Mon Oct 10 14:02:57 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 Mon Oct 10 2011 at 14:02:57 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: 304 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2011 !!! WARNING: HIR 237 has a net charge of 0.5140 !!! WARNING: GLM 283 has a net charge of -0.0940 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6762276 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): 6.992000 59.63700 ymin,ymax (A): 76.15000 122.9870 zmin,zma (A): -7.487000 33.43400 x,y,z range (A): 52.64500 46.83700 40.92100 scale (grids/A): 0.6762276 object centre (A): 33.31450 99.56850 12.97350 number of atom coordinates read : 2011 total number of charged atoms : 1872 net assigned charge : 2.920003 assigned positive charge : 300.1128 centred at (gu) : 88.01331 90.42619 90.89041 assigned negative charge : -297.1929 centred at (gu) : 88.10828 90.37882 90.78616 start vw surface at 9.0000004E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 6206 nv = 96 ne = 84 npr = 41332 no. pairs analyzed = 41332 no. exposed pairs = 2464 no. arc points = 17152 no. surface atoms = 838 nbur = 1173 mkacc time = 6.9999993E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 379 mr = 3466 m= 2 mr = 42 m= 0 mr = 0 time to grow re-entrant surface = 7.9999998E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.1700000 number of dielectric boundary points 3079 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1551 ## 127 charges are in solution ## iepsmp to db, and charging done at 0.2300000 number of grid points assigned charge 7008 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.0925259E-08 4.0740318E-08 midg,1,midg; midg,igrid,midg -1.0721294E-10 2.3182782E-08 1,midg,midg; igrid,midg,midg 4.8024596E-08 -7.2085484E-09 gauss-seidel spectral radius is 0.9886077 estimated iterations to convergence 76 setup time was (sec) 0.3500000 now iterating at: 14:02:58 rms-change max change #iterations 0.1654742 26.71684 at 10iterations 1.8811217E-02 3.028755 at 20iterations 2.1213493E-03 0.3252540 at 30iterations 2.9848274E-04 4.1692734E-02 at 40iterations 6.8822519E-05 1.0365486E-02 at 50iterations finished qdiffx linear iterations at : 14:03:00 total time elapsed so far: 3.200000 # loops : 50 mean,max change (kT/e) : 6.8822519E-05 1.0365486E-02 energy calculations done at 3.200000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.330000 DelPhi exited at 14:03:01 3.334u 0.156s 0:03.97 87.6% 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 14:03:01 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: 304 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2011 !!! WARNING: HIR 237 has a net charge of 0.5140 !!! WARNING: GLM 283 has a net charge of -0.0940 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.028683 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): 6.992000 59.63700 ymin,ymax (A): 76.15000 122.9870 zmin,zma (A): -7.487000 33.43400 x,y,z range (A): 52.64500 46.83700 40.92100 scale (grids/A): 2.028683 object centre (A): 33.31450 99.56850 12.97350 number of atom coordinates read : 2011 total number of charged atoms : 1872 net assigned charge : 2.920003 assigned positive charge : 300.1128 centred at (gu) : 84.03983 91.27823 92.67108 assigned negative charge : -297.1929 centred at (gu) : 84.32477 91.13631 92.35844 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 65934 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17152 grid for indexing accessible points = 1.400000 m= 25060 mr = 45721 m= 4545 mr = 18589 m= 321 mr = 2907 m= 9 mr = 128 m= 0 mr = 0 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3400000 number of dielectric boundary points 28524 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 63 iepsmp to db, and charging done at 0.4100000 number of grid points assigned charge 14821 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) : 0.6762276 object centre at (A) : 33.31450 99.56850 12.97350 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -4.9980432E-03 