Tue Oct 11 03:14:18 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 Tue Oct 11 2011 at 03:14:18 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3210 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: 0.5570072 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): -24.12100 33.31400 ymin,ymax (A): -39.01700 22.46100 zmin,zma (A): -31.65100 32.26200 x,y,z range (A): 57.43500 61.47800 63.91300 scale (grids/A): 0.5570072 object centre (A): 4.596499 -8.277999 0.3055000 number of atom coordinates read : 3210 total number of charged atoms : 3055 net assigned charge : -4.999985 assigned positive charge : 478.3609 centred at (gu) : 90.14242 91.36721 91.93561 assigned negative charge : -483.3623 centred at (gu) : 90.20511 91.27415 91.96387 start vw surface at 0.1700000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 6573 nv = 96 ne = 84 npr = 62894 no. pairs analyzed = 62894 no. exposed pairs = 4458 no. arc points = 30838 no. surface atoms = 1497 nbur = 1713 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 = 1.540000 m= 276 mr = 3201 m= 2 mr = 12 m= 0 mr = 0 time to grow re-entrant surface = 0.2100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4000000 number of dielectric boundary points 3638 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3055 ## 377 charges are in solution ## iepsmp to db, and charging done at 0.5200000 number of grid points assigned charge 8490 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.1650045E-10 -1.2555531E-09 midg,1,midg; midg,igrid,midg -1.0719459E-09 7.2771750E-10 1,midg,midg; igrid,midg,midg 1.8238697E-10 -1.1994354E-09 gauss-seidel spectral radius is 0.9834030 estimated iterations to convergence 64 setup time was (sec) 0.6700000 now iterating at: 03:14:19 rms-change max change #iterations 8.3580784E-02 13.78359 at 10iterations 5.9334310E-03 1.089093 at 20iterations 4.3005176E-04 6.9902420E-02 at 30iterations 4.2574466E-05 8.3341599E-03 at 40iterations 7.3309820E-06 1.8014908E-03 at 50iterations finished qdiffx linear iterations at : 03:14:23 total time elapsed so far: 4.020000 # loops : 50 mean,max change (kT/e) : 7.3309820E-06 1.8014908E-03 energy calculations done at 4.020000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.210000 DelPhi exited at 03:14:23 4.211u 0.281s 0:04.89 91.8% 0+0k 0+0io 6pf+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 Oct 11 2011 at 03:14:23 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3210 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: 1.671021 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): -24.12100 33.31400 ymin,ymax (A): -39.01700 22.46100 zmin,zma (A): -31.65100 32.26200 x,y,z range (A): 57.43500 61.47800 63.91300 scale (grids/A): 1.671021 object centre (A): 4.596499 -8.277999 0.3055000 number of atom coordinates read : 3210 total number of charged atoms : 3055 net assigned charge : -4.999985 assigned positive charge : 478.3609 centred at (gu) : 90.42665 94.10077 95.80634 assigned negative charge : -483.3623 centred at (gu) : 90.61510 93.82216 95.89133 start vw surface at 0.1800000 fill in re-entrant regions at 0.3000000 boundary points on vw surface= 72795 reading accessible surface arcs data from file ARCDAT no. of arc points read = 30838 grid for indexing accessible points = 1.400000 m= 21712 mr = 47809 m= 2065 mr = 14195 m= 55 mr = 834 m= 0 mr = 1 time to grow re-entrant surface = 0.3100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.6500000 number of dielectric boundary points 33788 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 285 ## 2 charges are in solution ## iepsmp to db, and charging done at 0.7900000 number of grid points assigned charge 23499 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) : 0.5570072 object centre at (A) : 4.596499 -8.277999 0.3055000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.9796869E-02 -9.6715242E-03 midg,1,midg; midg,igrid,midg -2.4150746E-02 -1.3273172E-02 1,midg,midg; igrid,midg,midg 8.3751883E-03 -9.3511837E-03 gauss-seidel spectral radius is 0.9983008 estimated iterations to convergence 193 setup time was (sec) 0.9600000 now iterating at: 03:14:25 rms-change max change #iterations 3.696674 161.6116 at 10iterations 1.565597 66.30795 at 20iterations 0.6705367 22.32775 at 30iterations 0.2860920 11.19042 at 40iterations 0.1232002 4.638709 at 50iterations 5.2722469E-02 1.819727 at 60iterations 2.2592587E-02 0.7947860 at 70iterations 9.6589318E-03 0.3585200 at 80iterations 4.1480996E-03 0.1486473 at 90iterations 1.7751879E-03 6.0358047E-02 at 100iterations 7.6480833E-04 2.5636196E-02 at 110iterations 3.3004288E-04 1.0947227E-02 at 120iterations finished qdiffx linear iterations at : 03:14:33 total time elapsed so far: 9.440000 # loops : 120 mean,max change (kT/e) : 3.3004288E-04 1.0947227E-02 energy calculations done at 9.440000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.630000 DelPhi exited at 03:14:34 9.637u 0.303s 0:10.33 96.1% 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 Oct 11 2011 at 03:14:34 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3210 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: 2.506532 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): -24.12100 33.31400 ymin,ymax (A): -39.01700 22.46100 zmin,zma (A): -31.65100 32.26200 x,y,z range (A): 57.43500 61.47800 63.91300 scale (grids/A): 2.506532 object centre (A): 4.596499 -8.277999 0.3055000 number of atom coordinates read : 3210 total number of charged atoms : 3055 net assigned charge : -4.999985 assigned positive charge : 478.3609 centred at (gu) : 90.63989 96.15096 98.70928 assigned negative charge : -483.3623 centred at (gu) : 90.92255 95.73322 98.83710 start vw surface at 0.1700000 fill in re-entrant regions at 0.5300000 boundary points on vw surface= 169022 reading accessible surface arcs data from file ARCDAT no. of arc points read = 30838 grid for indexing accessible points = 1.400000 m= 75403 mr = 117525 m= 20570 mr = 57941 m= 3018 mr = 14750 m= 208 mr = 1740 m= 2 mr = 78 m= 0 mr = 0 time to grow re-entrant surface = 0.9200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.590000 number of dielectric boundary points 76189 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 20 iepsmp to db, and charging done at 1.740000 number of grid points assigned charge 24425 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) : 1.671021 object centre at (A) : 4.596499 -8.277999 0.3055000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.4761060 -0.1016772 midg,1,midg; midg,igrid,midg -0.4604617 -0.2886457 1,midg,midg; igrid,midg,midg 0.1006177 -0.1149143 gauss-seidel spectral radius is 0.9991878 estimated iterations to convergence 277 setup time was (sec) 1.910000 now iterating at: 03:14:36 rms-change max change #iterations 9.497596 402.5074 at 10iterations 5.463984 125.7770 at 20iterations 3.121075 67.58028 at 30iterations 1.772984 40.63756 at 40iterations 1.003670 21.05418 at 50iterations 0.5644408 11.86950 at 60iterations 0.3179953 6.579601 at 70iterations 0.1787190 4.396664 at 80iterations 0.1002501 2.248453 at 90iterations 5.6138266E-02 1.051549 at 100iterations 3.1476993E-02 0.6250210 at 110iterations 1.7611049E-02 0.3713646 at 120iterations 9.8586418E-03 0.1862125 at 130iterations 5.5147214E-03 0.1055748 at 140iterations 3.0864710E-03 6.4363480E-02 at 150iterations 1.7254946E-03 3.6991119E-02 at 160iterations 9.6421334E-04 1.9999027E-02 at 170iterations 5.3940149E-04 9.4642639E-03 at 180iterations finished qdiffx linear iterations at : 03:14:50 total time elapsed so far: 16.02000 # loops : 180 mean,max change (kT/e) : 5.3940149E-04 9.4642639E-03 energy calculations done at 16.02000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 16.21000 DelPhi exited at 03:14:51 16.210u 0.330s 0:16.87 98.0% 0+0k 0+0io 0pf+0w