Sat Oct 15 13:17:36 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+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 Sat Oct 15 2011 at 13:17:36 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: 267 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3363 !!! WARNING: LLP 1 has a net charge of 1.7400 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: 0.5739344 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): -11.22200 50.80600 ymin,ymax (A): -12.70900 42.48800 zmin,zma (A): 17.67300 75.60201 x,y,z range (A): 62.02800 55.19700 57.92900 scale (grids/A): 0.5739344 object centre (A): 19.79200 14.88950 46.63750 number of atom coordinates read : 3363 total number of charged atoms : 3217 net assigned charge : 3.240021 assigned positive charge : 520.8698 centred at (gu) : 90.83980 89.81660 88.24122 assigned negative charge : -517.6310 centred at (gu) : 90.76971 89.90717 88.21786 start vw surface at 0.1400000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 7471 nv = 96 ne = 84 npr = 65140 no. pairs analyzed = 65140 no. exposed pairs = 4522 no. arc points = 32130 no. surface atoms = 1524 nbur = 1839 mkacc time = 0.1800000 writing accessible surface arcs data to file ARCDAT initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 360 mr = 3710 m= 1 mr = 34 m= 0 mr = 0 time to grow re-entrant surface = 0.2400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3900000 number of dielectric boundary points 4088 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3163 ## 308 charges are in solution ## iepsmp to db, and charging done at 0.5200000 number of grid points assigned charge 9314 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 9.6779799E-11 6.9728373E-10 midg,1,midg; midg,igrid,midg 2.5379763E-09 -1.2854720E-09 1,midg,midg; igrid,midg,midg -7.3942441E-10 2.4572611E-09 gauss-seidel spectral radius is 0.9843714 estimated iterations to convergence 66 setup time was (sec) 0.7200000 now iterating at: 13:17:37 rms-change max change #iterations 9.7010873E-02 13.81056 at 10iterations 7.3415283E-03 1.251931 at 20iterations 5.6311849E-04 9.6477509E-02 at 30iterations 4.3493303E-05 7.1954727E-03 at 40iterations 3.3666861E-06 4.6348572E-04 at 50iterations finished qdiffx linear iterations at : 13:17:41 total time elapsed so far: 5.190000 # loops : 50 mean,max change (kT/e) : 3.3666861E-06 4.6348572E-04 energy calculations done at 5.190000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 5.360000 DelPhi exited at 13:17:42 5.364u 0.445s 0:06.21 93.3% 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 15 2011 at 13:17:42 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: 267 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3363 !!! WARNING: LLP 1 has a net charge of 1.7400 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: 1.721803 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): -11.22200 50.80600 ymin,ymax (A): -12.70900 42.48800 zmin,zma (A): 17.67300 75.60201 x,y,z range (A): 62.02800 55.19700 57.92900 scale (grids/A): 1.721803 object centre (A): 19.79200 14.88950 46.63750 number of atom coordinates read : 3363 total number of charged atoms : 3217 net assigned charge : 3.240021 assigned positive charge : 520.8698 centred at (gu) : 92.51836 89.44890 84.72238 assigned negative charge : -517.6310 centred at (gu) : 92.30859 89.72126 84.65331 start vw surface at 0.1300000 fill in re-entrant regions at 0.2600000 boundary points on vw surface= 81397 reading accessible surface arcs data from file ARCDAT no. of arc points read = 32130 grid for indexing accessible points = 1.400000 m= 27144 mr = 54545 m= 3457 mr = 18119 m= 137 mr = 1774 m= 2 mr = 18 m= 0 mr = 0 time to grow re-entrant surface = 0.3800000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.7000000 number of dielectric boundary points 37681 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 296 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.8800000 number of grid points assigned charge 24933 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) : 0.5739344 object centre at (A) : 19.79200 14.88950 46.63750 