Sat Oct 8 21:47:38 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 Sat Oct 8 2011 at 21:47:38 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: 278 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1991 !!! WARNING: GLM 133 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= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6379929 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): -27.43500 28.36500 ymin,ymax (A): 46.24000 94.05700 zmin,zma (A): -7.699000 34.13700 x,y,z range (A): 55.80000 47.81700 41.83600 scale (grids/A): 0.6379929 object centre (A): 0.4650002 70.14850 13.21900 number of atom coordinates read : 1991 total number of charged atoms : 1851 net assigned charge : -1.093998 assigned positive charge : 295.4009 centred at (gu) : 92.22931 89.46716 91.09953 assigned negative charge : -296.4949 centred at (gu) : 92.12005 89.54586 91.02928 start vw surface at 9.0000004E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 5668 nv = 96 ne = 84 npr = 38872 no. pairs analyzed = 38872 no. exposed pairs = 2640 no. arc points = 18292 no. surface atoms = 889 nbur = 1102 mkacc time = 6.9999993E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 329 mr = 3056 m= 4 mr = 45 m= 0 mr = 0 time to grow re-entrant surface = 7.9999998E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.1700000 number of dielectric boundary points 2900 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1740 ## 147 charges are in solution ## iepsmp to db, and charging done at 0.2400000 number of grid points assigned charge 6543 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -6.1226757E-09 5.1461497E-09 midg,1,midg; midg,igrid,midg 5.3134914E-09 -7.5559319E-09 1,midg,midg; igrid,midg,midg -6.8771211E-09 1.1915037E-08 gauss-seidel spectral radius is 0.9872227 estimated iterations to convergence 72 setup time was (sec) 0.3500000 now iterating at: 21:47:39 rms-change max change #iterations 0.1251630 21.51789 at 10iterations 1.2386068E-02 2.219501 at 20iterations 1.2980662E-03 0.2343264 at 30iterations 1.8638541E-04 2.8575897E-02 at 40iterations 4.6069694E-05 8.0146790E-03 at 50iterations finished qdiffx linear iterations at : 21:47:42 total time elapsed so far: 3.210000 # loops : 50 mean,max change (kT/e) : 4.6069694E-05 8.0146790E-03 energy calculations done at 3.210000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.330000 DelPhi exited at 21:47:42 3.334u 0.187s 0:03.88 90.4% 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 Sat Oct 8 2011 at 21:47:42 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: 278 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1991 !!! WARNING: GLM 133 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= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.913979 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): -27.43500 28.36500 ymin,ymax (A): 46.24000 94.05700 zmin,zma (A): -7.699000 34.13700 x,y,z range (A): 55.80000 47.81700 41.83600 scale (grids/A): 1.913979 object centre (A): 0.4650002 70.14850 13.21900 number of atom coordinates read : 1991 total number of charged atoms : 1851 net assigned charge : -1.093998 assigned positive charge : 295.4009 centred at (gu) : 96.68806 88.40160 93.29849 assigned negative charge : -296.4949 centred at (gu) : 96.36032 88.63750 93.08765 start vw surface at 7.0000000E-02 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 61063 reading accessible surface arcs data from file ARCDAT no. of arc points read = 18292 grid for indexing accessible points = 1.400000 m= 23045 mr = 41978 m= 3798 mr = 17010 m= 241 mr = 2381 m= 3 mr = 110 m= 0 mr = 0 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3100000 number of dielectric boundary points 26671 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 112 iepsmp to db, and charging done at 0.3900000 number of grid points assigned charge 14590 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) : 0.6379929 object centre at (A) : 0.4650002 70.14850 13.21900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -6.3180281E-03 4.8629604E-03 