Wed Dec 21 14:20:48 PST 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 Wed Dec 21 2011 at 14:20:48 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: 228 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1919 !!! WARNING: LYS 7 has a net charge of 0.0200 !!! WARNING: LYS 41 has a net charge of 0.0200 !!! WARNING: LYS 70 has a net charge of 0.0200 !!! WARNING: LYS 119 has a net charge of 0.0200 !!! WARNING: LYS 140 has a net charge of 0.0200 !!! WARNING: LYS 142 has a net charge of 0.0200 !!! WARNING: LYS 154 has a net charge of 0.0200 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: 0.6109071 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): -9.039000 49.23500 ymin,ymax (A): 8.652000 47.48300 zmin,zma (A): -3.712000 38.68000 x,y,z range (A): 58.27400 38.83100 42.39200 scale (grids/A): 0.6109071 object centre (A): 20.09800 28.06750 17.48400 number of atom coordinates read : 1919 total number of charged atoms : 1787 net assigned charge : -2.859994 assigned positive charge : 279.8401 centred at (gu) : 90.12418 89.73030 90.50529 assigned negative charge : -282.7003 centred at (gu) : 90.05902 89.71210 90.62733 start vw surface at 7.0000000E-02 fill in re-entrant regions at 7.9999998E-02 boundary points on vw surface= 4861 nv = 96 ne = 84 npr = 39581 no. pairs analyzed = 39581 no. exposed pairs = 2407 no. arc points = 16702 no. surface atoms = 816 nbur = 1103 mkacc time = 6.0000002E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 195 mr = 2668 m= 0 mr = 15 time to grow re-entrant surface = 7.0000008E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.1500000 number of dielectric boundary points 2373 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1669 ## 174 charges are in solution ## iepsmp to db, and charging done at 0.2400000 number of grid points assigned charge 5830 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.4439994E-09 -7.0531576E-09 midg,1,midg; midg,igrid,midg -2.5300881E-09 -9.7987085E-10 1,midg,midg; igrid,midg,midg -4.0283155E-09 7.0956502E-10 gauss-seidel spectral radius is 0.9860697 estimated iterations to convergence 69 setup time was (sec) 0.3800000 now iterating at: 14:20:49 rms-change max change #iterations 0.1017459 15.72248 at 10iterations 8.9402720E-03 1.447581 at 20iterations 7.8611821E-04 0.1315536 at 30iterations 6.8099100E-05 1.1486053E-02 at 40iterations 6.0869224E-06 1.0356903E-03 at 50iterations finished qdiffx linear iterations at : 14:20:52 total time elapsed so far: 3.790000 # loops : 50 mean,max change (kT/e) : 6.0869224E-06 1.0356903E-03 energy calculations done at 3.790000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.920000 DelPhi exited at 14:20:53 3.924u 0.238s 0:04.84 85.7% 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 Wed Dec 21 2011 at 14:20:53 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: 228 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1919 !!! WARNING: LYS 7 has a net charge of 0.0200 !!! WARNING: LYS 41 has a net charge of 0.0200 !!! WARNING: LYS 70 has a net charge of 0.0200 !!! WARNING: LYS 119 has a net charge of 0.0200 !!! WARNING: LYS 140 has a net charge of 0.0200 !!! WARNING: LYS 142 has a net charge of 0.0200 !!! WARNING: LYS 154 has a net charge of 0.0200 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: 1.832721 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): -9.039000 49.23500 ymin,ymax (A): 8.652000 47.48300 zmin,zma (A): -3.712000 38.68000 x,y,z range (A): 58.27400 38.83100 42.39200 scale (grids/A): 1.832721 object centre (A): 20.09800 28.06750 17.48400 number of atom coordinates read : 1919 total number of charged atoms : 1787 net assigned charge : -2.859994 assigned positive charge : 279.8401 centred at (gu) : 90.37237 89.19106 91.51608 assigned negative charge : -282.7003 centred at (gu) : 90.17747 89.13646 91.88221 start vw surface at 7.0000000E-02 fill in re-entrant regions at 0.1300000 boundary points on vw surface= 52804 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16702 grid for indexing accessible points = 1.400000 m= 17943 mr = 36394 m= 2158 mr = 13355 m= 55 mr = 1250 m= 0 mr = 9 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 1288 time to turn everything in is 0.2800000 number of dielectric boundary points 21952 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 130 iepsmp to db, and charging done at 0.3800000 number of grid points assigned charge 14037 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) : 