Sat Oct 15 12:56:07 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 Sat Oct 15 2011 at 12:56:07 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: 300 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2433 !!! WARNING: GLM 182 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= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6920685 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): -6.332000 43.64200 ymin,ymax (A): -13.67100 37.76900 zmin,zma (A): 2.164000 44.70000 x,y,z range (A): 49.97400 51.43999 42.53600 scale (grids/A): 0.6920685 object centre (A): 18.65500 12.04900 23.43200 number of atom coordinates read : 2433 total number of charged atoms : 2287 net assigned charge : 5.406019 assigned positive charge : 374.8600 centred at (gu) : 89.62674 90.96037 91.03286 assigned negative charge : -369.4545 centred at (gu) : 89.58624 91.10458 91.14114 start vw surface at 7.9999998E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 7712 nv = 96 ne = 84 npr = 49523 no. pairs analyzed = 49523 no. exposed pairs = 2919 no. arc points = 20184 no. surface atoms = 998 nbur = 1435 mkacc time = 7.9999998E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 439 mr = 4312 m= 5 mr = 96 m= 0 mr = 0 time to grow re-entrant surface = 9.9999994E-02 no. cavity mid-points inaccessible to solvent = 3 time to turn everything in is 0.1900000 number of dielectric boundary points 3748 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1907 ## 178 charges are in solution ## iepsmp to db, and charging done at 0.2600000 number of grid points assigned charge 8943 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 6.2605579E-08 -1.5726103E-08 midg,1,midg; midg,igrid,midg 7.5363737E-08 -3.3925005E-08 1,midg,midg; igrid,midg,midg 1.7093440E-08 4.5833239E-08 gauss-seidel spectral radius is 0.9891535 estimated iterations to convergence 78 setup time was (sec) 0.3900000 now iterating at: 12:56:08 rms-change max change #iterations 0.1995860 28.16880 at 10iterations 2.4538955E-02 3.265704 at 20iterations 3.6300635E-03 0.5553818 at 30iterations 8.8518392E-04 0.1346207 at 40iterations 2.9339312E-04 4.0863037E-02 at 50iterations finished qdiffx linear iterations at : 12:56:11 total time elapsed so far: 3.410000 # loops : 50 mean,max change (kT/e) : 2.9339312E-04 4.0863037E-02 energy calculations done at 3.410000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.550000 DelPhi exited at 12:56:12 3.549u 0.195s 0:04.24 87.9% 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 Sat Oct 15 2011 at 12:56:12 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: 300 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2433 !!! WARNING: GLM 182 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= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.076205 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): -6.332000 43.64200 ymin,ymax (A): -13.67100 37.76900 zmin,zma (A): 2.164000 44.70000 x,y,z range (A): 49.97400 51.43999 42.53600 scale (grids/A): 2.076205 object centre (A): 18.65500 12.04900 23.43200 number of atom coordinates read : 2433 total number of charged atoms : 2287 net assigned charge : 5.406019 assigned positive charge : 374.8600 centred at (gu) : 88.87949 92.88026 93.09815 assigned negative charge : -369.4545 centred at (gu) : 88.75859 93.31353 93.42317 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 82615 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20184 grid for indexing accessible points = 1.400000 m= 31586 mr = 58258 m= 5727 mr = 23823 m= 496 mr = 3688 m= 17 mr = 251 m= 0 mr = 2 time to grow re-entrant surface = 0.2000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4100000 number of dielectric boundary points 34419 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 111 iepsmp to db, and charging done at 0.4900000 number of grid points assigned charge 18150 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) : 0.6920685 object centre at (A) : 18.65500 12.04900 23.43200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 