Tue Oct 11 02:21:30 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 Tue Oct 11 2011 at 02:21:30 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: 316 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2680 !!! WARNING: GLM 47 has a net charge of -0.0940 !!! WARNING: HIR 56 has a net charge of 0.5140 !!! WARNING: FMN 398 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: 0.6677420 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): 20.70800 67.24900 ymin,ymax (A): 14.65700 67.97100 zmin,zma (A): -17.36500 29.85700 x,y,z range (A): 46.54100 53.31400 47.22200 scale (grids/A): 0.6677420 object centre (A): 43.97850 41.31400 6.246000 number of atom coordinates read : 2680 total number of charged atoms : 2541 net assigned charge : 2.420011 assigned positive charge : 410.1055 centred at (gu) : 90.88238 90.33409 90.34644 assigned negative charge : -407.6864 centred at (gu) : 90.71650 90.54747 90.38588 start vw surface at 0.1000000 fill in re-entrant regions at 0.1100000 boundary points on vw surface= 8065 nv = 96 ne = 84 npr = 54972 no. pairs analyzed = 54972 no. exposed pairs = 3282 no. arc points = 22491 no. surface atoms = 1104 nbur = 1576 mkacc time = 9.0000004E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 442 mr = 4608 m= 3 mr = 55 m= 0 mr = 0 time to grow re-entrant surface = 0.1000000 no. cavity mid-points inaccessible to solvent = 28 time to turn everything in is 0.2200000 number of dielectric boundary points 3847 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2164 ## 176 charges are in solution ## iepsmp to db, and charging done at 0.2900000 number of grid points assigned charge 9424 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.6227165E-08 -2.7442664E-09 midg,1,midg; midg,igrid,midg 5.6186575E-08 -5.1183726E-08 1,midg,midg; igrid,midg,midg -2.9175821E-08 5.8575896E-08 gauss-seidel spectral radius is 0.9883811 estimated iterations to convergence 76 setup time was (sec) 0.4100000 now iterating at: 02:21:31 rms-change max change #iterations 0.1844439 29.46634 at 10iterations 2.0934302E-02 3.233376 at 20iterations 3.0732497E-03 0.5055122 at 30iterations 8.1985450E-04 0.1743126 at 40iterations 2.8812187E-04 6.2973022E-02 at 50iterations finished qdiffx linear iterations at : 02:21:33 total time elapsed so far: 3.290000 # loops : 50 mean,max change (kT/e) : 2.8812187E-04 6.2973022E-02 energy calculations done at 3.290000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.430000 DelPhi exited at 02:21:34 3.429u 0.160s 0:04.16 86.0% 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 Tue Oct 11 2011 at 02:21:34 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: 316 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2680 !!! WARNING: GLM 47 has a net charge of -0.0940 !!! WARNING: HIR 56 has a net charge of 0.5140 !!! WARNING: FMN 398 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: 2.003226 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): 20.70800 67.24900 ymin,ymax (A): 14.65700 67.97100 zmin,zma (A): -17.36500 29.85700 x,y,z range (A): 46.54100 53.31400 47.22200 scale (grids/A): 2.003226 object centre (A): 43.97850 41.31400 6.246000 number of atom coordinates read : 2680 total number of charged atoms : 2541 net assigned charge : 2.420011 assigned positive charge : 410.1055 centred at (gu) : 92.64664 91.00137 91.03844 assigned negative charge : -407.6864 centred at (gu) : 92.14938 91.64201 91.15714 start vw surface at 0.1000000 fill in re-entrant regions at 0.2000000 boundary points on vw surface= 87195 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22491 grid for indexing accessible points = 1.400000 m= 32745 mr = 62013 m= 5546 mr = 24761 m= 373 mr = 3606 m= 6 mr = 172 m= 0 mr = 0 time to grow re-entrant surface = 0.2000000 no. cavity mid-points inaccessible to solvent = 1555 time to turn everything in is 0.4400000 number of dielectric boundary points 35313 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 91 iepsmp to db, and charging done at 0.5200000 number of grid points assigned charge 20105 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) : 0.6677420 object