midg,1,midg; midg,igrid,midg 2.4173515E-02 -1.5500084E-03 1,midg,midg; igrid,midg,midg -4.2340465E-02 -2.7556235E-02 gauss-seidel spectral radius is 0.9985886 estimated iterations to convergence 211 setup time was (sec) 0.5300000 now iterating at: 21:47:43 rms-change max change #iterations 3.661957 182.9648 at 10iterations 1.697775 72.57315 at 20iterations 0.7871681 30.69052 at 30iterations 0.3626446 12.87796 at 40iterations 0.1674212 6.158830 at 50iterations 7.7491961E-02 2.682650 at 60iterations 3.5955120E-02 1.357112 at 70iterations 1.6649036E-02 0.6065292 at 80iterations 7.7344980E-03 0.2736206 at 90iterations 3.6026884E-03 0.1273513 at 100iterations 1.6904857E-03 6.5137863E-02 at 110iterations 8.0801029E-04 2.9051304E-02 at 120iterations finished qdiffx linear iterations at : 21:47:51 total time elapsed so far: 7.650000 # loops : 120 mean,max change (kT/e) : 8.0801029E-04 2.9051304E-02 energy calculations done at 7.650000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.780000 DelPhi exited at 21:47:51 7.780u 0.996s 0:09.09 96.4% 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 Sat Oct 8 2011 at 21:47:51 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: 278 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1991 !!! WARNING: GLM 133 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= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.870968 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): -27.43500 28.36500 ymin,ymax (A): 46.24000 94.05700 zmin,zma (A): -7.699000 34.13700 x,y,z range (A): 55.80000 47.81700 41.83600 scale (grids/A): 2.870968 object centre (A): 0.4650002 70.14850 13.21900 number of atom coordinates read : 1991 total number of charged atoms : 1851 net assigned charge : -1.093998 assigned positive charge : 295.4009 centred at (gu) : 100.0320 87.60225 94.94777 assigned negative charge : -296.4949 centred at (gu) : 99.54047 87.95636 94.63145 start vw surface at 7.0000000E-02 fill in re-entrant regions at 0.2600000 boundary points on vw surface= 140700 reading accessible surface arcs data from file ARCDAT no. of arc points read = 18292 grid for indexing accessible points = 1.400000 m= 73356 mr = 101534 m= 27414 mr = 59954 m= 6848 mr = 21943 m= 1075 mr = 5195 m= 65 mr = 760 m= 1 mr = 36 m= 0 mr = 0 time to grow re-entrant surface = 0.4700000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.8000000 number of dielectric boundary points 60037 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2 iepsmp to db, and charging done at 0.8800000 number of grid points assigned charge 14807 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) : 1.913979 object centre at (A) : 0.4650002 70.14850 13.21900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -4.3756694E-02 6.5554708E-02 midg,1,midg; midg,igrid,midg 0.2743336 -5.4912049E-02 1,midg,midg; igrid,midg,midg -0.7820237 -0.3742971 gauss-seidel spectral radius is 0.9992369 estimated iterations to convergence 286 setup time was (sec) 1.030000 now iterating at: 21:47:52 rms-change max change #iterations 8.768827 434.7830 at 10iterations 5.125259 128.9336 at 20iterations 2.966967 64.77811 at 30iterations 1.714901 38.06357 at 40iterations 0.9844073 21.63567 at 50iterations 0.5665569 12.29234 at 60iterations 0.3245454 6.606146 at 70iterations 0.1860792 3.820877 at 80iterations 0.1064224 2.133425 at 90iterations 6.0800191E-02 1.286446 at 100iterations 3.4695636E-02 0.6517724 at 110iterations 1.9815041E-02 0.4380970 at 120iterations 1.1362020E-02 0.2361612 at 130iterations 6.4931805E-03 0.1311455 at 140iterations 3.7326480E-03 8.4074020E-02 at 150iterations 2.1537554E-03 4.7727585E-02 at 160iterations 1.2527464E-03 2.5314331E-02 at 170iterations 7.4398326E-04 1.5346527E-02 at 180iterations finished qdiffx linear iterations at : 21:48:03 total time elapsed so far: 11.93000 # loops : 180 mean,max change (kT/e) : 7.4398326E-04 1.5346527E-02 energy calculations done at 11.93000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.06000 DelPhi exited at 21:48:04 12.066u 0.214s 0:12.62 97.2% 0+0k 0+0io 0pf+0w