0.6109071 object centre at (A) : 20.09800 28.06750 17.48400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 6.4351591E-03 -1.1742178E-02 midg,1,midg; midg,igrid,midg -1.6651535E-03 -2.8132675E-03 1,midg,midg; igrid,midg,midg 9.2318226E-03 1.5269145E-02 gauss-seidel spectral radius is 0.9984464 estimated iterations to convergence 201 setup time was (sec) 0.5900000 now iterating at: 14:20:54 rms-change max change #iterations 3.269875 168.8436 at 10iterations 1.456649 53.73071 at 20iterations 0.6488879 25.00053 at 30iterations 0.2890775 10.89062 at 40iterations 0.1285248 5.059753 at 50iterations 5.7135951E-02 2.115170 at 60iterations 2.5428994E-02 0.8811016 at 70iterations 1.1313575E-02 0.4342232 at 80iterations 5.0361780E-03 0.1893768 at 90iterations 2.2399656E-03 8.0682158E-02 at 100iterations 1.0012401E-03 3.6874771E-02 at 110iterations 4.4588320E-04 2.0290375E-02 at 120iterations finished qdiffx linear iterations at : 14:21:03 total time elapsed so far: 8.940000 # loops : 120 mean,max change (kT/e) : 4.4588320E-04 2.0290375E-02 energy calculations done at 8.940000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.080000 DelPhi exited at 14:21:04 9.078u 0.425s 0:11.03 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 Wed Dec 21 2011 at 14:21:05 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: 228 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1919 !!! WARNING: LYS 7 has a net charge of 0.0200 !!! WARNING: LYS 41 has a net charge of 0.0200 !!! WARNING: LYS 70 has a net charge of 0.0200 !!! WARNING: LYS 119 has a net charge of 0.0200 !!! WARNING: LYS 140 has a net charge of 0.0200 !!! WARNING: LYS 142 has a net charge of 0.0200 !!! WARNING: LYS 154 has a net charge of 0.0200 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: 2.749082 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): -9.039000 49.23500 ymin,ymax (A): 8.652000 47.48300 zmin,zma (A): -3.712000 38.68000 x,y,z range (A): 58.27400 38.83100 42.39200 scale (grids/A): 2.749082 object centre (A): 20.09800 28.06750 17.48400 number of atom coordinates read : 1919 total number of charged atoms : 1787 net assigned charge : -2.859994 assigned positive charge : 279.8401 centred at (gu) : 90.55859 88.78655 92.27412 assigned negative charge : -282.7003 centred at (gu) : 90.26620 88.70481 92.82331 start vw surface at 7.0000000E-02 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 122105 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16702 grid for indexing accessible points = 1.400000 m= 60157 mr = 88011 m= 19524 mr = 49543 m= 3609 mr = 15782 m= 280 mr = 2705 m= 3 mr = 132 m= 0 mr = 0 time to grow re-entrant surface = 0.3700000 no. cavity mid-points inaccessible to solvent = 4464 time to turn everything in is 0.6900000 number of dielectric boundary points 49505 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 0.7900000 number of grid points assigned charge 14296 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) : 1.832721 object centre at (A) : 20.09800 28.06750 17.48400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 5.7312917E-02 -9.8526739E-02 midg,1,midg; midg,igrid,midg 1.2063107E-02 -2.5311213E-02 1,midg,midg; igrid,midg,midg 0.2122378 0.2478140 gauss-seidel spectral radius is 0.9991886 estimated iterations to convergence 277 setup time was (sec) 0.9500000 now iterating at: 14:21:06 rms-change max change #iterations 7.829899 340.8216 at 10iterations 4.421773 135.6246 at 20iterations 2.481542 57.31103 at 30iterations 1.389356 31.91796 at 40iterations 0.7800716 17.20682 at 50iterations 0.4352705 9.330666 at 60iterations 0.2425756 5.967659 at 70iterations 0.1355721 3.007080 at 80iterations 7.5563148E-02 1.637184 at 90iterations 4.2242743E-02 0.9533653 at 100iterations 2.3588238E-02 0.5309410 at 110iterations 1.3165174E-02 0.2811928 at 120iterations 7.3533943E-03 0.1669922 at 130iterations 4.1077794E-03 8.9073181E-02 at 140iterations 2.2878267E-03 4.7811508E-02 at 150iterations 1.2789258E-03 2.7053833E-02 at 160iterations 7.1294006E-04 1.6038895E-02 at 170iterations 3.9834448E-04 8.5792542E-03 at 180iterations finished qdiffx linear iterations at : 14:21:20 total time elapsed so far: 14.68000 # loops : 180 mean,max change (kT/e) : 3.9834448E-04 8.5792542E-03 energy calculations done at 14.68000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 14.82000 DelPhi exited at 14:21:31 14.819u 0.301s 0:26.46 57.1% 0+0k 0+0io 0pf+0w