Sat Oct 15 11:28:25 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 11:28:25 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: 249 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4525 !!! WARNING: GLM 703 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= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 0.5763502 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): -6.275000 51.99100 ymin,ymax (A): 95.52700 157.2950 zmin,zma (A): -10.42900 48.10100 x,y,z range (A): 58.26600 61.76800 58.53000 scale (grids/A): 0.5763502 object centre (A): 22.85800 126.4110 18.83600 number of atom coordinates read : 4525 total number of charged atoms : 4351 net assigned charge : 4.906046 assigned positive charge : 691.1531 centred at (gu) : 89.41122 90.41772 90.56654 assigned negative charge : -686.2514 centred at (gu) : 89.40635 90.47475 90.53245 start vw surface at 0.1100000 fill in re-entrant regions at 0.1200000 boundary points on vw surface= 9708 nv = 96 ne = 84 npr = 92021 no. pairs analyzed = 92021 no. exposed pairs = 5532 no. arc points = 38094 no. surface atoms = 1858 nbur = 2667 mkacc time = 0.1600000 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 = 1.484000 m= 468 mr = 5290 m= 0 mr = 33 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3000000 number of dielectric boundary points 4853 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3899 ## 434 charges are in solution ## iepsmp to db, and charging done at 0.4100000 number of grid points assigned charge 12649 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -6.8235854E-11 2.2473547E-09 midg,1,midg; midg,igrid,midg 2.4019449E-09 -8.6980945E-10 1,midg,midg; igrid,midg,midg 9.1311136E-10 9.5427111E-10 gauss-seidel spectral radius is 0.9845812 estimated iterations to convergence 66 setup time was (sec) 0.5600000 now iterating at: 11:28:27 rms-change max change #iterations 0.1200485 17.13296 at 10iterations 1.0530767E-02 1.276596 at 20iterations 2.5656652E-03 0.3996162 at 30iterations 1.2962782E-03 0.2112465 at 40iterations 6.8706699E-04 0.1122818 at 50iterations finished qdiffx linear iterations at : 11:28:32 total time elapsed so far: 4.070000 # loops : 50 mean,max change (kT/e) : 6.8706699E-04 0.1122818 energy calculations done at 4.070000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.200000 DelPhi exited at 11:28:34 4.199u 0.292s 0:08.47 52.8% 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 11:28:34 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: 249 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4525 !!! WARNING: GLM 703 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= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 1.729051 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): -6.275000 51.99100 ymin,ymax (A): 95.52700 157.2950 zmin,zma (A): -10.42900 48.10100 x,y,z range (A): 58.26600 61.76800 58.53000 scale (grids/A): 1.729051 object centre (A): 22.85800 126.4110 18.83600 number of atom coordinates read : 4525 total number of charged atoms : 4351 net assigned charge : 4.906046 assigned positive charge : 691.1531 centred at (gu) : 88.23220 91.25135 91.69860 assigned negative charge : -686.2514 centred at (gu) : 88.21850 91.42401 91.59688 start vw surface at 0.1300000 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 107938 reading accessible surface arcs data from file ARCDAT no. of arc points read = 38094 grid for indexing accessible points = 1.400000 m= 36301 mr = 75987 m= 4803 mr = 25511 m= 219 mr = 2602 m= 3 mr = 45 m= 0 mr = 0 time to grow re-entrant surface = 0.2600000 no. cavity mid-points inaccessible to solvent = 538 time to turn everything in is 0.5500000 number of dielectric boundary points 45119 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 399 iepsmp to db, and charging done at 0.6600000 number of grid points assigned charge 33741 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) : 0.5763502 object centre at (A) : 22.85800 126.4110 18.83600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -8.5896207E-03 3.9294865E-02 