114808 midg,1,midg; midg,igrid,midg -0.1176557 0.6077362 1,midg,midg; igrid,midg,midg -7.9837158E-02 0.5721515 gauss-seidel spectral radius is 0.9992959 estimated iterations to convergence 297 setup time was (sec) 1.410000 now iterating at: 04:23:50 rms-change max change #iterations 11.07463 325.8232 at 10iterations 6.528361 137.9411 at 20iterations 3.843977 75.27457 at 30iterations 2.263865 41.99735 at 40iterations 1.331073 22.85081 at 50iterations 0.7804630 14.94864 at 60iterations 0.4575227 7.786285 at 70iterations 0.2680818 4.835529 at 80iterations 0.1561223 2.452328 at 90iterations 9.1593914E-02 1.622686 at 100iterations 5.3492658E-02 0.9003451 at 110iterations 3.1304419E-02 0.5400352 at 120iterations 1.8245419E-02 0.3006744 at 130iterations 1.0695662E-02 0.1756363 at 140iterations 6.2715812E-03 0.1064949 at 150iterations 3.6941622E-03 7.0251465E-02 at 160iterations 2.1933003E-03 3.5598755E-02 at 170iterations 1.3147555E-03 2.4406433E-02 at 180iterations finished qdiffx linear iterations at : 04:24:01 total time elapsed so far: 12.94000 # loops : 180 mean,max change (kT/e) : 1.3147555E-03 2.4406433E-02 energy calculations done at 12.94000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.07000 DelPhi exited at 04:24:02 13.071u 0.219s 0:13.58 97.7% 0+0k 0+0io 0pf+0w