Tue Nov 22 14:19:18 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+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 Nov 22 2011 at 14:19:22 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: 256 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1966 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: 0.5764995 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): -34.86000 10.11600 ymin,ymax (A): 1.505000 41.40000 zmin,zma (A): -4.673000 57.07900 x,y,z range (A): 44.97600 39.89500 61.75200 scale (grids/A): 0.5764995 object centre (A): -12.37200 21.45250 26.20300 number of atom coordinates read : 1966 total number of charged atoms : 1834 net assigned charge : 3.000004 assigned positive charge : 292.5259 centred at (gu) : 90.23969 89.54748 90.92270 assigned negative charge : -289.5262 centred at (gu) : 90.17577 89.66299 90.91883 start vw surface at 0.1300000 fill in re-entrant regions at 0.1300000 boundary points on vw surface= 4398 nv = 96 ne = 84 npr = 39575 no. pairs analyzed = 39575 no. exposed pairs = 2496 no. arc points = 17214 no. surface atoms = 843 nbur = 1123 mkacc time = 9.0000004E-02 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 = 1.512000 m= 184 mr = 2323 m= 3 mr = 32 m= 0 mr = 0 time to grow re-entrant surface = 9.9999994E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2400000 number of dielectric boundary points 2230 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1803 ## 222 charges are in solution ## iepsmp to db, and charging done at 0.3600000 number of grid points assigned charge 5477 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 4.2329801E-10 7.6647017E-10 midg,1,midg; midg,igrid,midg 2.2527913E-09 -8.2586321E-10 1,midg,midg; igrid,midg,midg -2.3550750E-10 1.4597066E-09 gauss-seidel spectral radius is 0.9843889 estimated iterations to convergence 66 setup time was (sec) 0.4800000 now iterating at: 14:19:26 rms-change max change #iterations 7.6381445E-02 13.84454 at 10iterations 5.8826632E-03 1.111580 at 20iterations 4.4964429E-04 8.3978653E-02 at 30iterations 3.3806038E-05 6.1244965E-03 at 40iterations 2.5789143E-06 4.0817261E-04 at 50iterations finished qdiffx linear iterations at : 14:19:33 total time elapsed so far: 3.200000 # loops : 50 mean,max change (kT/e) : 2.5789143E-06 4.0817261E-04 energy calculations done at 3.200000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.380000 DelPhi exited at 14:19:34 3.388u 0.163s 0:11.50 30.7% 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 Nov 22 2011 at 14:19:35 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: 256 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1966 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: 1.729499 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): -34.86000 10.11600 ymin,ymax (A): 1.505000 41.40000 zmin,zma (A): -4.673000 57.07900 x,y,z range (A): 44.97600 39.89500 61.75200 scale (grids/A): 1.729499 object centre (A): -12.37200 21.45250 26.20300 number of atom coordinates read : 1966 total number of charged atoms : 1834 net assigned charge : 3.000004 assigned positive charge : 292.5259 centred at (gu) : 90.71919 88.64208 92.76808 assigned negative charge : -289.5262 centred at (gu) : 90.52748 88.98914 92.75653 start vw surface at 0.1200000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 47644 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17214 grid for indexing accessible points = 1.400000 m= 16269 mr = 32398 m= 2107 mr = 11987 m= 74 mr = 1308 m= 2 mr = 11 m= 0 mr = 0 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 522 time to turn everything in is 0.3700000 number of dielectric boundary points 20392 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 195 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.5000000 number of grid points assigned charge 14225 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) : 0.5764995 object centre at (A) : -12.37200 21.45250 26.20300 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.6777080E-02 