Sun Oct 9 05:59:27 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 05:59:27 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: 269 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1866 !!! WARNING: HIR 132 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= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6532830 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): 18.84700 69.49300 ymin,ymax (A): 15.50100 69.99500 zmin,zma (A): 47.04900 92.65700 x,y,z range (A): 50.64600 54.49400 45.60800 scale (grids/A): 0.6532830 object centre (A): 44.17000 42.74800 69.85300 number of atom coordinates read : 1866 total number of charged atoms : 1724 net assigned charge : -8.985989 assigned positive charge : 290.2799 centred at (gu) : 89.96872 87.74902 88.86596 assigned negative charge : -299.2661 centred at (gu) : 90.20850 87.60602 89.17932 start vw surface at 7.0000000E-02 fill in re-entrant regions at 7.9999998E-02 boundary points on vw surface= 5482 nv = 96 ne = 84 npr = 36740 no. pairs analyzed = 36740 no. exposed pairs = 2541 no. arc points = 18139 no. surface atoms = 848 nbur = 1018 mkacc time = 6.0000002E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 312 mr = 2782 m= 1 mr = 26 m= 0 mr = 0 time to grow re-entrant surface = 7.0000008E-02 no. cavity mid-points inaccessible to solvent = 4 time to turn everything in is 0.1500000 number of dielectric boundary points 2987 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1791 ## 181 charges are in solution ## iepsmp to db, and charging done at 0.2200000 number of grid points assigned charge 6281 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.5555430E-08 -4.7387747E-08 midg,1,midg; midg,igrid,midg -6.0040357E-08 -8.5611812E-10 1,midg,midg; igrid,midg,midg 1.1020500E-08 -4.9819278E-08 gauss-seidel spectral radius is 0.9877986 estimated iterations to convergence 74 setup time was (sec) 0.3300000 now iterating at: 05:59:27 rms-change max change #iterations 0.1368771 22.37319 at 10iterations 1.3880109E-02 2.570370 at 20iterations 1.4230339E-03 0.2538147 at 30iterations 1.4629556E-04 2.5533199E-02 at 40iterations 1.5051893E-05 2.4197102E-03 at 50iterations finished qdiffx linear iterations at : 05:59:30 total time elapsed so far: 3.160000 # loops : 50 mean,max change (kT/e) : 1.5051893E-05 2.4197102E-03 energy calculations done at 3.160000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.290000 DelPhi exited at 05:59:30 3.292u 0.183s 0:03.73 93.0% 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 05:59:30 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: 269 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1866 !!! WARNING: HIR 132 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= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.959849 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): 18.84700 69.49300 ymin,ymax (A): 15.50100 69.99500 zmin,zma (A): 47.04900 92.65700 x,y,z range (A): 50.64600 54.49400 45.60800 scale (grids/A): 1.959849 object centre (A): 44.17000 42.74800 69.85300 number of atom coordinates read : 1866 total number of charged atoms : 1724 net assigned charge : -8.985989 assigned positive charge : 290.2799 centred at (gu) : 89.90593 83.24696 86.59821 assigned negative charge : -299.2661 centred at (gu) : 90.62563 82.81812 87.53797 start vw surface at 7.0000000E-02 fill in re-entrant regions at 0.1300000 boundary points on vw surface= 58270 reading accessible surface arcs data from file ARCDAT no. of arc points read = 18139 grid for indexing accessible points = 1.400000 m= 20055 mr = 38018 m= 3029 mr = 14252 m= 170 mr = 1794 m= 1 mr = 63 m= 0 mr = 0 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 360 time to turn everything in is 0.2800000 number of dielectric boundary points 27398 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 122 iepsmp to db, and charging done at 0.3500000 number of grid points assigned charge 13623 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) : 0.6532830 object centre at (A) : 44.17000 42.74800 69.85300 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 