Sun Jan 29 13:29:57 PST 2012 #!/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 Sun Jan 29 2012 at 13:29:57 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 ! Automatically converted by prot2crg.py # of charge parameter records: 291 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3239 !!! WARNING: DIC 166 has a net charge of -0.8000 !!! WARNING: HIY 168 has a net charge of 0.2000 !!! WARNING: DIC 255 has a net charge of -0.8000 !!! WARNING: ZN1 1075 has a net charge of 1.4000 !!! WARNING: ZN2 1078 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= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6030321 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): -59.73900 -10.23600 ymin,ymax (A): -5.553000 46.75200 zmin,zma (A): -68.73600 -9.700999 x,y,z range (A): 49.50300 52.30500 59.03500 scale (grids/A): 0.6030321 object centre (A): -34.98750 20.59950 -39.21850 number of atom coordinates read : 3239 total number of charged atoms : 3133 net assigned charge : -1.499957 assigned positive charge : 487.0540 centred at (gu) : 91.13331 89.34724 91.39588 assigned negative charge : -488.5550 centred at (gu) : 91.24194 89.54577 91.51466 start vw surface at 0.1000000 fill in re-entrant regions at 0.1100000 boundary points on vw surface= 7714 nv = 96 ne = 84 npr = 65848 no. pairs analyzed = 65848 no. exposed pairs = 4095 no. arc points = 27692 no. surface atoms = 1396 nbur = 1843 mkacc time = 0.1100000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 399 mr = 4227 m= 0 mr = 44 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2400000 number of dielectric boundary points 3842 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2664 ## 236 charges are in solution ## iepsmp to db, and charging done at 0.3100000 number of grid points assigned charge 9739 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 3.8358392E-09 -9.1753369E-09 midg,1,midg; midg,igrid,midg 1.0641060E-08 -9.3012931E-09 1,midg,midg; igrid,midg,midg 3.6893109E-09 -7.9508329E-09 gauss-seidel spectral radius is 0.9858170 estimated iterations to convergence 69 setup time was (sec) 0.4200000 now iterating at: 13:29:57 rms-change max change #iterations 0.1249680 20.52687 at 10iterations 1.1024157E-02 1.708736 at 20iterations 1.4026867E-03 0.2065725 at 30iterations 5.0928368E-04 8.9271545E-02 at 40iterations 2.5093241E-04 4.2606354E-02 at 50iterations finished qdiffx linear iterations at : 13:30:00 total time elapsed so far: 3.330000 # loops : 50 mean,max change (kT/e) : 2.5093241E-04 4.2606354E-02 energy calculations done at 3.330000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.460000 DelPhi exited at 13:30:01 3.468u 0.194s 0:04.21 86.6% 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 Sun Jan 29 2012 at 13:30:01 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 ! Automatically converted by prot2crg.py # of charge parameter records: 291 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3239 !!! WARNING: DIC 166 has a net charge of -0.8000 !!! WARNING: HIY 168 has a net charge of 0.2000 !!! WARNING: DIC 255 has a net charge of -0.8000 !!! WARNING: ZN1 1075 has a net charge of 1.4000 !!! WARNING: ZN2 1078 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= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.809096 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): -59.73900 -10.23600 ymin,ymax (A): -5.553000 46.75200 zmin,zma (A): -68.73600 -9.700999 x,y,z range (A): 49.50300 52.30500 59.03500 scale (grids/A): 1.809096 object centre (A): -34.98750 20.59950 -39.21850 number of atom coordinates read : 3239 total number of charged atoms : 3133 net assigned charge : -1.499957 assigned positive charge : 487.0540 centred at (gu) : 93.39912 88.04101 94.18701 assigned negative charge : -488.5550 centred at (gu) : 93.72556 88.63694 94.54330 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 84606 reading accessible surface arcs data from file ARCDAT no. of arc points read = 27692 grid for indexing accessible points = 1.400000 m= 29480 mr = 59211 m= 4175 mr = 21301 m= 200 mr = 2471 m= 1 mr = 67 m= 0 mr = 0 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 81 time to turn everything in is 0.4000000 number of dielectric boundary points 35412 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 200 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.4700000 number of grid points assigned charge 24515 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) : 0.6030321 object