Tue Oct 11 03:25:44 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 Tue Oct 11 2011 at 03:25:44 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: 316 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2963 !!! WARNING: HIT 129 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= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 0.5602593 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): -28.85500 24.34300 ymin,ymax (A): -67.82401 -8.929000 zmin,zma (A): -25.21800 38.32400 x,y,z range (A): 53.19800 58.89500 63.54200 scale (grids/A): 0.5602593 object centre (A): -2.256000 -38.37650 6.553000 number of atom coordinates read : 2963 total number of charged atoms : 2808 net assigned charge : -7.485990 assigned positive charge : 443.0352 centred at (gu) : 89.41570 91.83242 85.93792 assigned negative charge : -450.5224 centred at (gu) : 89.42913 91.84323 85.87786 start vw surface at 0.1800000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 6252 nv = 96 ne = 84 npr = 57430 no. pairs analyzed = 57430 no. exposed pairs = 4194 no. arc points = 29778 no. surface atoms = 1388 nbur = 1575 mkacc time = 0.1600000 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= 265 mr = 2999 m= 0 mr = 18 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3800000 number of dielectric boundary points 3500 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2922 ## 384 charges are in solution ## iepsmp to db, and charging done at 0.5000000 number of grid points assigned charge 7957 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -3.8454466E-09 -4.9336053E-11 midg,1,midg; midg,igrid,midg -4.1596784E-10 -1.3466135E-09 1,midg,midg; igrid,midg,midg -6.9112632E-10 -7.8468254E-10 gauss-seidel spectral radius is 0.9835764 estimated iterations to convergence 64 setup time was (sec) 0.6600000 now iterating at: 03:25:45 rms-change max change #iterations 8.3701409E-02 13.30754 at 10iterations 5.9387395E-03 1.009756 at 20iterations 4.2120411E-04 6.9932938E-02 at 30iterations 3.1804302E-05 5.0935745E-03 at 40iterations 2.8866234E-06 5.0354004E-04 at 50iterations finished qdiffx linear iterations at : 03:25:48 total time elapsed so far: 4.030000 # loops : 50 mean,max change (kT/e) : 2.8866234E-06 5.0354004E-04 energy calculations done at 4.030000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.210000 DelPhi exited at 03:25:49 4.213u 0.259s 0:05.10 87.4% 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 03:25:49 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: 316 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2963 !!! WARNING: HIT 129 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= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 1.680778 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): -28.85500 24.34300 ymin,ymax (A): -67.82401 -8.929000 zmin,zma (A): -25.21800 38.32400 x,y,z range (A): 53.19800 58.89500 63.54200 scale (grids/A): 1.680778 object centre (A): -2.256000 -38.37650 6.553000 number of atom coordinates read : 2963 total number of charged atoms : 2808 net assigned charge : -7.485990 assigned positive charge : 443.0352 centred at (gu) : 88.24638 95.49661 77.81291 assigned negative charge : -450.5224 centred at (gu) : 88.28705 95.52951 77.63358 start vw surface at 0.1800000 fill in re-entrant regions at 0.2900000 boundary points on vw surface= 67817 reading accessible surface arcs data from file ARCDAT no. of arc points read = 29778 grid for indexing accessible points = 1.400000 m= 20193 mr = 43436 m= 2268 mr = 13355 m= 76 mr = 1113 m= 0 mr = 4 time to grow re-entrant surface = 0.2800000 no. cavity mid-points inaccessible to solvent = 1412 time to turn everything in is 0.6100000 number of dielectric boundary points 32446 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 308 ## 3 charges are in solution ## iepsmp to db, and charging done at 0.7500000 number of grid points assigned charge 21647 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) : 0.5602593 object centre at (A) : -2.256000 -38.37650 6.553000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.1618772E-02 -8.7912409E-03 midg,1,midg; midg,igrid,midg -1.4522985E-02 -2.1555329E-02 1,midg,midg; igrid,midg,midg -2.6700634E-03 -1.1519104E-03 gauss-seidel spectral radius is 0.9982917 estimated iterations to convergence 192 setup time was (sec) 0.9100000 now iterating at: 03:25:50 rms-change max change #iterations 3.561166 162.8883 at 10iterations 1.518979 60.52862 at 20iterations 0.6513982 23.42630 at 30iterations 0.2782361 9.719785 at 40iterations 0.1191351 4.090241 at 50iterations 5.0681192E-02 1.932841 at 60iterations 2.1688432E-02 0.7617645 at 70iterations 9.2863226E-03 0.3459949 at 80iterations 3.9605163E-03 0.1297131 at 90iterations 1.6990332E-03 6.1774254E-02 at 100iterations 7.2471338E-04 2.4551392E-02 at 110iterations 3.1040102E-04 1.1482239E-02 at 120iterations finished qdiffx linear iterations at : 03:25:59 total time elapsed so far: 9.420000 # loops : 120 mean,max change (kT/e) : 3.1040102E-04 1.1482239E-02 energy calculations done at 9.420000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.600000 DelPhi exited at 03:25:59 9.602u 0.305s 0:10.30 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 03:25:59 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: 316 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2963 !!! WARNING: HIT 129 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= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 2.521167 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): -28.85500 24.34300 ymin,ymax (A): -67.82401 -8.929000 zmin,zma (A): -25.21800 38.32400 x,y,z range (A): 53.19800 58.89500 63.54200 scale (grids/A): 2.521167 object centre (A): -2.256000 -38.37650 6.553000 number of atom coordinates read : 2963 total number of charged atoms : 2808 net assigned charge : -7.485990 assigned positive charge : 443.0352 centred at (gu) : 87.36935 98.24464 71.71908 assigned negative charge : -450.5224 centred at (gu) : 87.43041 98.29414 71.45039 start vw surface at 0.1800000 fill in re-entrant regions at 0.5100000 boundary points on vw surface= 157377 reading accessible surface arcs data from file ARCDAT no. of arc points read = 29778 grid for indexing accessible points = 1.400000 m= 69101 mr = 107109 m= 20177 mr = 52825 m= 3558 mr = 14886 m= 290 mr = 2365 m= 5 mr = 124 m= 0 mr = 0 time to grow re-entrant surface = 0.8600001 no. cavity mid-points inaccessible to solvent = 4754 time to turn everything in is 1.480000 number of dielectric boundary points 73199 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 8 iepsmp to db, and charging done at 1.620000 number of grid points assigned charge 22445 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) : 1.680778 object centre at (A) : -2.256000 -38.37650 6.553000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1367676 -0.2678266 midg,1,midg; midg,igrid,midg -0.2456616 -0.1507652 1,midg,midg; igrid,midg,midg -3.2098997E-02 -4.7729569E-03 gauss-seidel spectral radius is 0.9991777 estimated iterations to convergence 275 setup time was (sec) 1.800000 now iterating at: 03:26:02 rms-change max change #iterations 9.265389 285.9108 at 10iterations 5.324362 137.2839 at 20iterations 3.044467 83.18774 at 30iterations 1.727041 40.66978 at 40iterations 0.9751311 20.49962 at 50iterations 0.5500290 12.38998 at 60iterations 0.3090543 7.438255 at 70iterations 0.1731253 3.633224 at 80iterations 9.6919030E-02 2.196475 at 90iterations 5.4165214E-02 1.229614 at 100iterations 3.0222820E-02 0.7596741 at 110iterations 1.6894210E-02 0.3351898 at 120iterations 9.4114291E-03 0.1766787 at 130iterations 5.2599246E-03 0.1127930 at 140iterations 2.9336698E-03 5.8369637E-02 at 150iterations 1.6356623E-03 3.5659313E-02 at 160iterations 9.1092079E-04 1.8144369E-02 at 170iterations 5.0824258E-04 9.7694397E-03 at 180iterations finished qdiffx linear iterations at : 03:26:16 total time elapsed so far: 15.85000 # loops : 180 mean,max change (kT/e) : 5.0824258E-04 9.7694397E-03 energy calculations done at 15.85000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 16.03000 DelPhi exited at 03:26:16 16.028u 0.336s 0:16.75 97.6% 0+0k 0+0io 0pf+0w