Mon Oct 10 16:13:52 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 16:13:52 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: 320 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4762 !!! WARNING: GLM 130 has a net charge of -0.0940 !!! WARNING: ASP 606 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= 0.1100000 grid size : 179 scale,in grids/A, set to be: 0.5518097 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): -23.65700 31.42700 ymin,ymax (A): -34.64700 29.51100 zmin,zma (A): -29.25200 35.26300 x,y,z range (A): 55.08400 64.15800 64.51500 scale (grids/A): 0.5518097 object centre (A): 3.885000 -2.568002 3.005501 number of atom coordinates read : 4762 total number of charged atoms : 4600 net assigned charge : 5.906026 assigned positive charge : 720.6137 centred at (gu) : 90.38278 89.95494 88.40867 assigned negative charge : -714.7120 centred at (gu) : 90.42799 89.97889 88.40346 start vw surface at 0.2000000 fill in re-entrant regions at 0.2100000 boundary points on vw surface= 9280 nv = 96 ne = 84 npr = 98207 no. pairs analyzed = 98207 no. exposed pairs = 5768 no. arc points = 39005 no. surface atoms = 1941 nbur = 2821 mkacc time = 0.2400000 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= 366 mr = 5164 m= 2 mr = 20 m= 0 mr = 0 time to grow re-entrant surface = 0.2700000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5000000 number of dielectric boundary points 4464 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3989 ## 537 charges are in solution ## iepsmp to db, and charging done at 0.6300000 number of grid points assigned charge 12284 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 5.7566080E-10 3.6483230E-10 midg,1,midg; midg,igrid,midg 7.8735524E-10 1.4425666E-10 1,midg,midg; igrid,midg,midg 9.6319397E-10 -1.5393670E-10 gauss-seidel spectral radius is 0.9831922 estimated iterations to convergence 63 setup time was (sec) 0.7700000 now iterating at: 16:13:53 rms-change max change #iterations 0.1019413 13.48154 at 10iterations 7.6412801E-03 1.108143 at 20iterations 1.2649075E-03 0.2228508 at 30iterations 4.8392295E-04 7.4573517E-02 at 40iterations 2.1048842E-04 2.7645111E-02 at 50iterations finished qdiffx linear iterations at : 16:13:56 total time elapsed so far: 4.130000 # loops : 50 mean,max change (kT/e) : 2.1048842E-04 2.7645111E-02 energy calculations done at 4.130000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.320000 DelPhi exited at 16:13:57 4.325u 0.224s 0:04.82 94.1% 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 Mon Oct 10 2011 at 16:13:57 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: 320 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4762 !!! WARNING: GLM 130 has a net charge of -0.0940 !!! WARNING: ASP 606 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= 0.1100000 grid size : 179 scale,in grids/A, set to be: 1.655429 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): -23.65700 31.42700 ymin,ymax (A): -34.64700 29.51100 zmin,zma (A): -29.25200 35.26300 x,y,z range (A): 55.08400 64.15800 64.51500 scale (grids/A): 1.655429 object centre (A): 3.885000 -2.568002 3.005501 number of atom coordinates read : 4762 total number of charged atoms : 4600 net assigned charge : 5.906026 assigned positive charge : 720.6137 centred at (gu) : 91.14690 89.86330 85.22451 assigned negative charge : -714.7120 centred at (gu) : 91.28363 89.93589 85.20991 start vw surface at 0.2000000 fill in re-entrant regions at 0.3400000 boundary points on vw surface= 103997 reading accessible surface arcs data from file ARCDAT no. of arc points read = 39005 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 33174 mr = 74089 m= 3516 mr = 23377 m= 104 mr = 1725 m= 0 mr = 17 time to grow re-entrant surface = 0.3600000 no. cavity mid-points inaccessible to solvent = 999 time to turn everything in is 0.7500000 number of dielectric boundary points 41583 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 415 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.8900000 number of grid points assigned charge 35332 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) : 0.5518097 object centre at (A) : 3.885000 -2.568002 3.005501 