midg,1,midg; midg,igrid,midg 3.4887005E-02 -3.6623530E-02 1,midg,midg; igrid,midg,midg -4.1971952E-04 3.3525147E-02 gauss-seidel spectral radius is 0.9985376 estimated iterations to convergence 207 setup time was (sec) 0.8100000 now iterating at: 11:28:36 rms-change max change #iterations 4.852773 165.3507 at 10iterations 2.203501 66.54580 at 20iterations 1.003485 28.80707 at 30iterations 0.4575512 12.70825 at 40iterations 0.2090454 6.380634 at 50iterations 9.5766753E-02 2.802823 at 60iterations 4.4071760E-02 1.223890 at 70iterations 2.0539830E-02 0.5197468 at 80iterations 9.8678330E-03 0.2732430 at 90iterations 5.1540034E-03 0.1657104 at 100iterations 3.0759163E-03 0.1009712 at 110iterations 2.0980875E-03 6.9646835E-02 at 120iterations finished qdiffx linear iterations at : 11:28:51 total time elapsed so far: 9.620000 # loops : 120 mean,max change (kT/e) : 2.0980875E-03 6.9646835E-02 energy calculations done at 9.620000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.760000 DelPhi exited at 11:28:51 9.760u 0.275s 0:16.90 59.3% 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 Sat Oct 15 2011 at 11:28:52 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: 249 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4525 !!! WARNING: GLM 703 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= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 2.593576 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): -6.275000 51.99100 ymin,ymax (A): 95.52700 157.2950 zmin,zma (A): -10.42900 48.10100 x,y,z range (A): 58.26600 61.76800 58.53000 scale (grids/A): 2.593576 object centre (A): 22.85800 126.4110 18.83600 number of atom coordinates read : 4525 total number of charged atoms : 4351 net assigned charge : 4.906046 assigned positive charge : 691.1531 centred at (gu) : 87.34785 91.87679 92.54754 assigned negative charge : -686.2514 centred at (gu) : 87.32757 92.13569 92.39518 start vw surface at 0.1300000 fill in re-entrant regions at 0.4700000 boundary points on vw surface= 250474 reading accessible surface arcs data from file ARCDAT no. of arc points read = 38094 grid for indexing accessible points = 1.400000 m= 122673 mr = 185272 m= 38630 mr = 98381 m= 7944 mr = 29238 m= 906 mr = 5525 m= 22 mr = 493 m= 0 mr = 2 time to grow re-entrant surface = 0.7700000 no. cavity mid-points inaccessible to solvent = 1758 time to turn everything in is 1.360000 number of dielectric boundary points 101738 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 9 iepsmp to db, and charging done at 1.480000 number of grid points assigned charge 34785 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) : 1.729051 object centre at (A) : 22.85800 126.4110 18.83600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.2026454 0.5022838 midg,1,midg; midg,igrid,midg 0.7516505 -0.6722755 1,midg,midg; igrid,midg,midg -4.7936603E-02 0.6262145 gauss-seidel spectral radius is 0.9992737 estimated iterations to convergence 293 setup time was (sec) 1.640000 now iterating at: 11:28:55 rms-change max change #iterations 11.94924 320.6134 at 10iterations 7.071336 151.0134 at 20iterations 4.156447 80.11792 at 30iterations 2.438715 43.70779 at 40iterations 1.425996 27.13601 at 50iterations 0.8316106 13.88006 at 60iterations 0.4831391 7.592527 at 70iterations 0.2816358 5.306215 at 80iterations 0.1635388 2.762920 at 90iterations 9.5112555E-02 1.627033 at 100iterations 5.5213537E-02 0.8730984 at 110iterations 3.2222621E-02 0.5056801 at 120iterations 1.8973432E-02 0.3484955 at 130iterations 1.1293609E-02 0.2158928 at 140iterations 6.9669783E-03 0.1308861 at 150iterations 4.5366730E-03 9.0517044E-02 at 160iterations 3.1781041E-03 6.5237999E-02 at 170iterations 2.4079159E-03 4.8824310E-02 at 180iterations finished qdiffx linear iterations at : 11:29:19 total time elapsed so far: 15.70000 # loops : 180 mean,max change (kT/e) : 2.4079159E-03 4.8824310E-02 energy calculations done at 15.70000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.83000 DelPhi exited at 11:29:20 15.829u 0.327s 0:28.30 57.0% 0+0k 0+0io 0pf+0w