Sun Oct 9 11:06:36 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 Sun Oct 9 2011 at 11:06:36 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: 281 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2819 !!! WARNING: HIR 206 has a net charge of 0.5140 !!! WARNING: CME 307 has a net charge of -0.3480 !!! WARNING: CME 1 has a net charge of -0.0350 !!! WARNING: CME 3 has a net charge of -0.0350 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 0.6312616 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): -24.93100 29.45600 ymin,ymax (A): -25.25400 26.19800 zmin,zma (A): -15.41000 40.98500 x,y,z range (A): 54.38700 51.45200 56.39500 scale (grids/A): 0.6312616 object centre (A): 2.262500 0.4720001 12.78750 number of atom coordinates read : 2819 total number of charged atoms : 2737 net assigned charge : 4.096034 assigned positive charge : 424.0162 centred at (gu) : 89.75152 89.14405 92.29954 assigned negative charge : -419.9219 centred at (gu) : 89.74060 89.19246 92.39903 start vw surface at 0.1600000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 7922 nv = 96 ne = 84 npr = 54267 no. pairs analyzed = 54267 no. exposed pairs = 3890 no. arc points = 27368 no. surface atoms = 1289 nbur = 1530 mkacc time = 0.1300000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 454 mr = 4109 m= 2 mr = 61 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 0.3200000 number of dielectric boundary points 4208 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2570 ## 225 charges are in solution ## iepsmp to db, and charging done at 0.4300000 number of grid points assigned charge 9355 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 8.8595904E-09 -8.7463610E-09 midg,1,midg; midg,igrid,midg 1.1491021E-08 5.3565527E-11 1,midg,midg; igrid,midg,midg 3.9293693E-09 5.5810734E-09 gauss-seidel spectral radius is 0.9870366 estimated iterations to convergence 72 setup time was (sec) 0.5500000 now iterating at: 11:06:37 rms-change max change #iterations 0.1428789 22.11815 at 10iterations 1.3960070E-02 2.024990 at 20iterations 1.4657513E-03 0.2119122 at 30iterations 2.3440692E-04 3.1759262E-02 at 40iterations 6.1107050E-05 9.4733238E-03 at 50iterations finished qdiffx linear iterations at : 11:06:40 total time elapsed so far: 3.210000 # loops : 50 mean,max change (kT/e) : 6.1107050E-05 9.4733238E-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) 3.380000 DelPhi exited at 11:06:40 3.388u 0.186s 0:03.93 90.5% 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 Sun Oct 9 2011 at 11:06:40 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: 281 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2819 !!! WARNING: HIR 206 has a net charge of 0.5140 !!! WARNING: CME 307 has a net charge of -0.3480 !!! WARNING: CME 1 has a net charge of -0.0350 !!! WARNING: CME 3 has a net charge of -0.0350 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 1.893785 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): -24.93100 29.45600 ymin,ymax (A): -25.25400 26.19800 zmin,zma (A): -15.41000 40.98500 x,y,z range (A): 54.38700 51.45200 56.39500 scale (grids/A): 1.893785 object centre (A): 2.262500 0.4720001 12.78750 number of atom coordinates read : 2819 total number of charged atoms : 2737 net assigned charge : 4.096034 assigned positive charge : 424.0162 centred at (gu) : 89.25368 87.43131 96.89777 assigned negative charge : -419.9219 centred at (gu) : 89.22186 87.57708 97.19687 start vw surface at 0.1500000 fill in re-entrant regions at 0.2600000 boundary points on vw surface= 85421 reading accessible surface arcs data from file ARCDAT no. of arc points read = 27368 grid for indexing accessible points = 1.400000 m= 30858 mr = 57882 m= 5374 mr = 21779 m= 359 mr = 3322 m= 2 mr = 113 m= 0 mr = 0 time to grow re-entrant surface = 0.2900000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.6000000 number of dielectric boundary points 38918 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 145 iepsmp to db, and charging done at 0.7200000 number of grid points assigned charge 21509 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) : 0.6312616 object centre at (A) : 2.262500 0.4720001 12.78750 