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.4788054E-02 -5.6844242E-03 midg,1,midg; midg,igrid,midg 1.6005646E-02 2.0075930E-02 1,midg,midg; igrid,midg,midg 6.8451911E-03 7.4268214E-04 gauss-seidel spectral radius is 0.9984054 estimated iterations to convergence 199 setup time was (sec) 1.070000 now iterating at: 16:13:58 rms-change max change #iterations 4.487920 217.0265 at 10iterations 1.985732 60.94222 at 20iterations 0.8727321 25.56281 at 30iterations 0.3849308 10.37301 at 40iterations 0.1698043 4.891777 at 50iterations 7.4880123E-02 2.085497 at 60iterations 3.3274483E-02 0.9524565 at 70iterations 1.4747848E-02 0.4422302 at 80iterations 6.6716596E-03 0.2085590 at 90iterations 3.0969933E-03 0.1049023 at 100iterations 1.5214432E-03 4.7992706E-02 at 110iterations 8.4346451E-04 2.7912140E-02 at 120iterations finished qdiffx linear iterations at : 16:14:07 total time elapsed so far: 9.510000 # loops : 120 mean,max change (kT/e) : 8.4346451E-04 2.7912140E-02 energy calculations done at 9.510000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.690000 DelPhi exited at 16:14:07 9.693u 0.250s 0:10.21 97.3% 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 16:14:07 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: 320 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4762 !!! WARNING: GLM 130 has a net charge of -0.0940 !!! WARNING: ASP 606 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= 0.1100000 grid size : 179 scale,in grids/A, set to be: 2.483144 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): -23.65700 31.42700 ymin,ymax (A): -34.64700 29.51100 zmin,zma (A): -29.25200 35.26300 x,y,z range (A): 55.08400 64.15800 64.51500 scale (grids/A): 2.483144 object centre (A): 3.885000 -2.568002 3.005501 number of atom coordinates read : 4762 total number of charged atoms : 4600 net assigned charge : 5.906026 assigned positive charge : 720.6137 centred at (gu) : 91.72009 89.79443 82.83631 assigned negative charge : -714.7120 centred at (gu) : 91.92543 89.90377 82.81458 start vw surface at 0.1900000 fill in re-entrant regions at 0.6900000 boundary points on vw surface= 242130 reading accessible surface arcs data from file ARCDAT no. of arc points read = 39005 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 115391 mr = 181079 m= 33386 mr = 92631 m= 5575 mr = 25419 m= 448 mr = 3699 m= 18 mr = 220 m= 0 mr = 0 time to grow re-entrant surface = 1.250000 no. cavity mid-points inaccessible to solvent = 3389 time to turn everything in is 2.070000 number of dielectric boundary points 93900 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 30 iepsmp to db, and charging done at 2.220000 number of grid points assigned charge 36750 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) : 1.655429 object centre at (A) : 3.885000 -2.568002 3.005501 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.4252885 -0.1108523 midg,1,midg; midg,igrid,midg 0.1686887 0.3769166 1,midg,midg; igrid,midg,midg 0.1099577 1.6500467E-02 gauss-seidel spectral radius is 0.9992419 estimated iterations to convergence 287 setup time was (sec) 2.430000 now iterating at: 16:14:10 rms-change max change #iterations 11.52228 363.2263 at 10iterations 6.785079 153.2056 at 20iterations 3.962473 90.22551 at 30iterations 2.311988 43.45760 at 40iterations 1.340193 26.21320 at 50iterations 0.7769587 15.23098 at 60iterations 0.4482309 7.919872 at 70iterations 0.2581664 4.819588 at 80iterations 0.1489107 2.820015 at 90iterations 8.5417658E-02 1.599472 at 100iterations 4.9075034E-02 0.7590179 at 110iterations 2.8178018E-02 0.4810216 at 120iterations 1.6202722E-02 0.3485260 at 130iterations 9.3181888E-03 0.1815643 at 140iterations 5.3750277E-03 9.5037460E-02 at 150iterations 3.1197474E-03 5.9675217E-02 at 160iterations 1.8297384E-03 3.1261444E-02 at 170iterations 1.1014617E-03 1.9260406E-02 at 180iterations finished qdiffx linear iterations at : 16:14:24 total time elapsed so far: 16.34000 # loops : 180 mean,max change (kT/e) : 1.1014617E-03 1.9260406E-02 energy calculations done at 16.34000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 16.52000 DelPhi exited at 16:14:24 16.521u 0.327s 0:17.12 98.3% 0+0k 0+0io 0pf+0w