Mon Oct 10 14:37:53 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 14:37:53 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: 228 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2105 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: 0.7378238 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): 46.25500 91.41800 ymin,ymax (A): -8.962000 38.20000 zmin,zma (A): -3.644000 44.60600 x,y,z range (A): 45.16300 47.16200 48.25000 scale (grids/A): 0.7378238 object centre (A): 68.83650 14.61900 20.48100 number of atom coordinates read : 2105 total number of charged atoms : 1967 net assigned charge : -4.999990 assigned positive charge : 315.2119 centred at (gu) : 89.24453 90.03422 89.97307 assigned negative charge : -320.2120 centred at (gu) : 89.25278 90.07091 90.13086 start vw surface at 0.1200000 fill in re-entrant regions at 0.1300000 boundary points on vw surface= 7748 nv = 96 ne = 84 npr = 43959 no. pairs analyzed = 43959 no. exposed pairs = 2629 no. arc points = 18557 no. surface atoms = 892 nbur = 1213 mkacc time = 0.1100000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 512 mr = 4270 m= 5 mr = 116 m= 0 mr = 0 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 3 time to turn everything in is 0.2700000 number of dielectric boundary points 3879 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1588 ## 112 charges are in solution ## iepsmp to db, and charging done at 0.3700000 number of grid points assigned charge 8377 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 6.7454991E-08 -2.3853332E-07 midg,1,midg; midg,igrid,midg -4.8178247E-08 -1.2055278E-07 1,midg,midg; igrid,midg,midg -8.7062361E-08 -8.0282575E-08 gauss-seidel spectral radius is 0.9904261 estimated iterations to convergence 83 setup time was (sec) 0.5400000 now iterating at: 14:37:54 rms-change max change #iterations 0.2412670 29.78059 at 10iterations 3.2287255E-02 4.252402 at 20iterations 4.3173479E-03 0.5737572 at 30iterations 5.7408487E-04 6.8782806E-02 at 40iterations 7.7548582E-05 1.0181352E-02 at 50iterations finished qdiffx linear iterations at : 14:37:58 total time elapsed so far: 4.350000 # loops : 50 mean,max change (kT/e) : 7.7548582E-05 1.0181352E-02 energy calculations done at 4.350000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.520000 DelPhi exited at 14:37:59 4.524u 0.373s 0:05.40 90.5% 0+0k 0+0io 1pf+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 14:37:59 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: 228 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2105 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: 2.213471 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): 46.25500 91.41800 ymin,ymax (A): -8.962000 38.20000 zmin,zma (A): -3.644000 44.60600 x,y,z range (A): 45.16300 47.16200 48.25000 scale (grids/A): 2.213471 object centre (A): 68.83650 14.61900 20.48100 number of atom coordinates read : 2105 total number of charged atoms : 1967 net assigned charge : -4.999990 assigned positive charge : 315.2119 centred at (gu) : 87.73377 90.10262 89.91903 assigned negative charge : -320.2120 centred at (gu) : 87.75842 90.21288 90.39263 start vw surface at 0.1200000 fill in re-entrant regions at 0.2700000 boundary points on vw surface= 81944 reading accessible surface arcs data from file ARCDAT no. of arc points read = 18557 grid for indexing accessible points = 1.400000 m= 32224 mr = 56510 m= 6761 mr = 24495 m= 678 mr = 4747 m= 23 mr = 404 m= 0 mr = 0 time to grow re-entrant surface = 0.3600000 no. cavity mid-points inaccessible to solvent = 172 time to turn everything in is 0.7000000 number of dielectric boundary points 35474 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 53 iepsmp to db, and charging done at 0.8700000 number of grid points assigned charge 15672 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) : 0.7378238 object centre at (A) : 68.83650 14.61900 20.48100 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.8455942E-04 -0.1278452 midg,1,midg; midg,igrid,midg -2.3810554E-02 -2.5489103E-02 1,midg,midg; igrid,midg,midg -1.6838944E-03 8.0216965E-03 gauss-seidel spectral radius is 0.9989188 estimated iterations to convergence 241 setup time was (sec) 1.050000 now iterating at: 14:38:00 rms-change max change #iterations 5.026035 215.9473 at 10iterations 2.544648 76.91852 at 20iterations 1.292689 39.40708 at 30iterations 0.6580890 19.96940 at 40iterations 0.3344481 9.541281 at 50iterations 0.1701795 5.146541 at 60iterations 8.6181007E-02 2.751863 at 70iterations 4.3995444E-02 1.189844 at 80iterations 2.2432491E-02 0.6582990 at 90iterations 1.1359884E-02 0.2927530 at 100iterations 5.7797199E-03 0.1576252 at 110iterations 2.9451095E-03 8.6910248E-02 at 120iterations finished qdiffx linear iterations at : 14:38:10 total time elapsed so far: 10.68000 # loops : 120 mean,max change (kT/e) : 2.9451095E-03 8.6910248E-02 energy calculations done at 10.68000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.85000 DelPhi exited at 14:38:11 10.857u 0.453s 0:11.89 95.0% 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 Mon Oct 10 2011 at 14:38:11 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: 228 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2105 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: 3.320207 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): 46.25500 91.41800 ymin,ymax (A): -8.962000 38.20000 zmin,zma (A): -3.644000 44.60600 x,y,z range (A): 45.16300 47.16200 48.25000 scale (grids/A): 3.320207 object centre (A): 68.83650 14.61900 20.48100 number of atom coordinates read : 2105 total number of charged atoms : 1967 net assigned charge : -4.999990 assigned positive charge : 315.2119 centred at (gu) : 86.60060 90.15398 89.87863 assigned negative charge : -320.2120 centred at (gu) : 86.63754 90.31929 90.58891 start vw surface at 0.1200000 fill in re-entrant regions at 0.8900000 boundary points on vw surface= 188778 reading accessible surface arcs data from file ARCDAT no. of arc points read = 18557 grid for indexing accessible points = 1.400000 m= 99478 mr = 136388 m= 41749 mr = 82307 m= 12894 mr = 34665 m= 2912 mr = 10372 m= 334 mr = 2293 m= 18 mr = 224 m= 0 mr = 3 time to grow re-entrant surface = 1.140000 no. cavity mid-points inaccessible to solvent = 702 time to turn everything in is 2.160000 number of dielectric boundary points 79911 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.310000 number of grid points assigned charge 15736 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) : 2.213471 object centre at (A) : 68.83650 14.61900 20.48100 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.9820650E-02 -1.356983 midg,1,midg; midg,igrid,midg -0.1935187 -0.1120600 1,midg,midg; igrid,midg,midg 3.8016289E-02 6.8880387E-02 gauss-seidel spectral radius is 0.9993155 estimated iterations to convergence 302 setup time was (sec) 2.500000 now iterating at: 14:38:14 rms-change max change #iterations 10.81315 348.8622 at 10iterations 6.339232 111.1394 at 20iterations 3.734001 61.50485 at 30iterations 2.189970 35.39053 at 40iterations 1.285577 23.20615 at 50iterations 0.7554748 12.30230 at 60iterations 0.4421155 6.882844 at 70iterations 0.2601198 4.261436 at 80iterations 0.1521700 2.430789 at 90iterations 8.9326173E-02 1.488232 at 100iterations 5.2368790E-02 0.8226471 at 110iterations 3.0685153E-02 0.4955101 at 120iterations 1.8029524E-02 0.3186252 at 130iterations 1.0560364E-02 0.1876526 at 140iterations 6.1832154E-03 0.1023674 at 150iterations 3.6270372E-03 6.4245224E-02 at 160iterations 2.1238730E-03 3.5285950E-02 at 170iterations 1.2481656E-03 2.2331238E-02 at 180iterations finished qdiffx linear iterations at : 14:38:31 total time elapsed so far: 19.27000 # loops : 180 mean,max change (kT/e) : 1.2481656E-03 2.2331238E-02 energy calculations done at 19.27000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 19.45000 DelPhi exited at 14:38:31 19.455u 0.477s 0:20.43 97.5% 0+0k 0+0io 0pf+0w