6.1339345E-02 1.0982360E-02 midg,1,midg; midg,igrid,midg 3.5480224E-02 -2.7067551E-02 1,midg,midg; igrid,midg,midg 4.7408678E-02 3.2889468E-03 gauss-seidel spectral radius is 0.9988198 estimated iterations to convergence 230 setup time was (sec) 0.6400000 now iterating at: 12:56:13 rms-change max change #iterations 4.913737 219.4471 at 10iterations 2.411845 96.58151 at 20iterations 1.198341 39.21264 at 30iterations 0.5924221 19.29564 at 40iterations 0.2928835 8.803972 at 50iterations 0.1449634 4.374329 at 60iterations 7.1755603E-02 2.105338 at 70iterations 3.5853334E-02 1.043226 at 80iterations 1.7951570E-02 0.5417686 at 90iterations 9.1253472E-03 0.2957973 at 100iterations 4.7209384E-03 0.1391525 at 110iterations 2.5894644E-03 8.7242126E-02 at 120iterations finished qdiffx linear iterations at : 12:56:20 total time elapsed so far: 8.030000 # loops : 120 mean,max change (kT/e) : 2.5894644E-03 8.7242126E-02 energy calculations done at 8.030000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.160000 DelPhi exited at 12:56:21 8.166u 0.250s 0:08.96 93.8% 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 Sat Oct 15 2011 at 12:56:21 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: 300 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2433 !!! WARNING: GLM 182 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= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 3.114308 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): -6.332000 43.64200 ymin,ymax (A): -13.67100 37.76900 zmin,zma (A): 2.164000 44.70000 x,y,z range (A): 49.97400 51.43999 42.53600 scale (grids/A): 3.114308 object centre (A): 18.65500 12.04900 23.43200 number of atom coordinates read : 2433 total number of charged atoms : 2287 net assigned charge : 5.406019 assigned positive charge : 374.8600 centred at (gu) : 88.31920 94.32021 94.64722 assigned negative charge : -369.4545 centred at (gu) : 88.13794 94.97024 95.13473 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.5300000 boundary points on vw surface= 190999 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20184 grid for indexing accessible points = 1.400000 m= 100216 mr = 140968 m= 38791 mr = 83034 m= 10643 mr = 31652 m= 2089 mr = 8180 m= 244 mr = 1510 m= 17 mr = 165 m= 0 mr = 2 time to grow re-entrant surface = 0.6300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.260000 number of dielectric boundary points 77488 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.350000 number of grid points assigned charge 18296 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) : 2.076205 object centre at (A) : 18.65500 12.04900 23.43200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.5717027 5.6686084E-04 midg,1,midg; midg,igrid,midg 0.7021814 -0.2975570 1,midg,midg; igrid,midg,midg 0.5495064 -0.1588008 gauss-seidel spectral radius is 0.9992949 estimated iterations to convergence 297 setup time was (sec) 1.500000 now iterating at: 12:56:23 rms-change max change #iterations 11.07956 374.7158 at 10iterations 6.552470 132.3802 at 20iterations 3.864113 79.51001 at 30iterations 2.277916 40.82801 at 40iterations 1.338577 26.44846 at 50iterations 0.7865801 14.24504 at 60iterations 0.4615368 7.349506 at 70iterations 0.2701678 4.493854 at 80iterations 0.1579506 2.562695 at 90iterations 9.2849210E-02 1.553909 at 100iterations 5.4565445E-02 0.9274902 at 110iterations 3.2149501E-02 0.5497799 at 120iterations 1.9226514E-02 0.3118439 at 130iterations 1.1706309E-02 0.2192974 at 140iterations 7.3898509E-03 0.1372757 at 150iterations 4.9193837E-03 0.1020737 at 160iterations 3.4804489E-03 8.4926605E-02 at 170iterations 2.6210130E-03 5.5862427E-02 at 180iterations finished qdiffx linear iterations at : 12:56:35 total time elapsed so far: 13.51000 # loops : 180 mean,max change (kT/e) : 2.6210130E-03 5.5862427E-02 energy calculations done at 13.51000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.65000 DelPhi exited at 12:56:35 13.650u 0.218s 0:14.62 94.8% 0+0k 0+0io 0pf+0w