Tue Oct 11 04:24:20 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 04:24:21 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: 254 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2768 !!! WARNING: TYS 1 has a net charge of -0.3600 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: 0.6598092 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): -14.50200 33.53600 ymin,ymax (A): 6.796000 55.05400 zmin,zma (A): 25.47100 79.42599 x,y,z range (A): 48.03800 48.25800 53.95499 scale (grids/A): 0.6598092 object centre (A): 9.517000 30.92500 52.44850 number of atom coordinates read : 2768 total number of charged atoms : 2616 net assigned charge : 3.140009 assigned positive charge : 417.3656 centred at (gu) : 89.96148 90.43707 88.54774 assigned negative charge : -414.2263 centred at (gu) : 90.25626 90.25038 88.55247 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1000000 boundary points on vw surface= 8044 nv = 96 ne = 84 npr = 57163 no. pairs analyzed = 57163 no. exposed pairs = 3383 no. arc points = 23480 no. surface atoms = 1138 nbur = 1630 mkacc time = 0.1000000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 461 mr = 4560 m= 3 mr = 61 m= 0 mr = 0 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 12 time to turn everything in is 0.2100000 number of dielectric boundary points 3887 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2301 ## 220 charges are in solution ## iepsmp to db, and charging done at 0.2800000 number of grid points assigned charge 9544 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.1856222E-08 5.1377995E-09 midg,1,midg; midg,igrid,midg -2.9230943E-08 5.0682299E-08 1,midg,midg; igrid,midg,midg 6.8314812E-08 -5.5513809E-08 gauss-seidel spectral radius is 0.9881063 estimated iterations to convergence 75 setup time was (sec) 0.4000000 now iterating at: 04:24:21 rms-change max change #iterations 0.1728867 22.05149 at 10iterations 1.8957341E-02 2.567835 at 20iterations 2.0872438E-03 0.2942295 at 30iterations 2.7031027E-04 3.6106110E-02 at 40iterations 5.2873322E-05 6.3400269E-03 at 50iterations finished qdiffx linear iterations at : 04:24:24 total time elapsed so far: 3.230000 # loops : 50 mean,max change (kT/e) : 5.2873322E-05 6.3400269E-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) 3.370000 DelPhi exited at 04:24:25 3.370u 0.160s 0:04.04 87.3% 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 Tue Oct 11 2011 at 04:24:25 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: 254 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2768 !!! WARNING: TYS 1 has a net charge of -0.3600 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: 1.979427 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): -14.50200 33.53600 ymin,ymax (A): 6.796000 55.05400 zmin,zma (A): 25.47100 79.42599 x,y,z range (A): 48.03800 48.25800 53.95499 scale (grids/A): 1.979427 object centre (A): 9.517000 30.92500 52.44850 number of atom coordinates read : 2768 total number of charged atoms : 2616 net assigned charge : 3.140009 assigned positive charge : 417.3656 centred at (gu) : 89.88400 91.31082 85.64291 assigned negative charge : -414.2263 centred at (gu) : 90.76833 90.75068 85.65705 start vw surface at 0.1000000 fill in re-entrant regions at 0.2000000 boundary points on vw surface= 86644 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23480 grid for indexing accessible points = 1.400000 m= 32263 mr = 61286 m= 5313 mr = 24088 m= 340 mr = 3315 m= 6 mr = 130 m= 0 mr = 0 time to grow re-entrant surface = 0.2100000 no. cavity mid-points inaccessible to solvent = 627 time to turn everything in is 0.4300000 number of dielectric boundary points 35747 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 115 iepsmp to db, and charging done at 0.5200000 number of grid points assigned charge 20644 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) : 0.6598092 object centre at (A) : 9.517000 30.92500 52.44850 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -6.0811951E-03 -2.0184247E-02 midg,1,midg; midg,igrid,midg -1.4834923E-02 4.2998731E-02 1,midg,midg; igrid,midg,midg 7.2684385E-02 -1.5151693E-02 gauss-seidel spectral radius is 0.9987478 estimated iterations to convergence 224 setup time was (sec) 0.6600000 now iterating at: 04:24:25 rms-change max change #iterations 4.798796 189.3712 at 10iterations 2.329422 70.60648 at 20iterations 1.125653 36.23014 at 30iterations 0.5465028 18.13879 at 40iterations 0.2649428 7.278994 at 50iterations 0.1280688 3.688919 at 60iterations 6.2302891E-02 1.721638 at 70iterations 3.0183041E-02 0.9051056 at 80iterations 1.4677149E-02 0.4914808 at 90iterations 7.1171541E-03 0.2194595 at 100iterations 3.4774391E-03 9.8838806E-02 at 110iterations 1.7108225E-03 5.0663948E-02 at 120iterations finished qdiffx linear iterations at : 04:24:33 total time elapsed so far: 7.740000 # loops : 120 mean,max change (kT/e) : 1.7108225E-03 5.0663948E-02 energy calculations done at 7.740000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.870000 DelPhi exited at 04:24:34 7.871u 0.207s 0:09.38 86.0% 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 Tue Oct 11 2011 at 04:24:34 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: 254 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2768 !!! WARNING: TYS 1 has a net charge of -0.3600 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: 2.969141 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): -14.50200 33.53600 ymin,ymax (A): 6.796000 55.05400 zmin,zma (A): 25.47100 79.42599 x,y,z range (A): 48.03800 48.25800 53.95499 scale (grids/A): 2.969141 object centre (A): 9.517000 30.92500 52.44850 number of atom coordinates read : 2768 total number of charged atoms : 2616 net assigned charge : 3.140009 assigned positive charge : 417.3656 centred at (gu) : 89.82587 91.96609 83.46407 assigned negative charge : -414.2263 centred at (gu) : 91.15242 91.12598 83.48557 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.3800000 boundary points on vw surface= 200104 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23480 grid for indexing accessible points = 1.400000 m= 104171 mr = 148198 m= 38648 mr = 86037 m= 9721 mr = 31121 m= 1436 mr = 7271 m= 93 mr = 963 m= 1 mr = 35 m= 0 mr = 0 time to grow re-entrant surface = 0.6500000 no. cavity mid-points inaccessible to solvent = 2131 time to turn everything in is 1.120000 number of dielectric boundary points 80549 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.210000 number of grid points assigned charge 20919 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) : 1.979427 object centre at (A) : 9.517000 30.92500 52.44850 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2099096 -0.2744810 midg,1,midg; midg,igrid,midg -0.1707274 0.4953710 1,midg,midg; igrid,midg,midg 0.5678369 -7.0199169E-02 gauss-seidel spectral radius is 0.9992877 estimated iterations to convergence 296 setup time was (sec) 1.360000 now iterating at: 04:24:36 rms-change max change #iterations 10.94436 451.1395 at 10iterations 6.446386 136.6049 at 20iterations 3.796054 73.32088 at 30iterations 2.230403 41.55238 at 40iterations 1.308308 26.32896 at 50iterations 0.7667454 15.62978 at 60iterations 0.4478602 8.066345 at 70iterations 0.2616728 4.563227 at 80iterations 0.1524332 2.645378 at 90iterations 8.9063525E-02 1.556774 at 100iterations 5.1888768E-02 0.8905735 at 110iterations 3.0385269E-02 0.5773411 at 120iterations 1.7705446E-02 0.2870865 at 130iterations 1.0369594E-02 0.1896064 at 140iterations 6.0933759E-03 0.1131630 at 150iterations 3.6181395E-03 6.5418243E-02 at 160iterations 2.1688556E-03 3.8173676E-02 at 170iterations 1.3270333E-03 2.5379181E-02 at 180iterations finished qdiffx linear iterations at : 04:24:47 total time elapsed so far: 12.71000 # loops : 180 mean,max change (kT/e) : 1.3270333E-03 2.5379181E-02 energy calculations done at 12.71000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.83000 DelPhi exited at 04:24:47 12.834u 0.231s 0:13.44 97.1% 0+0k 0+0io 0pf+0w