Fri Oct 28 23:56:04 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 Fri Oct 28 2011 at 23:56:04 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: 327 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3807 !!! WARNING: HEM 500 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= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 0.5351774 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): -27.21000 39.31000 ymin,ymax (A): 1.452000 55.11700 zmin,zma (A): -33.48600 25.43300 x,y,z range (A): 66.52000 53.66500 58.91900 scale (grids/A): 0.5351774 object centre (A): 6.050001 28.28450 -4.026500 number of atom coordinates read : 3807 total number of charged atoms : 3659 net assigned charge : -1.999984 assigned positive charge : 564.5784 centred at (gu) : 89.66506 89.33783 91.50578 assigned negative charge : -566.5803 centred at (gu) : 89.63177 89.34888 91.56337 start vw surface at 0.1100000 fill in re-entrant regions at 0.1200000 boundary points on vw surface= 6932 nv = 96 ne = 84 npr = 79112 no. pairs analyzed = 79112 no. exposed pairs = 4816 no. arc points = 33775 no. surface atoms = 1605 nbur = 2202 mkacc time = 0.1400000 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= 277 mr = 3556 m= 1 mr = 14 m= 0 mr = 0 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2800000 number of dielectric boundary points 3640 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3321 ## 399 charges are in solution ## iepsmp to db, and charging done at 0.3400000 number of grid points assigned charge 9267 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.6595852E-10 -5.8753724E-10 midg,1,midg; midg,igrid,midg -1.4907594E-11 -1.1604723E-10 1,midg,midg; igrid,midg,midg -2.8503011E-10 1.0107220E-10 gauss-seidel spectral radius is 0.9820713 estimated iterations to convergence 62 setup time was (sec) 0.4700000 now iterating at: 23:56:04 rms-change max change #iterations 7.4259080E-02 11.81226 at 10iterations 4.7372235E-03 0.7303603 at 20iterations 3.8073509E-04 7.7335358E-02 at 30iterations 5.7964200E-05 1.4743805E-02 at 40iterations 1.3273697E-05 3.4332275E-03 at 50iterations finished qdiffx linear iterations at : 23:56:08 total time elapsed so far: 3.420000 # loops : 50 mean,max change (kT/e) : 1.3273697E-05 3.4332275E-03 energy calculations done at 3.420000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.550000 DelPhi exited at 23:56:08 3.557u 0.264s 0:04.45 85.6% 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 Fri Oct 28 2011 at 23:56:08 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: 327 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3807 !!! WARNING: HEM 500 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= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 1.605532 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): -27.21000 39.31000 ymin,ymax (A): 1.452000 55.11700 zmin,zma (A): -33.48600 25.43300 x,y,z range (A): 66.52000 53.66500 58.91900 scale (grids/A): 1.605532 object centre (A): 6.050001 28.28450 -4.026500 number of atom coordinates read : 3807 total number of charged atoms : 3659 net assigned charge : -1.999984 assigned positive charge : 564.5784 centred at (gu) : 88.99408 88.01210 94.51615 assigned negative charge : -566.5803 centred at (gu) : 88.89492 88.04610 94.68989 start vw surface at 0.1200000 fill in re-entrant regions at 0.2000000 boundary points on vw surface= 77617 reading accessible surface arcs data from file ARCDAT no. of arc points read = 33775 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 23761 mr = 52646 m= 2488 mr = 16298 m= 60 mr = 1256 m= 1 mr = 2 m= 0 mr = 0 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 589 time to turn everything in is 0.4000000 number of dielectric boundary points 33725 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 348 ## 4 charges are in solution ## iepsmp to db, and charging done at 0.4800000 number of grid points assigned charge 27954 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) : 0.5351774 object centre at (A) : 6.050001 28.28450 -4.026500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -3.9765271E-03 -1.6408756E-02 midg,1,midg; midg,igrid,midg 7.6725408E-03 4.2805094E-03 1,midg,midg; igrid,midg,midg 6.5215427E-05 -8.0805942E-03 gauss-seidel spectral radius is 0.9982136 estimated iterations to convergence 188 setup time was (sec) 0.6200000 now iterating at: 23:56:09 rms-change max change #iterations 3.676014 167.6601 at 10iterations 1.543090 58.94918 at 20iterations 0.6457324 22.31076 at 30iterations 0.2716068 9.715866 at 40iterations 0.1140463 4.149275 at 50iterations 4.7814373E-02 1.852005 at 60iterations 2.0210331E-02 0.6607208 at 70iterations 8.5092690E-03 0.2576237 at 80iterations 3.5844012E-03 0.1150017 at 90iterations 1.5152572E-03 4.8010826E-02 at 100iterations 6.4257311E-04 2.3111343E-02 at 110iterations 2.7366725E-04 9.4375610E-03 at 120iterations finished qdiffx linear iterations at : 23:56:17 total time elapsed so far: 8.100000 # loops : 120 mean,max change (kT/e) : 2.7366725E-04 9.4375610E-03 energy calculations done at 8.100000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.240000 DelPhi exited at 23:56:17 8.242u 0.210s 0:08.97 94.2% 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 Fri Oct 28 2011 at 23:56:17 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: 327 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3807 !!! WARNING: HEM 500 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= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 2.408298 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): -27.21000 39.31000 ymin,ymax (A): 1.452000 55.11700 zmin,zma (A): -33.48600 25.43300 x,y,z range (A): 66.52000 53.66500 58.91900 scale (grids/A): 2.408298 object centre (A): 6.050001 28.28450 -4.026500 number of atom coordinates read : 3807 total number of charged atoms : 3659 net assigned charge : -1.999984 assigned positive charge : 564.5784 centred at (gu) : 88.49084 87.01790 96.77379 assigned negative charge : -566.5803 centred at (gu) : 88.34206 87.06900 97.03477 start vw surface at 0.1200000 fill in re-entrant regions at 0.3400000 boundary points on vw surface= 180755 reading accessible surface arcs data from file ARCDAT no. of arc points read = 33775 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 82505 mr = 129438 m= 23724 mr = 64700 m= 3818 mr = 18000 m= 242 mr = 2574 m= 0 mr = 107 time to grow re-entrant surface = 0.5500000 no. cavity mid-points inaccessible to solvent = 1941 time to turn everything in is 0.9700000 number of dielectric boundary points 76225 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 32 iepsmp to db, and charging done at 1.070000 number of grid points assigned charge 29230 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) : 1.605532 object centre at (A) : 6.050001 28.28450 -4.026500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -8.0905341E-02 -0.2481004 midg,1,midg; midg,igrid,midg 0.1339210 9.7315267E-02 1,midg,midg; igrid,midg,midg 0.1178759 -8.8185430E-02 gauss-seidel spectral radius is 0.9991693 estimated iterations to convergence 274 setup time was (sec) 1.210000 now iterating at: 23:56:19 rms-change max change #iterations 9.556051 290.9684 at 10iterations 5.416121 119.5100 at 20iterations 3.061146 72.29342 at 30iterations 1.717072 34.22208 at 40iterations 0.9618270 19.38054 at 50iterations 0.5385163 10.20439 at 60iterations 0.3009753 6.307011 at 70iterations 0.1677507 3.628674 at 80iterations 9.3371063E-02 1.832108 at 90iterations 5.1899534E-02 0.9348869 at 100iterations 2.8881520E-02 0.5613594 at 110iterations 1.6062640E-02 0.2908783 at 120iterations 8.9465817E-03 0.1722693 at 130iterations 4.9648536E-03 9.4558716E-02 at 140iterations 2.7639777E-03 5.1484108E-02 at 150iterations 1.5361230E-03 3.0586243E-02 at 160iterations 8.5530605E-04 1.7251015E-02 at 170iterations 4.7656192E-04 9.1552734E-03 at 180iterations finished qdiffx linear iterations at : 23:56:31 total time elapsed so far: 13.36000 # loops : 180 mean,max change (kT/e) : 4.7656192E-04 9.1552734E-03 energy calculations done at 13.36000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.48000 DelPhi exited at 23:56:32 13.484u 0.276s 0:14.43 95.2% 0+0k 0+0io 0pf+0w