Mon Oct 10 14:38:10 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 Mon Oct 10 2011 at 14:38:10 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: 263 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2690 !!! WARNING: ADP 662 has a net charge of -2.0000 !!! WARNING: MG6 664 has a net charge of 1.4000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.5854108 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): -8.087000 52.72500 ymin,ymax (A): -15.81600 34.31300 zmin,zma (A): 77.48800 130.7630 x,y,z range (A): 60.81200 50.12900 53.27500 scale (grids/A): 0.5854108 object centre (A): 22.31900 9.248500 104.1255 number of atom coordinates read : 2690 total number of charged atoms : 2548 net assigned charge : -3.599991 assigned positive charge : 417.6435 centred at (gu) : 92.08064 89.86182 89.59454 assigned negative charge : -421.2444 centred at (gu) : 92.00947 89.94354 89.65512 start vw surface at 0.1200000 fill in re-entrant regions at 0.1300000 boundary points on vw surface= 6213 nv = 96 ne = 84 npr = 52093 no. pairs analyzed = 52093 no. exposed pairs = 3719 no. arc points = 26122 no. surface atoms = 1255 nbur = 1435 mkacc time = 0.1400000 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 = 1.456000 m= 318 mr = 3102 m= 2 mr = 23 m= 0 mr = 0 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3100000 number of dielectric boundary points 3408 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2594 ## 286 charges are in solution ## iepsmp to db, and charging done at 0.4100000 number of grid points assigned charge 7675 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 5.5494587E-10 -2.2818221E-09 midg,1,midg; midg,igrid,midg 1.0506047E-09 -2.9435114E-09 1,midg,midg; igrid,midg,midg -1.7199364E-09 1.2861129E-09 gauss-seidel spectral radius is 0.9849196 estimated iterations to convergence 67 setup time was (sec) 0.5800000 now iterating at: 14:38:11 rms-change max change #iterations 0.1000838 18.00673 at 10iterations 7.9799052E-03 1.235490 at 20iterations 6.5036363E-04 0.1073468 at 30iterations 6.6525150E-05 1.2184143E-02 at 40iterations 1.2816819E-05 2.5787354E-03 at 50iterations finished qdiffx linear iterations at : 14:38:15 total time elapsed so far: 4.670000 # loops : 50 mean,max change (kT/e) : 1.2816819E-05 2.5787354E-03 energy calculations done at 4.670000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.840000 DelPhi exited at 14:38:16 4.842u 0.382s 0:05.69 91.7% 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 Mon Oct 10 2011 at 14:38:17 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: 263 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2690 !!! WARNING: ADP 662 has a net charge of -2.0000 !!! WARNING: MG6 664 has a net charge of 1.4000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.756232 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): -8.087000 52.72500 ymin,ymax (A): -15.81600 34.31300 zmin,zma (A): 77.48800 130.7630 x,y,z range (A): 60.81200 50.12900 53.27500 scale (grids/A): 1.756232 object centre (A): 22.31900 9.248500 104.1255 number of atom coordinates read : 2690 total number of charged atoms : 2548 net assigned charge : -3.599991 assigned positive charge : 417.6435 centred at (gu) : 96.24119 89.58487 88.78304 assigned negative charge : -421.2444 centred at (gu) : 96.02818 89.83049 88.96503 start vw surface at 0.1100000 fill in re-entrant regions at 0.2200000 boundary points on vw surface= 66933 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26122 grid for indexing accessible points = 1.400000 m= 22497 mr = 44204 m= 3151 mr = 15261 m= 130 mr = 1631 m= 0 mr = 24 time to grow re-entrant surface = 0.2900000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5500000 number of dielectric boundary points 31591 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 242 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.6700000 number of grid points assigned charge 19790 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) : 0.5854108 object centre at (A) : 22.31900 9.248500 104.1255 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -9.4715143E-03 -2.7880432E-02 midg,1,midg; midg,igrid,midg -5.2800695E-03 -1.5657505E-02 1,midg,midg; igrid,midg,midg 1.6456351E-02 3.4494195E-02 gauss-seidel spectral radius is 0.9984233 estimated iterations to convergence 200 setup time was (sec) 0.8600000 now iterating at: 14:38:18 rms-change max change #iterations 3.785492 158.3075 at 10iterations 1.666522 68.00409 at 20iterations 0.7381543 29.27210 at 30iterations 0.3264777 10.93929 at 40iterations 0.1443185 5.474834 at 50iterations 6.3765116E-02 2.108269 at 60iterations 2.8300397E-02 1.000373 at 70iterations 1.2495751E-02 0.4612122 at 80iterations 5.5284458E-03 0.2117215 at 90iterations 2.4515963E-03 8.9599609E-02 at 100iterations 1.0865319E-03 3.6750793E-02 at 110iterations 4.8048978E-04 1.6075134E-02 at 120iterations finished qdiffx linear iterations at : 14:38:28 total time elapsed so far: 11.09000 # loops : 120 mean,max change (kT/e) : 4.8048978E-04 1.6075134E-02 energy calculations done at 11.09000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.26000 DelPhi exited at 14:38:29 11.267u 0.484s 0:12.38 94.8% 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 Mon Oct 10 2011 at 14:38:29 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: 263 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2690 !!! WARNING: ADP 662 has a net charge of -2.0000 !!! WARNING: MG6 664 has a net charge of 1.4000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.634349 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): -8.087000 52.72500 ymin,ymax (A): -15.81600 34.31300 zmin,zma (A): 77.48800 130.7630 x,y,z range (A): 60.81200 50.12900 53.27500 scale (grids/A): 2.634349 object centre (A): 22.31900 9.248500 104.1255 number of atom coordinates read : 2690 total number of charged atoms : 2548 net assigned charge : -3.599991 assigned positive charge : 417.6435 centred at (gu) : 99.36164 89.37717 88.17437 assigned negative charge : -421.2444 centred at (gu) : 99.04208 89.74563 88.44745 start vw surface at 0.1200000 fill in re-entrant regions at 0.4600000 boundary points on vw surface= 154889 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26122 grid for indexing accessible points = 1.400000 m= 74119 mr = 108243 m= 24864 mr = 57713 m= 5132 mr = 18638 m= 595 mr = 3454 m= 21 mr = 336 m= 0 mr = 4 time to grow re-entrant surface = 0.9000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.470000 number of dielectric boundary points 71232 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4 iepsmp to db, and charging done at 1.620000 number of grid points assigned charge 20380 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) : 1.756232 object centre at (A) : 22.31900 9.248500 104.1255 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1020073 -0.3736036 midg,1,midg; midg,igrid,midg -8.5788429E-02 -0.1697800 1,midg,midg; igrid,midg,midg 0.3553252 0.3934926 gauss-seidel spectral radius is 0.9992086 estimated iterations to convergence 281 setup time was (sec) 1.840000 now iterating at: 14:38:31 rms-change max change #iterations 9.425742 323.4579 at 10iterations 5.462606 171.2280 at 20iterations 3.134169 69.52637 at 30iterations 1.789644 38.71944 at 40iterations 1.018048 20.32094 at 50iterations 0.5802378 13.55982 at 60iterations 0.3288375 6.893407 at 70iterations 0.1861279 3.764707 at 80iterations 0.1051674 2.112043 at 90iterations 5.9421305E-02 1.194706 at 100iterations 3.3537630E-02 0.6294060 at 110iterations 1.8950608E-02 0.3557739 at 120iterations 1.0691782E-02 0.2369995 at 130iterations 6.0334443E-03 0.1410923 at 140iterations 3.4069307E-03 7.2631836E-02 at 150iterations 1.9208554E-03 3.7395477E-02 at 160iterations 1.0833459E-03 2.3973465E-02 at 170iterations 6.1119965E-04 1.2513161E-02 at 180iterations finished qdiffx linear iterations at : 14:38:49 total time elapsed so far: 19.39000 # loops : 180 mean,max change (kT/e) : 6.1119965E-04 1.2513161E-02 energy calculations done at 19.39000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 19.55000 DelPhi exited at 14:38:50 19.559u 0.546s 0:20.73 96.9% 0+0k 0+0io 0pf+0w