7.5330329E-03 -4.7212671E-02 midg,1,midg; midg,igrid,midg -9.7986594E-02 -1.8794492E-02 1,midg,midg; igrid,midg,midg 2.8542899E-02 -5.2066267E-02 gauss-seidel spectral radius is 0.9986378 estimated iterations to convergence 215 setup time was (sec) 0.4900000 now iterating at: 05:59:31 rms-change max change #iterations 3.887429 170.6172 at 10iterations 1.817278 70.92256 at 20iterations 0.8455503 29.26696 at 30iterations 0.3970060 14.08502 at 40iterations 0.1857335 7.858028 at 50iterations 8.6441107E-02 3.051618 at 60iterations 4.0539064E-02 1.496756 at 70iterations 1.8897375E-02 0.6853092 at 80iterations 8.8605722E-03 0.3188181 at 90iterations 4.1487175E-03 0.1476364 at 100iterations 1.9369138E-03 7.2647095E-02 at 110iterations 9.0513739E-04 3.2073975E-02 at 120iterations finished qdiffx linear iterations at : 05:59:38 total time elapsed so far: 7.440000 # loops : 120 mean,max change (kT/e) : 9.0513739E-04 3.2073975E-02 energy calculations done at 7.440000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.560000 DelPhi exited at 05:59:38 7.566u 0.204s 0:08.09 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 Sun Oct 9 2011 at 05:59:38 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: 269 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1866 !!! WARNING: HIR 132 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= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.939773 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): 18.84700 69.49300 ymin,ymax (A): 15.50100 69.99500 zmin,zma (A): 47.04900 92.65700 x,y,z range (A): 50.64600 54.49400 45.60800 scale (grids/A): 2.939773 object centre (A): 44.17000 42.74800 69.85300 number of atom coordinates read : 1866 total number of charged atoms : 1724 net assigned charge : -8.985989 assigned positive charge : 290.2799 centred at (gu) : 89.85883 79.87051 84.89724 assigned negative charge : -299.2661 centred at (gu) : 90.93848 79.22724 86.30707 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.2600000 boundary points on vw surface= 134330 reading accessible surface arcs data from file ARCDAT no. of arc points read = 18139 grid for indexing accessible points = 1.400000 m= 65022 mr = 92305 m= 22582 mr = 52101 m= 5374 mr = 17571 m= 789 mr = 3885 m= 43 mr = 504 m= 0 mr = 14 time to grow re-entrant surface = 0.4000000 no. cavity mid-points inaccessible to solvent = 1250 time to turn everything in is 0.7500000 number of dielectric boundary points 61760 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 0.8300000 number of grid points assigned charge 13791 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) : 1.959849 object centre at (A) : 44.17000 42.74800 69.85300 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 5.0729461E-02 -0.4895340 midg,1,midg; midg,igrid,midg -0.8628610 -0.1367128 1,midg,midg; igrid,midg,midg 0.1719459 -0.8195517 gauss-seidel spectral radius is 0.9992484 estimated iterations to convergence 288 setup time was (sec) 0.9700000 now iterating at: 05:59:40 rms-change max change #iterations 9.203056 476.2441 at 10iterations 5.346329 198.9065 at 20iterations 3.077928 78.42325 at 30iterations 1.771417 40.21570 at 40iterations 1.016275 22.92752 at 50iterations 0.5827517 15.81747 at 60iterations 0.3344460 6.626221 at 70iterations 0.1911536 4.315738 at 80iterations 0.1095682 2.547782 at 90iterations 6.2633008E-02 1.287315 at 100iterations 3.5793934E-02 0.7766037 at 110iterations 2.0434229E-02 0.3999310 at 120iterations 1.1695328E-02 0.2439143 at 130iterations 6.6752168E-03 0.1380575 at 140iterations 3.8139434E-03 7.5378418E-02 at 150iterations 2.1846849E-03 4.6791077E-02 at 160iterations 1.2484373E-03 2.4410248E-02 at 170iterations 7.1611581E-04 1.4495850E-02 at 180iterations finished qdiffx linear iterations at : 05:59:51 total time elapsed so far: 11.94000 # loops : 180 mean,max change (kT/e) : 7.1611581E-04 1.4495850E-02 energy calculations done at 11.94000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.07000 DelPhi exited at 05:59:51 12.077u 0.205s 0:12.54 97.8% 0+0k 0+0io 0pf+0w