Tue Oct 11 07:55:21 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 07:55:21 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: 295 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2382 !!! WARNING: HIQ 54 has a net charge of 0.5140 !!! WARNING: SEP 206 has a net charge of -0.4750 !!! WARNING: GLM 208 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= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6444722 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): -8.843000 39.86600 ymin,ymax (A): -14.32800 40.91100 zmin,zma (A): 5.310000 52.73600 x,y,z range (A): 48.70900 55.23900 47.42600 scale (grids/A): 0.6444722 object centre (A): 15.51150 13.29150 29.02300 number of atom coordinates read : 2382 total number of charged atoms : 2240 net assigned charge : 3.945009 assigned positive charge : 358.9263 centred at (gu) : 89.43311 88.49921 90.59258 assigned negative charge : -354.9818 centred at (gu) : 89.35171 88.51813 90.75943 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 6681 nv = 96 ne = 84 npr = 47663 no. pairs analyzed = 47663 no. exposed pairs = 2856 no. arc points = 19925 no. surface atoms = 966 nbur = 1416 mkacc time = 0.1400000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 366 mr = 3745 m= 2 mr = 64 m= 0 mr = 0 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 17 time to turn everything in is 0.3200000 number of dielectric boundary points 3240 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2018 ## 196 charges are in solution ## iepsmp to db, and charging done at 0.4500000 number of grid points assigned charge 7908 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.3229811E-08 -1.5652455E-08 midg,1,midg; midg,igrid,midg 1.2274701E-08 3.2772878E-09 1,midg,midg; igrid,midg,midg -3.6393448E-09 1.4522797E-08 gauss-seidel spectral radius is 0.9875051 estimated iterations to convergence 73 setup time was (sec) 0.6100000 now iterating at: 07:55:21 rms-change max change #iterations 0.1473624 24.62050 at 10iterations 1.5426075E-02 2.291176 at 20iterations 1.6281173E-03 0.2594910 at 30iterations 1.9123746E-04 3.2562256E-02 at 40iterations 2.5619278E-05 4.1580200E-03 at 50iterations finished qdiffx linear iterations at : 07:55:25 total time elapsed so far: 3.930000 # loops : 50 mean,max change (kT/e) : 2.5619278E-05 4.1580200E-03 energy calculations done at 3.930000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.110000 DelPhi exited at 07:55:25 4.114u 0.264s 0:04.71 92.7% 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 07:55:25 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: 295 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2382 !!! WARNING: HIQ 54 has a net charge of 0.5140 !!! WARNING: SEP 206 has a net charge of -0.4750 !!! WARNING: GLM 208 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= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.933416 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): -8.843000 39.86600 ymin,ymax (A): -14.32800 40.91100 zmin,zma (A): 5.310000 52.73600 x,y,z range (A): 48.70900 55.23900 47.42600 scale (grids/A): 1.933416 object centre (A): 15.51150 13.29150 29.02300 number of atom coordinates read : 2382 total number of charged atoms : 2240 net assigned charge : 3.945009 assigned positive charge : 358.9263 centred at (gu) : 88.29881 85.49724 91.77745 assigned negative charge : -354.9818 centred at (gu) : 88.05505 85.55408 92.27834 start vw surface at 0.1500000 fill in re-entrant regions at 0.2800000 boundary points on vw surface= 71841 reading accessible surface arcs data from file ARCDAT no. of arc points read = 19925 grid for indexing accessible points = 1.400000 m= 27285 mr = 50418 m= 4628 mr = 20691 m= 333 mr = 3072 m= 3 mr = 158 m= 0 mr = 0 time to grow re-entrant surface = 0.3300000 no. cavity mid-points inaccessible to solvent = 1370 time to turn everything in is 0.6500000 number of dielectric boundary points 29751 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 150 iepsmp to db, and charging done at 0.7900000 number of grid points assigned charge 17625 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) : 0.6444722 object centre at (A) : 15.51150 13.29150 29.02300 