Sun Oct 9 07:03:03 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 07:03:03 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: 313 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2001 !!! WARNING: SEP 59 has a net charge of -0.4750 !!! WARNING: ASP 186 has a net charge of -2.0000 !!! WARNING: NDP 188 has a net charge of -3.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 0.6957746 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): -24.19900 25.29900 ymin,ymax (A): 0.7770001 45.61900 zmin,zma (A): -23.69000 27.47600 x,y,z range (A): 49.49800 44.84200 51.16600 scale (grids/A): 0.6957746 object centre (A): 0.5499992 23.19800 1.893000 number of atom coordinates read : 2001 total number of charged atoms : 1860 net assigned charge : -2.974986 assigned positive charge : 300.3760 centred at (gu) : 89.32986 89.66646 89.34111 assigned negative charge : -303.3510 centred at (gu) : 89.25278 89.86393 89.32520 start vw surface at 0.1400000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 6493 nv = 96 ne = 84 npr = 42370 no. pairs analyzed = 42370 no. exposed pairs = 2496 no. arc points = 17277 no. surface atoms = 842 nbur = 1159 mkacc time = 0.1200000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 357 mr = 3611 m= 0 mr = 48 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 33 time to turn everything in is 0.2900000 number of dielectric boundary points 3191 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1567 ## 126 charges are in solution ## iepsmp to db, and charging done at 0.4200000 number of grid points assigned charge 7349 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -2.8133655E-08 -1.1525071E-08 midg,1,midg; midg,igrid,midg 5.6269297E-08 -8.7162810E-08 1,midg,midg; igrid,midg,midg -5.4299466E-08 8.0200904E-09 gauss-seidel spectral radius is 0.9892309 estimated iterations to convergence 78 setup time was (sec) 0.5600000 now iterating at: 07:03:04 rms-change max change #iterations 0.1858405 28.16518 at 10iterations 2.2631833E-02 3.250336 at 20iterations 2.6422874E-03 0.3765602 at 30iterations 3.1544629E-04 4.5983315E-02 at 40iterations 3.7289185E-05 5.5770874E-03 at 50iterations finished qdiffx linear iterations at : 07:03:07 total time elapsed so far: 3.830000 # loops : 50 mean,max change (kT/e) : 3.7289185E-05 5.5770874E-03 energy calculations done at 3.830000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.000000 DelPhi exited at 07:03:08 3.999u 0.271s 0:04.54 93.8% 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 Sun Oct 9 2011 at 07:03:08 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: 313 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2001 !!! WARNING: SEP 59 has a net charge of -0.4750 !!! WARNING: ASP 186 has a net charge of -2.0000 !!! WARNING: NDP 188 has a net charge of -3.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 2.087324 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): -24.19900 25.29900 ymin,ymax (A): 0.7770001 45.61900 zmin,zma (A): -23.69000 27.47600 x,y,z range (A): 49.49800 44.84200 51.16600 scale (grids/A): 2.087324 object centre (A): 0.5499992 23.19800 1.893000 number of atom coordinates read : 2001 total number of charged atoms : 1860 net assigned charge : -2.974986 assigned positive charge : 300.3760 centred at (gu) : 87.98978 88.99943 88.02325 assigned negative charge : -303.3510 centred at (gu) : 87.75836 89.59195 87.97559 start vw surface at 0.1500000 fill in re-entrant regions at 0.2800000 boundary points on vw surface= 69564 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17277 grid for indexing accessible points = 1.400000 m= 25650 mr = 48279 m= 4395 mr = 19187 m= 340 mr = 2902 m= 7 mr = 163 m= 0 mr = 0 time to grow re-entrant surface = 0.3100000 no. cavity mid-points inaccessible to solvent = 1214 time to turn everything in is 0.6300000 number of dielectric boundary points 29425 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 71 iepsmp to db, and charging done at 0.7600000 number of grid points assigned charge 14755 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) : 0.6957746 object centre at (A) : 0.5499992 23.19800 