2.9089281E-02 midg,1,midg; midg,igrid,midg 7.2045196E-03 3.3533394E-02 1,midg,midg; igrid,midg,midg -2.1051759E-02 -2.2008821E-02 gauss-seidel spectral radius is 0.9987273 estimated iterations to convergence 222 setup time was (sec) 0.5500000 now iterating at: 14:03:02 rms-change max change #iterations 4.177305 262.0699 at 10iterations 2.010517 66.35114 at 20iterations 0.9678398 32.76318 at 30iterations 0.4639858 15.70930 at 40iterations 0.2245201 7.471741 at 50iterations 0.1080306 3.385448 at 60iterations 5.1963411E-02 1.848822 at 70iterations 2.5026521E-02 0.7929230 at 80iterations 1.1994616E-02 0.4145432 at 90iterations 5.8201593E-03 0.1904945 at 100iterations 2.8137949E-03 0.1056824 at 110iterations 1.3641950E-03 4.1664124E-02 at 120iterations finished qdiffx linear iterations at : 14:03:09 total time elapsed so far: 7.530000 # loops : 120 mean,max change (kT/e) : 1.3641950E-03 4.1664124E-02 energy calculations done at 7.530000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.660000 DelPhi exited at 14:03:09 7.665u 0.189s 0:08.17 95.9% 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 14:03:09 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: 304 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2011 !!! WARNING: HIR 237 has a net charge of 0.5140 !!! WARNING: GLM 283 has a net charge of -0.0940 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 3.043024 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): 6.992000 59.63700 ymin,ymax (A): 76.15000 122.9870 zmin,zma (A): -7.487000 33.43400 x,y,z range (A): 52.64500 46.83700 40.92100 scale (grids/A): 3.043024 object centre (A): 33.31450 99.56850 12.97350 number of atom coordinates read : 2011 total number of charged atoms : 1872 net assigned charge : 2.920003 assigned positive charge : 300.1128 centred at (gu) : 81.05970 91.91741 94.00662 assigned negative charge : -297.1929 centred at (gu) : 81.48721 91.70437 93.53770 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.3000000 boundary points on vw surface= 152296 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17152 grid for indexing accessible points = 1.400000 m= 78804 mr = 110704 m= 30596 mr = 64684 m= 8568 mr = 24701 m= 1536 mr = 6472 m= 135 mr = 1077 m= 2 mr = 73 m= 0 mr = 0 time to grow re-entrant surface = 0.4900000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.8700000 number of dielectric boundary points 64226 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 0.9500000 number of grid points assigned charge 14976 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) : 2.028683 object centre at (A) : 33.31450 99.56850 12.97350 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -6.5351866E-02 0.2726253 midg,1,midg; midg,igrid,midg -1.4523947E-02 0.2311934 1,midg,midg; igrid,midg,midg -0.3458464 -0.1641551 gauss-seidel spectral radius is 0.9992708 estimated iterations to convergence 292 setup time was (sec) 1.100000 now iterating at: 14:03:11 rms-change max change #iterations 9.577665 404.7346 at 10iterations 5.626184 119.5543 at 20iterations 3.290572 82.62781 at 30iterations 1.919085 38.33968 at 40iterations 1.116222 22.21097 at 50iterations 0.6489617 12.70838 at 60iterations 0.3769594 7.530052 at 70iterations 0.2195072 4.295757 at 80iterations 0.1270484 2.464027 at 90iterations 7.3452555E-02 1.382476 at 100iterations 4.2557541E-02 0.8315296 at 110iterations 2.4637891E-02 0.4632730 at 120iterations 1.4236632E-02 0.2738714 at 130iterations 8.2447417E-03 0.1460762 at 140iterations 4.7734058E-03 9.2991829E-02 at 150iterations 2.7631389E-03 5.2875519E-02 at 160iterations 1.6095558E-03 2.8435707E-02 at 170iterations 9.4363780E-04 1.7773628E-02 at 180iterations finished qdiffx linear iterations at : 14:03:22 total time elapsed so far: 12.22000 # loops : 180 mean,max change (kT/e) : 9.4363780E-04 1.7773628E-02 energy calculations done at 12.22000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.36000 DelPhi exited at 14:03:23 12.363u 0.207s 0:13.29 94.5% 0+0k 0+0io 0pf+0w