2.4722774E-02 midg,1,midg; midg,igrid,midg -5.0727435E-04 -5.0690528E-03 1,midg,midg; igrid,midg,midg 1.3524252E-04 -3.7691125E-04 gauss-seidel spectral radius is 0.9982681 estimated iterations to convergence 191 setup time was (sec) 0.6800000 now iterating at: 14:19:40 rms-change max change #iterations 3.004982 157.1441 at 10iterations 1.268049 56.89656 at 20iterations 0.5403925 23.68787 at 30iterations 0.2299253 8.588682 at 40iterations 9.7910605E-02 3.801620 at 50iterations 4.1541815E-02 1.674320 at 60iterations 1.7646039E-02 0.7265596 at 70iterations 7.4988329E-03 0.2861500 at 80iterations 3.2104373E-03 0.1240274 at 90iterations 1.3636200E-03 5.4976940E-02 at 100iterations 5.8122992E-04 2.1583557E-02 at 110iterations 2.4679527E-04 9.3610287E-03 at 120iterations finished qdiffx linear iterations at : 14:19:55 total time elapsed so far: 7.240000 # loops : 120 mean,max change (kT/e) : 2.4679527E-04 9.3610287E-03 energy calculations done at 7.240000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.430000 DelPhi exited at 14:19:56 7.432u 0.186s 0:20.65 36.8% 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 Nov 22 2011 at 14:19:56 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: 256 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1966 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: 2.594248 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): -34.86000 10.11600 ymin,ymax (A): 1.505000 41.40000 zmin,zma (A): -4.673000 57.07900 x,y,z range (A): 44.97600 39.89500 61.75200 scale (grids/A): 2.594248 object centre (A): -12.37200 21.45250 26.20300 number of atom coordinates read : 1966 total number of charged atoms : 1834 net assigned charge : 3.000004 assigned positive charge : 292.5259 centred at (gu) : 91.07870 87.96312 94.15197 assigned negative charge : -289.5262 centred at (gu) : 90.79119 88.48385 94.13486 start vw surface at 0.1200000 fill in re-entrant regions at 0.3000000 boundary points on vw surface= 110273 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17214 grid for indexing accessible points = 1.400000 m= 54193 mr = 78738 m= 18054 mr = 44188 m= 3714 mr = 14617 m= 352 mr = 2792 m= 5 mr = 204 m= 0 mr = 0 time to grow re-entrant surface = 0.5100000 no. cavity mid-points inaccessible to solvent = 1732 time to turn everything in is 0.8900000 number of dielectric boundary points 46052 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 8 iepsmp to db, and charging done at 1.020000 number of grid points assigned charge 14667 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) : 1.729499 object centre at (A) : -12.37200 21.45250 26.20300 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1528387 0.2341203 midg,1,midg; midg,igrid,midg -4.6517219E-02 -8.0345981E-02 1,midg,midg; igrid,midg,midg -1.2122255E-02 -3.0250261E-02 gauss-seidel spectral radius is 0.9991288 estimated iterations to convergence 268 setup time was (sec) 1.190000 now iterating at: 14:19:58 rms-change max change #iterations 7.367048 245.6818 at 10iterations 4.095830 115.7004 at 20iterations 2.260377 56.72536 at 30iterations 1.243029 30.09570 at 40iterations 0.6850485 17.06049 at 50iterations 0.3746442 11.19921 at 60iterations 0.2050035 4.988275 at 70iterations 0.1123151 2.444186 at 80iterations 6.1507348E-02 1.745834 at 90iterations 3.3724904E-02 0.8290749 at 100iterations 1.8378882E-02 0.4280014 at 110iterations 1.0058111E-02 0.2302971 at 120iterations 5.5166758E-03 0.1355038 at 130iterations 3.0166591E-03 6.9641113E-02 at 140iterations 1.6478035E-03 3.7830353E-02 at 150iterations 9.0293505E-04 2.0191193E-02 at 160iterations 4.9245951E-04 1.0780334E-02 at 170iterations 2.6966800E-04 7.6065063E-03 at 180iterations finished qdiffx linear iterations at : 14:20:30 total time elapsed so far: 11.61000 # loops : 180 mean,max change (kT/e) : 2.6966800E-04 7.6065063E-03 energy calculations done at 11.61000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.79000 DelPhi exited at 14:20:32 11.793u 0.164s 0:36.07 33.1% 0+0k 0+0io 0pf+0w