Sun Oct 9 07:36:24 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 07:36:24 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: 307 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1697 !!! WARNING: NAP 164 has a net charge of -2.0000 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: 0.6984227 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): -8.198000 33.76400 ymin,ymax (A): 2.226000 43.06600 zmin,zma (A): 9.329000 60.30100 x,y,z range (A): 41.96200 40.84000 50.97200 scale (grids/A): 0.6984227 object centre (A): 12.78300 22.64600 34.81500 number of atom coordinates read : 1697 total number of charged atoms : 1560 net assigned charge : -11.49999 assigned positive charge : 252.6242 centred at (gu) : 91.61620 89.49018 89.54067 assigned negative charge : -264.1241 centred at (gu) : 91.41008 89.68603 89.78463 start vw surface at 0.1500000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 5545 nv = 96 ne = 84 npr = 36900 no. pairs analyzed = 36900 no. exposed pairs = 2053 no. arc points = 14551 no. surface atoms = 698 nbur = 999 mkacc time = 7.9999998E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 340 mr = 3125 m= 2 mr = 54 m= 0 mr = 0 time to grow re-entrant surface = 9.0000004E-02 no. cavity mid-points inaccessible to solvent = 32 time to turn everything in is 0.2500000 number of dielectric boundary points 2708 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1292 ## 85 charges are in solution ## iepsmp to db, and charging done at 0.3600000 number of grid points assigned charge 6148 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.9393698E-09 -1.5080197E-07 midg,1,midg; midg,igrid,midg -1.5377948E-08 -1.3385582E-07 1,midg,midg; igrid,midg,midg -1.1071437E-07 -1.3197636E-08 gauss-seidel spectral radius is 0.9892810 estimated iterations to convergence 79 setup time was (sec) 0.4800000 now iterating at: 07:36:25 rms-change max change #iterations 0.1822556 35.44305 at 10iterations 2.1596756E-02 3.442823 at 20iterations 2.5918314E-03 0.4252014 at 30iterations 3.0409911E-04 4.3308258E-02 at 40iterations 3.6306876E-05 5.3863525E-03 at 50iterations finished qdiffx linear iterations at : 07:36:28 total time elapsed so far: 3.130000 # loops : 50 mean,max change (kT/e) : 3.6306876E-05 5.3863525E-03 energy calculations done at 3.130000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.310000 DelPhi exited at 07:36:28 3.315u 0.170s 0:03.75 92.8% 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 Sun Oct 9 2011 at 07:36:28 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: 307 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1697 !!! WARNING: NAP 164 has a net charge of -2.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 2.095268 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): -8.198000 33.76400 ymin,ymax (A): 2.226000 43.06600 zmin,zma (A): 9.329000 60.30100 x,y,z range (A): 41.96200 40.84000 50.97200 scale (grids/A): 2.095268 object centre (A): 12.78300 22.64600 34.81500 number of atom coordinates read : 1697 total number of charged atoms : 1560 net assigned charge : -11.49999 assigned positive charge : 252.6242 centred at (gu) : 94.84882 88.47066 88.62200 assigned negative charge : -264.1241 centred at (gu) : 94.23041 89.05820 89.35410 start vw surface at 0.1200000 fill in re-entrant regions at 0.2100000 boundary points on vw surface= 57998 reading accessible surface arcs data from file ARCDAT no. of arc points read = 14551 grid for indexing accessible points = 1.400000 m= 23009 mr = 39920 m= 4338 mr = 17813 m= 347 mr = 2933 m= 8 mr = 162 m= 0 mr = 2 time to grow re-entrant surface = 0.2000000 no. cavity mid-points inaccessible to solvent = 716 time to turn everything in is 0.4400000 number of dielectric boundary points 24870 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 54 iepsmp to db, and charging done at 0.5600000 number of grid points assigned charge 12408 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) : 0.6984227 object centre at (A) : 12.78300 22.64600 