centre at (A) : 43.97850 41.31400 6.246000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.7905617E-02 -3.4056045E-02 midg,1,midg; midg,igrid,midg 6.0565185E-02 -5.3738587E-02 1,midg,midg; igrid,midg,midg -2.2867817E-02 5.2826099E-02 gauss-seidel spectral radius is 0.9987696 estimated iterations to convergence 226 setup time was (sec) 0.6600000 now iterating at: 02:21:35 rms-change max change #iterations 4.858335 191.1858 at 10iterations 2.363964 84.44601 at 20iterations 1.151919 35.17557 at 30iterations 0.5618368 16.80777 at 40iterations 0.2734370 8.254433 at 50iterations 0.1333294 3.978768 at 60iterations 6.5273799E-02 2.019283 at 70iterations 3.1885106E-02 0.9212623 at 80iterations 1.5823124E-02 0.4724960 at 90iterations 7.9815071E-03 0.2554703 at 100iterations 4.1640056E-03 0.1361008 at 110iterations 2.2948289E-03 8.4003448E-02 at 120iterations finished qdiffx linear iterations at : 02:21:42 total time elapsed so far: 7.820000 # loops : 120 mean,max change (kT/e) : 2.2948289E-03 8.4003448E-02 energy calculations done at 7.820000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.950000 DelPhi exited at 02:21:43 7.957u 0.197s 0:08.84 92.0% 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 Tue Oct 11 2011 at 02:21:43 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: 316 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2680 !!! WARNING: GLM 47 has a net charge of -0.0940 !!! WARNING: HIR 56 has a net charge of 0.5140 !!! WARNING: FMN 398 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: 3.004839 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): 20.70800 67.24900 ymin,ymax (A): 14.65700 67.97100 zmin,zma (A): -17.36500 29.85700 x,y,z range (A): 46.54100 53.31400 47.22200 scale (grids/A): 3.004839 object centre (A): 43.97850 41.31400 6.246000 number of atom coordinates read : 2680 total number of charged atoms : 2541 net assigned charge : 2.420011 assigned positive charge : 410.1055 centred at (gu) : 93.96974 91.50181 91.55754 assigned negative charge : -407.6864 centred at (gu) : 93.22409 92.46301 91.73567 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.3800000 boundary points on vw surface= 201431 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22491 grid for indexing accessible points = 1.400000 m= 104925 mr = 149893 m= 39769 mr = 87049 m= 10239 mr = 32533 m= 1695 mr = 7853 m= 123 mr = 1224 m= 2 mr = 65 m= 0 mr = 0 time to grow re-entrant surface = 0.6500000 no. cavity mid-points inaccessible to solvent = 5161 time to turn everything in is 1.120000 number of dielectric boundary points 79567 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.200000 number of grid points assigned charge 20327 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) : 2.003226 object centre at (A) : 43.97850 41.31400 6.246000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.2127491 -0.3899167 midg,1,midg; midg,igrid,midg 0.8463537 -0.6768721 1,midg,midg; igrid,midg,midg -0.2447650 0.4319420 gauss-seidel spectral radius is 0.9992923 estimated iterations to convergence 297 setup time was (sec) 1.350000 now iterating at: 02:21:45 rms-change max change #iterations 11.09766 469.1649 at 10iterations 6.550059 132.3803 at 20iterations 3.862184 75.69623 at 30iterations 2.266168 39.42388 at 40iterations 1.331466 23.74113 at 50iterations 0.7779159 13.60182 at 60iterations 0.4554283 7.921116 at 70iterations 0.2664762 5.789833 at 80iterations 0.1556476 3.055832 at 90iterations 9.0757042E-02 1.509293 at 100iterations 5.3129785E-02 0.8542442 at 110iterations 3.1035710E-02 0.5266457 at 120iterations 1.8274430E-02 0.3116875 at 130iterations 1.0794863E-02 0.2113838 at 140iterations 6.5007899E-03 0.1359329 at 150iterations 4.0028454E-03 8.5739136E-02 at 160iterations 2.5908996E-03 5.7540894E-02 at 170iterations 1.7727256E-03 4.1687012E-02 at 180iterations finished qdiffx linear iterations at : 02:21:56 total time elapsed so far: 12.87000 # loops : 180 mean,max change (kT/e) : 1.7727256E-03 4.1687012E-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) 13.01000 DelPhi exited at 02:21:57 13.008u 0.218s 0:13.73 96.2% 0+0k 0+0io 0pf+0w