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 6.1275000E-03 -2.3091475E-02 midg,1,midg; midg,igrid,midg 4.8010390E-02 1.2713148E-02 1,midg,midg; igrid,midg,midg -2.3640487E-03 2.7649842E-02 gauss-seidel spectral radius is 0.9986688 estimated iterations to convergence 217 setup time was (sec) 0.8900000 now iterating at: 11:06:41 rms-change max change #iterations 4.397336 222.4674 at 10iterations 2.072083 68.60968 at 20iterations 0.9799719 30.27759 at 30iterations 0.4641985 13.63176 at 40iterations 0.2184658 6.738996 at 50iterations 0.1037854 3.179542 at 60iterations 4.9043063E-02 1.678547 at 70iterations 2.3166824E-02 0.6978455 at 80iterations 1.0940436E-02 0.3351746 at 90iterations 5.1864763E-03 0.1822205 at 100iterations 2.4609677E-03 7.8347206E-02 at 110iterations 1.1716584E-03 3.5423517E-02 at 120iterations finished qdiffx linear iterations at : 11:06:48 total time elapsed so far: 7.710000 # loops : 120 mean,max change (kT/e) : 1.1716584E-03 3.5423517E-02 energy calculations done at 7.710000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.890000 DelPhi exited at 11:06:49 7.892u 0.249s 0:08.45 96.2% 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 Sun Oct 9 2011 at 11:06:49 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: 281 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2819 !!! WARNING: HIR 206 has a net charge of 0.5140 !!! WARNING: CME 307 has a net charge of -0.3480 !!! WARNING: CME 1 has a net charge of -0.0350 !!! WARNING: CME 3 has a net charge of -0.0350 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 2.840677 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): -24.93100 29.45600 ymin,ymax (A): -25.25400 26.19800 zmin,zma (A): -15.41000 40.98500 x,y,z range (A): 54.38700 51.45200 56.39500 scale (grids/A): 2.840677 object centre (A): 2.262500 0.4720001 12.78750 number of atom coordinates read : 2819 total number of charged atoms : 2737 net assigned charge : 4.096034 assigned positive charge : 424.0162 centred at (gu) : 88.88044 86.14665 100.3464 assigned negative charge : -419.9219 centred at (gu) : 88.83280 86.36581 100.7954 start vw surface at 0.1500000 fill in re-entrant regions at 0.4800000 boundary points on vw surface= 197661 reading accessible surface arcs data from file ARCDAT no. of arc points read = 27368 grid for indexing accessible points = 1.400000 m= 98412 mr = 141208 m= 36684 mr = 78273 m= 9788 mr = 28602 m= 1510 mr = 7250 m= 86 mr = 1001 m= 0 mr = 23 time to grow re-entrant surface = 0.9100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.520000 number of dielectric boundary points 87784 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.670000 number of grid points assigned charge 21886 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) : 1.893785 object centre at (A) : 2.262500 0.4720001 12.78750 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1297036 -0.1217598 midg,1,midg; midg,igrid,midg 0.5066785 0.1347820 1,midg,midg; igrid,midg,midg -9.4762193E-03 0.3519551 gauss-seidel spectral radius is 0.9992886 estimated iterations to convergence 296 setup time was (sec) 1.850000 now iterating at: 11:06:51 rms-change max change #iterations 10.51228 329.9626 at 10iterations 6.292039 166.9419 at 20iterations 3.726645 79.09566 at 30iterations 2.204079 53.05021 at 40iterations 1.301103 27.08587 at 50iterations 0.7633639 14.32753 at 60iterations 0.4470091 8.879250 at 70iterations 0.2615954 5.202011 at 80iterations 0.1527781 2.755241 at 90iterations 8.9243710E-02 1.792873 at 100iterations 5.1992632E-02 0.9595337 at 110iterations 3.0332688E-02 0.5102577 at 120iterations 1.7699577E-02 0.3062286 at 130iterations 1.0292309E-02 0.1737633 at 140iterations 6.0058651E-03 0.1225462 at 150iterations 3.5088884E-03 6.0207367E-02 at 160iterations 2.0507807E-03 3.8103104E-02 at 170iterations 1.2060446E-03 2.0538330E-02 at 180iterations finished qdiffx linear iterations at : 11:07:02 total time elapsed so far: 13.02000 # loops : 180 mean,max change (kT/e) : 1.2060446E-03 2.0538330E-02 energy calculations done at 13.02000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.19000 DelPhi exited at 11:07:03 13.195u 0.245s 0:13.93 96.4% 0+0k 0+0io 0pf+0w