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.2921659E-02 -2.3573456E-02 midg,1,midg; midg,igrid,midg 2.6162433E-02 1.8400202E-02 1,midg,midg; igrid,midg,midg -5.3370837E-03 4.1998425E-03 gauss-seidel spectral radius is 0.9986508 estimated iterations to convergence 216 setup time was (sec) 0.9600000 now iterating at: 07:55:27 rms-change max change #iterations 4.141320 197.7073 at 10iterations 1.947567 67.31776 at 20iterations 0.9202396 31.82818 at 30iterations 0.4344743 16.12554 at 40iterations 0.2052064 6.755387 at 50iterations 9.6317671E-02 3.524475 at 60iterations 4.5543741E-02 1.337112 at 70iterations 2.1545187E-02 0.7779102 at 80iterations 1.0163348E-02 0.3048782 at 90iterations 4.8136050E-03 0.1571631 at 100iterations 2.2786926E-03 7.4593902E-02 at 110iterations 1.0838640E-03 3.4673691E-02 at 120iterations finished qdiffx linear iterations at : 07:55:35 total time elapsed so far: 9.360000 # loops : 120 mean,max change (kT/e) : 1.0838640E-03 3.4673691E-02 energy calculations done at 9.360000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.540000 DelPhi exited at 07:55:36 9.545u 0.296s 0:10.46 93.9% 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 Tue Oct 11 2011 at 07:55:36 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: 295 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2382 !!! WARNING: HIQ 54 has a net charge of 0.5140 !!! WARNING: SEP 206 has a net charge of -0.4750 !!! WARNING: GLM 208 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= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.900125 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): -8.843000 39.86600 ymin,ymax (A): -14.32800 40.91100 zmin,zma (A): 5.310000 52.73600 x,y,z range (A): 48.70900 55.23900 47.42600 scale (grids/A): 2.900125 object centre (A): 15.51150 13.29150 29.02300 number of atom coordinates read : 2382 total number of charged atoms : 2240 net assigned charge : 3.945009 assigned positive charge : 358.9263 centred at (gu) : 87.44820 83.24567 92.66630 assigned negative charge : -354.9818 centred at (gu) : 87.08259 83.33105 93.41740 start vw surface at 0.1600000 fill in re-entrant regions at 0.5600000 boundary points on vw surface= 165981 reading accessible surface arcs data from file ARCDAT no. of arc points read = 19925 grid for indexing accessible points = 1.400000 m= 87143 mr = 121911 m= 32965 mr = 72397 m= 8505 mr = 26967 m= 1410 mr = 6715 m= 132 mr = 1038 m= 1 mr = 81 m= 0 mr = 0 time to grow re-entrant surface = 1.010000 no. cavity mid-points inaccessible to solvent = 4962 time to turn everything in is 1.690000 number of dielectric boundary points 67028 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.850000 number of grid points assigned charge 17908 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) : 1.933416 object centre at (A) : 15.51150 13.29150 29.02300 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.4837497 -0.3588933 midg,1,midg; midg,igrid,midg 0.1878281 0.2131898 1,midg,midg; igrid,midg,midg -4.4335466E-02 -2.2343526E-02 gauss-seidel spectral radius is 0.9992556 estimated iterations to convergence 289 setup time was (sec) 2.030000 now iterating at: 07:55:38 rms-change max change #iterations 9.723674 470.8535 at 10iterations 5.687071 164.0275 at 20iterations 3.300052 69.32326 at 30iterations 1.912333 41.81652 at 40iterations 1.105580 22.91198 at 50iterations 0.6371235 13.99393 at 60iterations 0.3668530 7.075990 at 70iterations 0.2115074 4.289404 at 80iterations 0.1214799 2.276714 at 90iterations 6.9883280E-02 1.315186 at 100iterations 4.0205661E-02 0.8276682 at 110iterations 2.3054658E-02 0.4220352 at 120iterations 1.3281275E-02 0.2435608 at 130iterations 7.6326961E-03 0.1406136 at 140iterations 4.3940344E-03 7.6871872E-02 at 150iterations 2.5417246E-03 4.8412323E-02 at 160iterations 1.4768924E-03 2.7935028E-02 at 170iterations 8.6766365E-04 1.5018463E-02 at 180iterations finished qdiffx linear iterations at : 07:55:52 total time elapsed so far: 15.89000 # loops : 180 mean,max change (kT/e) : 8.6766365E-04 1.5018463E-02 energy calculations done at 15.89000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 16.08000 DelPhi exited at 07:55:53 16.080u 0.298s 0:16.65 98.3% 0+0k 0+0io 0pf+0w