1.893000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -6.2698334E-02 6.4815078E-03 midg,1,midg; midg,igrid,midg 6.3613027E-02 -4.8163466E-02 1,midg,midg; igrid,midg,midg -5.7497766E-02 -1.1342199E-02 gauss-seidel spectral radius is 0.9987919 estimated iterations to convergence 228 setup time was (sec) 0.9200000 now iterating at: 07:03:09 rms-change max change #iterations 4.496797 200.2114 at 10iterations 2.192390 82.89079 at 20iterations 1.072739 37.78954 at 30iterations 0.5249218 18.37172 at 40iterations 0.2568153 9.017196 at 50iterations 0.1259995 3.948367 at 60iterations 6.1762635E-02 1.812409 at 70iterations 3.0296966E-02 0.9862165 at 80iterations 1.4753461E-02 0.4176483 at 90iterations 7.2745057E-03 0.2379255 at 100iterations 3.5553549E-03 0.1098270 at 110iterations 1.7346187E-03 5.3833008E-02 at 120iterations finished qdiffx linear iterations at : 07:03:17 total time elapsed so far: 9.160000 # loops : 120 mean,max change (kT/e) : 1.7346187E-03 5.3833008E-02 energy calculations done at 9.160000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.340000 DelPhi exited at 07:03:18 9.340u 0.299s 0:09.94 96.8% 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 Sun Oct 9 2011 at 07:03:18 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: 313 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2001 !!! WARNING: SEP 59 has a net charge of -0.4750 !!! WARNING: ASP 186 has a net charge of -2.0000 !!! WARNING: NDP 188 has a net charge of -3.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 3.130985 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): -24.19900 25.29900 ymin,ymax (A): 0.7770001 45.61900 zmin,zma (A): -23.69000 27.47600 x,y,z range (A): 49.49800 44.84200 51.16600 scale (grids/A): 3.130985 object centre (A): 0.5499992 23.19800 1.893000 number of atom coordinates read : 2001 total number of charged atoms : 1860 net assigned charge : -2.974986 assigned positive charge : 300.3760 centred at (gu) : 86.98465 88.49904 87.03490 assigned negative charge : -303.3510 centred at (gu) : 86.63748 89.38789 86.96329 start vw surface at 0.1400000 fill in re-entrant regions at 0.9300000 boundary points on vw surface= 160740 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17277 grid for indexing accessible points = 1.400000 m= 81834 mr = 116518 m= 30694 mr = 67675 m= 8157 mr = 25023 m= 1429 mr = 6322 m= 134 mr = 986 m= 6 mr = 84 m= 0 mr = 4 time to grow re-entrant surface = 0.9600000 no. cavity mid-points inaccessible to solvent = 4085 time to turn everything in is 2.010000 number of dielectric boundary points 66382 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.150000 number of grid points assigned charge 14880 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) : 2.087324 object centre at (A) : 0.5499992 23.19800 1.893000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.7992624 0.5123830 midg,1,midg; midg,igrid,midg 0.7549129 -0.5203755 1,midg,midg; igrid,midg,midg -0.5087655 -0.1125454 gauss-seidel spectral radius is 0.9992878 estimated iterations to convergence 296 setup time was (sec) 2.340000 now iterating at: 07:03:20 rms-change max change #iterations 10.07792 357.9028 at 10iterations 5.860145 119.8447 at 20iterations 3.404851 74.35574 at 30iterations 1.981213 39.36202 at 40iterations 1.150354 21.34180 at 50iterations 0.6662751 12.01112 at 60iterations 0.3864622 7.165981 at 70iterations 0.2242275 3.799438 at 80iterations 0.1300089 2.370950 at 90iterations 7.5486794E-02 1.423156 at 100iterations 4.3670945E-02 0.7179041 at 110iterations 2.5323240E-02 0.4513206 at 120iterations 1.4666947E-02 0.2616520 at 130iterations 8.5300216E-03 0.1555901 at 140iterations 4.9330620E-03 8.2573891E-02 at 150iterations 2.8613473E-03 5.8924675E-02 at 160iterations 1.6595758E-03 3.2056808E-02 at 170iterations 9.6314464E-04 1.6739368E-02 at 180iterations finished qdiffx linear iterations at : 07:03:35 total time elapsed so far: 17.46000 # loops : 180 mean,max change (kT/e) : 9.6314464E-04 1.6739368E-02 energy calculations done at 17.46000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 17.64000 DelPhi exited at 07:03:36 17.642u 0.302s 0:18.21 98.5% 0+0k 0+0io 0pf+0w