centre at (A) : -34.98750 20.59950 -39.21850 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.2048636E-03 -2.1912742E-02 midg,1,midg; midg,igrid,midg 3.1115782E-02 -6.2492304E-03 1,midg,midg; igrid,midg,midg 1.2691048E-03 -2.8420277E-02 gauss-seidel spectral radius is 0.9985513 estimated iterations to convergence 208 setup time was (sec) 0.6100000 now iterating at: 13:30:02 rms-change max change #iterations 4.377564 170.3136 at 10iterations 1.998666 74.01700 at 20iterations 0.9130298 29.26250 at 30iterations 0.4178286 14.23740 at 40iterations 0.1918302 5.898696 at 50iterations 8.8179000E-02 2.656670 at 60iterations 4.0603641E-02 1.273354 at 70iterations 1.8628919E-02 0.5428162 at 80iterations 8.6960457E-03 0.2461491 at 90iterations 4.1986653E-03 0.1439438 at 100iterations 2.1516047E-03 8.1621170E-02 at 110iterations 1.2572875E-03 4.7674179E-02 at 120iterations finished qdiffx linear iterations at : 13:30:09 total time elapsed so far: 7.800000 # loops : 120 mean,max change (kT/e) : 1.2572875E-03 4.7674179E-02 energy calculations done at 7.800000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.920000 DelPhi exited at 13:30:10 7.926u 0.239s 0:08.49 95.9% 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 Sun Jan 29 2012 at 13:30:10 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 ! Automatically converted by prot2crg.py # of charge parameter records: 291 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3239 !!! WARNING: DIC 166 has a net charge of -0.8000 !!! WARNING: HIY 168 has a net charge of 0.2000 !!! WARNING: DIC 255 has a net charge of -0.8000 !!! WARNING: ZN1 1075 has a net charge of 1.4000 !!! WARNING: ZN2 1078 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= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 2.713645 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): -59.73900 -10.23600 ymin,ymax (A): -5.553000 46.75200 zmin,zma (A): -68.73600 -9.700999 x,y,z range (A): 49.50300 52.30500 59.03500 scale (grids/A): 2.713645 object centre (A): -34.98750 20.59950 -39.21850 number of atom coordinates read : 3239 total number of charged atoms : 3133 net assigned charge : -1.499957 assigned positive charge : 487.0540 centred at (gu) : 95.09847 87.06137 96.28029 assigned negative charge : -488.5550 centred at (gu) : 95.58804 87.95525 96.81491 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.3600000 boundary points on vw surface= 195822 reading accessible surface arcs data from file ARCDAT no. of arc points read = 27692 grid for indexing accessible points = 1.400000 m= 97586 mr = 143929 m= 33382 mr = 79028 m= 7173 mr = 26173 m= 966 mr = 5283 m= 55 mr = 671 m= 0 mr = 25 time to grow re-entrant surface = 0.6300000 no. cavity mid-points inaccessible to solvent = 332 time to turn everything in is 1.070000 number of dielectric boundary points 79875 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3 iepsmp to db, and charging done at 1.160000 number of grid points assigned charge 25063 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) : 1.809096 object centre at (A) : -34.98750 20.59950 -39.21850 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.3775443E-02 -0.2203135 midg,1,midg; midg,igrid,midg 0.4308032 1.3766125E-02 1,midg,midg; igrid,midg,midg -8.5786907E-03 -0.3682119 gauss-seidel spectral radius is 0.9992458 estimated iterations to convergence 287 setup time was (sec) 1.310000 now iterating at: 13:30:11 rms-change max change #iterations 10.62870 336.2260 at 10iterations 6.276113 176.9324 at 20iterations 3.663946 97.87535 at 30iterations 2.130708 43.97404 at 40iterations 1.237698 25.24706 at 50iterations 0.7137141 13.53537 at 60iterations 0.4126155 8.266856 at 70iterations 0.2373566 4.258682 at 80iterations 0.1366187 2.679768 at 90iterations 7.8625292E-02 1.386841 at 100iterations 4.5244418E-02 0.9195099 at 110iterations 2.6019448E-02 0.5412521 at 120iterations 1.4989427E-02 0.2649384 at 130iterations 8.7043308E-03 0.1706467 at 140iterations 5.1307874E-03 0.1090298 at 150iterations 3.1238515E-03 7.4600220E-02 at 160iterations 2.0067603E-03 4.1029930E-02 at 170iterations 1.4003568E-03 3.1509399E-02 at 180iterations finished qdiffx linear iterations at : 13:30:23 total time elapsed so far: 12.87000 # loops : 180 mean,max change (kT/e) : 1.4003568E-03 3.1509399E-02 energy calculations done at 12.87000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.00000 DelPhi exited at 13:30:23 13.006u 0.232s 0:13.56 97.5% 0+0k 0+0io 0pf+0w