Mon Oct 10 17:01:02 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 Mon Oct 10 2011 at 17:01:02 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: 354 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4612 !!! WARNING: GLM 169 has a net charge of -0.0940 !!! WARNING: HEM 818 has a net charge of -3.4000 !!! WARNING: FE 2 has a net charge of 1.4000 !!! WARNING: FE 3 has a net charge of 1.4000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1500000 grid size : 179 scale,in grids/A, set to be: 0.5121418 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): -18.26900 36.06900 ymin,ymax (A): -30.35400 31.48700 zmin,zma (A): -4.014000 65.49800 x,y,z range (A): 54.33800 61.84100 69.51200 scale (grids/A): 0.5121418 object centre (A): 8.900001 0.5664997 30.74200 number of atom coordinates read : 4612 total number of charged atoms : 4406 net assigned charge : 5.306046 assigned positive charge : 694.4147 centred at (gu) : 90.46407 90.72408 88.17075 assigned negative charge : -689.1129 centred at (gu) : 90.38202 90.76353 88.22774 start vw surface at 0.2600000 fill in re-entrant regions at 0.2600000 boundary points on vw surface= 7475 nv = 96 ne = 84 npr = 94644 no. pairs analyzed = 94644 no. exposed pairs = 5867 no. arc points = 41118 no. surface atoms = 1959 nbur = 2653 mkacc time = 0.2400000 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 = 1.652000 m= 278 mr = 3796 m= 1 mr = 0 m= 0 mr = 0 time to grow re-entrant surface = 0.2800000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5700000 number of dielectric boundary points 3958 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3919 ## 552 charges are in solution ## iepsmp to db, and charging done at 0.6900000 number of grid points assigned charge 10123 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 3.6979136E-10 -4.5712861E-11 midg,1,midg; midg,igrid,midg 1.5018399E-10 -3.5492352E-11 1,midg,midg; igrid,midg,midg -1.2666605E-10 3.3115610E-10 gauss-seidel spectral radius is 0.9804860 estimated iterations to convergence 59 setup time was (sec) 0.8000000 now iterating at: 17:01:03 rms-change max change #iterations 6.7728393E-02 10.17180 at 10iterations 3.8811294E-03 0.6864386 at 20iterations 2.8028278E-04 3.6361694E-02 at 30iterations 6.3082276E-05 9.8543167E-03 at 40iterations 2.2584598E-05 3.4561157E-03 at 50iterations finished qdiffx linear iterations at : 17:01:06 total time elapsed so far: 3.420000 # loops : 50 mean,max change (kT/e) : 2.2584598E-05 3.4561157E-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) 3.620000 DelPhi exited at 17:01:06 3.619u 0.155s 0:04.15 90.6% 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 Mon Oct 10 2011 at 17:01:06 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: 354 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4612 !!! WARNING: GLM 169 has a net charge of -0.0940 !!! WARNING: HEM 818 has a net charge of -3.4000 !!! WARNING: FE 2 has a net charge of 1.4000 !!! WARNING: FE 3 has a net charge of 1.4000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1500000 grid size : 179 scale,in grids/A, set to be: 1.536425 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): -18.26900 36.06900 ymin,ymax (A): -30.35400 31.48700 zmin,zma (A): -4.014000 65.49800 x,y,z range (A): 54.33800 61.84100 69.51200 scale (grids/A): 1.536425 object centre (A): 8.900001 0.5664997 30.74200 number of atom coordinates read : 4612 total number of charged atoms : 4406 net assigned charge : 5.306046 assigned positive charge : 694.4147 centred at (gu) : 91.39066 92.17095 84.51059 assigned negative charge : -689.1129 centred at (gu) : 91.14576 92.29008 84.68300 start vw surface at 0.2400000 fill in re-entrant regions at 0.3500000 boundary points on vw surface= 84699 reading accessible surface arcs data from file ARCDAT no. of arc points read = 41118 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.568000 m= 23600 mr = 57549 m= 2036 mr = 15265 m= 46 mr = 836 m= 0 mr = 3 time to grow re-entrant surface = 0.3200000 no. cavity mid-points inaccessible to solvent = 324 time to turn everything in is 0.7200000 number of dielectric boundary points 36728 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 512 ## 7 charges are in solution ## iepsmp to db, and charging done at 0.8400000 number of grid points assigned charge 33112 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) : 0.5121418 