34.81500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.0732204E-02 -8.5847110E-02 midg,1,midg; midg,igrid,midg -9.8622693E-03 -4.8083860E-02 1,midg,midg; igrid,midg,midg -6.3729666E-02 -7.7846502E-03 gauss-seidel spectral radius is 0.9987642 estimated iterations to convergence 225 setup time was (sec) 0.7300000 now iterating at: 07:36:29 rms-change max change #iterations 4.167032 195.2941 at 10iterations 2.025538 71.23488 at 20iterations 0.9843965 38.42636 at 30iterations 0.4810886 17.16142 at 40iterations 0.2334949 8.475223 at 50iterations 0.1130299 3.784093 at 60iterations 5.4977756E-02 1.877106 at 70iterations 2.6793910E-02 0.9193974 at 80iterations 1.3024305E-02 0.4739475 at 90iterations 6.3575893E-03 0.2236996 at 100iterations 3.0951777E-03 0.1058502 at 110iterations 1.4951837E-03 5.0827026E-02 at 120iterations finished qdiffx linear iterations at : 07:36:36 total time elapsed so far: 7.420000 # loops : 120 mean,max change (kT/e) : 1.4951837E-03 5.0827026E-02 energy calculations done at 7.420000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.600000 DelPhi exited at 07:36:36 7.606u 0.231s 0:08.11 96.5% 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 07:36:36 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: 307 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1697 !!! WARNING: NAP 164 has a net charge of -2.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 3.142902 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): -8.198000 33.76400 ymin,ymax (A): 2.226000 43.06600 zmin,zma (A): 9.329000 60.30100 x,y,z range (A): 41.96200 40.84000 50.97200 scale (grids/A): 3.142902 object centre (A): 12.78300 22.64600 34.81500 number of atom coordinates read : 1697 total number of charged atoms : 1560 net assigned charge : -11.49999 assigned positive charge : 252.6242 centred at (gu) : 97.27323 87.70607 87.93311 assigned negative charge : -264.1241 centred at (gu) : 96.34561 88.58736 89.03108 start vw surface at 0.1100000 fill in re-entrant regions at 0.6400000 boundary points on vw surface= 133614 reading accessible surface arcs data from file ARCDAT no. of arc points read = 14551 grid for indexing accessible points = 1.400000 m= 71205 mr = 96284 m= 29828 mr = 59515 m= 8081 mr = 24959 m= 1368 mr = 6291 m= 147 mr = 939 m= 8 mr = 109 m= 0 mr = 2 time to grow re-entrant surface = 0.6300001 no. cavity mid-points inaccessible to solvent = 2362 time to turn everything in is 1.360000 number of dielectric boundary points 56152 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.490000 number of grid points assigned charge 12480 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) : 2.095268 object centre at (A) : 12.78300 22.64600 34.81500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1059806 -0.7246019 midg,1,midg; midg,igrid,midg -0.1129967 -0.3650186 1,midg,midg; igrid,midg,midg -0.5596504 -6.2035520E-02 gauss-seidel spectral radius is 0.9992716 estimated iterations to convergence 292 setup time was (sec) 1.660000 now iterating at: 07:36:38 rms-change max change #iterations 9.285355 431.4930 at 10iterations 5.332329 129.8487 at 20iterations 3.081448 65.11888 at 30iterations 1.776252 39.37820 at 40iterations 1.026848 24.84176 at 50iterations 0.5916131 11.65050 at 60iterations 0.3411847 6.497112 at 70iterations 0.1968055 3.940506 at 80iterations 0.1136184 2.024581 at 90iterations 6.5433070E-02 1.228183 at 100iterations 3.7663467E-02 0.7024345 at 110iterations 2.1694040E-02 0.4222503 at 120iterations 1.2548556E-02 0.2393303 at 130iterations 7.2238329E-03 0.1394920 at 140iterations 4.1545215E-03 8.0041885E-02 at 150iterations 2.4016083E-03 4.5440674E-02 at 160iterations 1.3852691E-03 2.6830673E-02 at 170iterations 7.9653552E-04 1.6693115E-02 at 180iterations finished qdiffx linear iterations at : 07:36:49 total time elapsed so far: 12.24000 # loops : 180 mean,max change (kT/e) : 7.9653552E-04 1.6693115E-02 energy calculations done at 12.24000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.42000 DelPhi exited at 07:36:49 12.427u 0.252s 0:12.96 97.7% 0+0k 0+0io 0pf+0w