Mon Oct 10 19:01:15 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 19:01:15 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: 279 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2603 !!! WARNING: HIR 242 has a net charge of 0.5140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1100000 grid size : 179 scale,in grids/A, set to be: 0.6368515 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): 1.960000 56.74900 ymin,ymax (A): -18.89800 19.39100 zmin,zma (A): -26.10500 29.79500 x,y,z range (A): 54.78900 38.28900 55.90000 scale (grids/A): 0.6368515 object centre (A): 29.35450 0.2465000 1.845000 number of atom coordinates read : 2603 total number of charged atoms : 2466 net assigned charge : 1.014006 assigned positive charge : 389.7369 centred at (gu) : 89.32696 90.06955 90.24388 assigned negative charge : -388.7240 centred at (gu) : 89.29353 90.01965 90.28086 start vw surface at 0.2000000 fill in re-entrant regions at 0.2100000 boundary points on vw surface= 7021 nv = 96 ne = 84 npr = 53055 no. pairs analyzed = 53055 no. exposed pairs = 3424 no. arc points = 23870 no. surface atoms = 1148 nbur = 1455 mkacc time = 0.1600000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 476 mr = 3678 m= 2 mr = 65 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 0.3900000 number of dielectric boundary points 3756 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2339 ## 182 charges are in solution ## iepsmp to db, and charging done at 0.5400000 number of grid points assigned charge 8510 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 5.0578617E-09 -2.7438338E-09 midg,1,midg; midg,igrid,midg -3.9331849E-09 6.8044925E-09 1,midg,midg; igrid,midg,midg -2.5788001E-09 4.2853117E-09 gauss-seidel spectral radius is 0.9872308 estimated iterations to convergence 72 setup time was (sec) 0.6900000 now iterating at: 19:01:16 rms-change max change #iterations 0.1415858 21.01846 at 10iterations 1.3504855E-02 2.169111 at 20iterations 1.3521069E-03 0.2120850 at 30iterations 1.5606514E-04 2.0674229E-02 at 40iterations 3.1770556E-05 5.3882599E-03 at 50iterations finished qdiffx linear iterations at : 19:01:19 total time elapsed so far: 4.000000 # loops : 50 mean,max change (kT/e) : 3.1770556E-05 5.3882599E-03 energy calculations done at 4.000000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.250000 DelPhi exited at 19:01:20 4.255u 0.215s 0:04.80 92.9% 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 19:01:20 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: 279 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2603 !!! WARNING: HIR 242 has a net charge of 0.5140 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: 1.910555 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): 1.960000 56.74900 ymin,ymax (A): -18.89800 19.39100 zmin,zma (A): -26.10500 29.79500 x,y,z range (A): 54.78900 38.28900 55.90000 scale (grids/A): 1.910555 object centre (A): 29.35450 0.2465000 1.845000 number of atom coordinates read : 2603 total number of charged atoms : 2466 net assigned charge : 1.014006 assigned positive charge : 389.7369 centred at (gu) : 87.98054 90.20816 90.73120 assigned negative charge : -388.7240 centred at (gu) : 87.88062 90.05897 90.84270 start vw surface at 0.1800000 fill in re-entrant regions at 0.3200000 boundary points on vw surface= 75648 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23870 grid for indexing accessible points = 1.400000 m= 27783 mr = 51267 m= 5180 mr = 19978 m= 352 mr = 3247 m= 8 mr = 143 m= 0 mr = 0 time to grow re-entrant surface = 0.3500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.7200000 number of dielectric boundary points 34336 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 146 iepsmp to db, and charging done at 0.8800000 number of grid points assigned charge 19393 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) : 0.6368515 object centre at (A) : 29.35450 0.2465000 1.845000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.9757323E-02 -2.0818885E-03 midg,1,midg; midg,igrid,midg -2.4936728E-03 6.0206982E-03 1,midg,midg; igrid,midg,midg 1.7482616E-02 -1.4432603E-02 gauss-seidel spectral radius is 0.9986506 estimated iterations to convergence 216 setup time was (sec) 1.090000 now iterating at: 19:01:21 rms-change max change #iterations 4.297905 199.8398 at 10iterations 2.010840 66.56406 at 20iterations 0.9453202 29.46969 at 30iterations 0.4420438 15.22307 at 40iterations 0.2078137 6.740606 at 50iterations 9.8012537E-02 3.021006 at 60iterations 4.6057027E-02 1.413944 at 70iterations 2.1589551E-02 0.7037110 at 80iterations 1.0194140E-02 0.2963257 at 90iterations 4.7999630E-03 0.1441460 at 100iterations 2.2572267E-03 7.5012207E-02 at 110iterations 1.0603227E-03 3.9594650E-02 at 120iterations finished qdiffx linear iterations at : 19:01:29 total time elapsed so far: 9.350000 # loops : 120 mean,max change (kT/e) : 1.0603227E-03 3.9594650E-02 energy calculations done at 9.350000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.600000 DelPhi exited at 19:01:30 9.600u 0.216s 0:10.30 95.2% 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 19:01:30 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: 279 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2603 !!! WARNING: HIR 242 has a net charge of 0.5140 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: 2.865832 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): 1.960000 56.74900 ymin,ymax (A): -18.89800 19.39100 zmin,zma (A): -26.10500 29.79500 x,y,z range (A): 54.78900 38.28900 55.90000 scale (grids/A): 2.865832 object centre (A): 29.35450 0.2465000 1.845000 number of atom coordinates read : 2603 total number of charged atoms : 2466 net assigned charge : 1.014006 assigned positive charge : 389.7369 centred at (gu) : 86.97061 90.31206 91.09674 assigned negative charge : -388.7240 centred at (gu) : 86.82101 90.08842 91.26385 start vw surface at 0.1900000 fill in re-entrant regions at 0.6000000 boundary points on vw surface= 174845 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23870 grid for indexing accessible points = 1.400000 m= 87455 mr = 124626 m= 34289 mr = 70128 m= 9528 mr = 27224 m= 1580 mr = 7217 m= 112 mr = 1108 m= 0 mr = 53 time to grow re-entrant surface = 1.080000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.810000 number of dielectric boundary points 77453 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.970000 number of grid points assigned charge 19726 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) : 1.910555 object centre at (A) : 29.35450 0.2465000 1.845000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.3551387 9.7732238E-02 midg,1,midg; midg,igrid,midg -2.5262237E-02 1.0687488E-02 1,midg,midg; igrid,midg,midg 0.1480613 -0.2684166 gauss-seidel spectral radius is 0.9992698 estimated iterations to convergence 292 setup time was (sec) 2.180000 now iterating at: 19:01:33 rms-change max change #iterations 10.36933 361.1757 at 10iterations 6.182757 181.6861 at 20iterations 3.662838 78.64835 at 30iterations 2.145403 40.39355 at 40iterations 1.259349 28.64691 at 50iterations 0.7331836 13.55583 at 60iterations 0.4274071 8.341946 at 70iterations 0.2485107 5.271173 at 80iterations 0.1441651 3.006935 at 90iterations 8.3407439E-02 1.791861 at 100iterations 4.8307512E-02 0.9708452 at 110iterations 2.8010638E-02 0.5434437 at 120iterations 1.6229955E-02 0.3281364 at 130iterations 9.4106710E-03 0.1779003 at 140iterations 5.4646218E-03 0.1016085 at 150iterations 3.2082717E-03 5.7010651E-02 at 160iterations 1.9073343E-03 3.7014008E-02 at 170iterations 1.1575089E-03 2.1315336E-02 at 180iterations finished qdiffx linear iterations at : 19:01:46 total time elapsed so far: 15.86000 # loops : 180 mean,max change (kT/e) : 1.1575089E-03 2.1315336E-02 energy calculations done at 15.86000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 16.10000 DelPhi exited at 19:01:47 16.101u 0.241s 0:16.64 98.1% 0+0k 0+0io 0pf+0w