object centre at (A) : 8.900001 0.5664997 30.74200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 5.0314264E-03 -5.1602945E-03 midg,1,midg; midg,igrid,midg 8.6381352E-03 -7.9372870E-03 1,midg,midg; igrid,midg,midg -1.3578854E-03 1.1126301E-02 gauss-seidel spectral radius is 0.9981043 estimated iterations to convergence 183 setup time was (sec) 1.010000 now iterating at: 17:01:08 rms-change max change #iterations 3.747247 150.7604 at 10iterations 1.527733 59.08200 at 20iterations 0.6245241 19.91835 at 30iterations 0.2560410 8.464075 at 40iterations 0.1046524 3.594034 at 50iterations 4.2876713E-02 1.672243 at 60iterations 1.7578285E-02 0.5926361 at 70iterations 7.2223935E-03 0.2368851 at 80iterations 2.9688303E-03 9.8514557E-02 at 90iterations 1.2294803E-03 4.0744066E-02 at 100iterations 5.1233917E-04 1.9720554E-02 at 110iterations 2.2053164E-04 7.6217651E-03 at 120iterations finished qdiffx linear iterations at : 17:01:15 total time elapsed so far: 8.120000 # loops : 120 mean,max change (kT/e) : 2.2053164E-04 7.6217651E-03 energy calculations done at 8.120000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.310000 DelPhi exited at 17:01:16 8.315u 0.182s 0:09.55 88.9% 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 Mon Oct 10 2011 at 17:01:16 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: 354 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4612 !!! WARNING: GLM 169 has a net charge of -0.0940 !!! WARNING: HEM 818 has a net charge of -3.4000 !!! WARNING: FE 2 has a net charge of 1.4000 !!! WARNING: FE 3 has a net charge of 1.4000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1300000 grid size : 179 scale,in grids/A, set to be: 2.304638 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): -18.26900 36.06900 ymin,ymax (A): -30.35400 31.48700 zmin,zma (A): -4.014000 65.49800 x,y,z range (A): 54.33800 61.84100 69.51200 scale (grids/A): 2.304638 object centre (A): 8.900001 0.5664997 30.74200 number of atom coordinates read : 4612 total number of charged atoms : 4406 net assigned charge : 5.306046 assigned positive charge : 694.4147 centred at (gu) : 92.08558 93.25614 81.76550 assigned negative charge : -689.1129 centred at (gu) : 91.71873 93.43495 82.02438 start vw surface at 0.2100000 fill in re-entrant regions at 0.5200000 boundary points on vw surface= 197340 reading accessible surface arcs data from file ARCDAT no. of arc points read = 41118 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.540000 m= 85112 mr = 141476 m= 20656 mr = 65538 m= 2787 mr = 14396 m= 124 mr = 1598 m= 0 mr = 24 time to grow re-entrant surface = 0.8800000 no. cavity mid-points inaccessible to solvent = 1098 time to turn everything in is 1.520000 number of dielectric boundary points 82987 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 67 iepsmp to db, and charging done at 1.660000 number of grid points assigned charge 35169 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) : 1.536425 object centre at (A) : 8.900001 0.5664997 30.74200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1548830 -0.1557052 midg,1,midg; midg,igrid,midg 0.1235201 -0.2215060 1,midg,midg; igrid,midg,midg -2.3634894E-02 0.1638982 gauss-seidel spectral radius is 0.9991539 estimated iterations to convergence 272 setup time was (sec) 1.830000 now iterating at: 17:01:18 rms-change max change #iterations 10.14323 272.3805 at 10iterations 5.798761 127.3816 at 20iterations 3.284883 74.57399 at 30iterations 1.849703 40.73664 at 40iterations 1.039600 22.59826 at 50iterations 0.5808576 12.13626 at 60iterations 0.3251141 6.897750 at 70iterations 0.1810480 4.606396 at 80iterations 0.1008423 2.013073 at 90iterations 5.6023244E-02 1.040726 at 100iterations 3.1142568E-02 0.6389217 at 110iterations 1.7269038E-02 0.3215134 at 120iterations 9.5974943E-03 0.1870990 at 130iterations 5.3111850E-03 0.1053667 at 140iterations 2.9409768E-03 5.5923462E-02 at 150iterations 1.6304686E-03 3.3271790E-02 at 160iterations 9.0408465E-04 1.7340660E-02 at 170iterations 5.0002732E-04 9.4375610E-03 at 180iterations finished qdiffx linear iterations at : 17:01:30 total time elapsed so far: 13.41000 # loops : 180 mean,max change (kT/e) : 5.0002732E-04 9.4375610E-03 energy calculations done at 13.41000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.60000 DelPhi exited at 17:01:31 13.604u 0.221s 0:15.46 89.3% 0+0k 0+0io 0pf+0w