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.8636654E-03 7.6523190E-03 midg,1,midg; midg,igrid,midg 2.2710226E-02 -9.6826339E-03 1,midg,midg; igrid,midg,midg -1.3133959E-02 -7.7808592E-03 gauss-seidel spectral radius is 0.9984202 estimated iterations to convergence 200 setup time was (sec) 1.110000 now iterating at: 13:17:44 rms-change max change #iterations 4.125755 154.8193 at 10iterations 1.819776 61.15544 at 20iterations 0.8079489 29.55244 at 30iterations 0.3575875 12.88743 at 40iterations 0.1581900 4.805371 at 50iterations 7.0443638E-02 2.396305 at 60iterations 3.1281203E-02 1.027361 at 70iterations 1.3904467E-02 0.5207081 at 80iterations 6.1898045E-03 0.2303658 at 90iterations 2.7880603E-03 9.7927094E-02 at 100iterations 1.2945512E-03 5.2188873E-02 at 110iterations 6.5520557E-04 2.3496628E-02 at 120iterations finished qdiffx linear iterations at : 13:17:56 total time elapsed so far: 13.05000 # loops : 120 mean,max change (kT/e) : 6.5520557E-04 2.3496628E-02 energy calculations done at 13.05000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.22000 DelPhi exited at 13:17:56 13.225u 0.528s 0:14.05 97.7% 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 Sat Oct 15 2011 at 13:17:56 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: 267 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3363 !!! WARNING: LLP 1 has a net charge of 1.7400 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: 2.582705 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): -11.22200 50.80600 ymin,ymax (A): -12.70900 42.48800 zmin,zma (A): 17.67300 75.60201 x,y,z range (A): 62.02800 55.19700 57.92900 scale (grids/A): 2.582705 object centre (A): 19.79200 14.88950 46.63750 number of atom coordinates read : 3363 total number of charged atoms : 3217 net assigned charge : 3.240021 assigned positive charge : 520.8698 centred at (gu) : 93.77753 89.17323 82.08338 assigned negative charge : -517.6310 centred at (gu) : 93.46281 89.58183 81.97993 start vw surface at 0.1400000 fill in re-entrant regions at 0.5300000 boundary points on vw surface= 188623 reading accessible surface arcs data from file ARCDAT no. of arc points read = 32130 grid for indexing accessible points = 1.400000 m= 90001 mr = 133302 m= 28819 mr = 70241 m= 5842 mr = 21141 m= 600 mr = 3871 m= 18 mr = 301 m= 0 mr = 0 time to grow re-entrant surface = 1.100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.770000 number of dielectric boundary points 85047 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 7 iepsmp to db, and charging done at 1.940000 number of grid points assigned charge 25715 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) : 1.721803 object centre at (A) : 19.79200 14.88950 46.63750 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 9.0800911E-02 9.0458706E-02 midg,1,midg; midg,igrid,midg 0.3681840 -0.1102873 1,midg,midg; igrid,midg,midg 1.3684940E-02 -0.5505162 gauss-seidel spectral radius is 0.9992263 estimated iterations to convergence 284 setup time was (sec) 2.160000 now iterating at: 13:17:59 rms-change max change #iterations 10.54053 290.4468 at 10iterations 6.242624 152.7904 at 20iterations 3.641852 85.15608 at 30iterations 2.108989 50.37781 at 40iterations 1.219787 31.17934 at 50iterations 0.7009825 15.88861 at 60iterations 0.4018923 9.649207 at 70iterations 0.2298179 4.707651 at 80iterations 0.1312882 2.513451 at 90iterations 7.5133368E-02 1.528953 at 100iterations 4.2861190E-02 0.8164835 at 110iterations 2.4413025E-02 0.4833832 at 120iterations 1.3902407E-02 0.2805624 at 130iterations 7.9340013E-03 0.1689736 at 140iterations 4.5324801E-03 8.8022232E-02 at 150iterations 2.5929841E-03 5.0197601E-02 at 160iterations 1.4965339E-03 2.8072119E-02 at 170iterations 8.8655326E-04 1.8960953E-02 at 180iterations finished qdiffx linear iterations at : 13:18:19 total time elapsed so far: 22.16000 # loops : 180 mean,max change (kT/e) : 8.8655326E-04 1.8960953E-02 energy calculations done at 22.16000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 22.33000 DelPhi exited at 13:18:20 22.336u 0.568s 0:23.34 98.0% 0+0k 0+0io 0pf+0w