Mon Oct 10 17:02:22 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+sph.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 = amb.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 17:02:22 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3666 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: 0.5559025 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): -14.00100 50.03900 ymin,ymax (A): -27.32200 21.41500 zmin,zma (A): -36.65800 27.31200 x,y,z range (A): 64.04000 48.73700 63.97000 scale (grids/A): 0.5559025 object centre (A): 18.01900 -2.953501 -4.672998 number of atom coordinates read : 3666 total number of charged atoms : 3521 net assigned charge : -5.499963 assigned positive charge : 554.8162 centred at (gu) : 89.78307 89.52460 90.69514 assigned negative charge : -560.3185 centred at (gu) : 89.76373 89.44114 90.84833 start vw surface at 0.1100000 fill in re-entrant regions at 0.1100000 boundary points on vw surface= 7523 nv = 96 ne = 84 npr = 71251 no. pairs analyzed = 71251 no. exposed pairs = 5090 no. arc points = 36145 no. surface atoms = 1713 nbur = 1953 mkacc time = 0.1200000 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 = 1.568000 m= 299 mr = 3562 m= 2 mr = 15 m= 0 mr = 0 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2500000 number of dielectric boundary points 4247 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3691 ## 429 charges are in solution ## iepsmp to db, and charging done at 0.3100000 number of grid points assigned charge 9721 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.1194292E-09 -2.8027629E-09 midg,1,midg; midg,igrid,midg -1.6803121E-09 4.5682400E-10 1,midg,midg; igrid,midg,midg -7.5100615E-10 -2.3500804E-10 gauss-seidel spectral radius is 0.9833795 estimated iterations to convergence 64 setup time was (sec) 0.4300000 now iterating at: 17:02:23 rms-change max change #iterations 8.6949609E-02 13.09426 at 10iterations 6.1139679E-03 0.9483895 at 20iterations 4.3845151E-04 7.7112556E-02 at 30iterations 3.8902584E-05 6.6108704E-03 at 40iterations 6.5095833E-06 1.4429092E-03 at 50iterations finished qdiffx linear iterations at : 17:02:26 total time elapsed so far: 3.320000 # loops : 50 mean,max change (kT/e) : 6.5095833E-06 1.4429092E-03 energy calculations done at 3.320000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.450000 DelPhi exited at 17:02:26 3.453u 0.196s 0:04.34 83.8% 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 Mon Oct 10 2011 at 17:02:26 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3666 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: 1.667708 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): -14.00100 50.03900 ymin,ymax (A): -27.32200 21.41500 zmin,zma (A): -36.65800 27.31200 x,y,z range (A): 64.04000 48.73700 63.97000 scale (grids/A): 1.667708 object centre (A): 18.01900 -2.953501 -4.672998 number of atom coordinates read : 3666 total number of charged atoms : 3521 net assigned charge : -5.499963 assigned positive charge : 554.8162 centred at (gu) : 89.34821 88.57260 92.08407 assigned negative charge : -560.3185 centred at (gu) : 89.29047 88.32310 92.54463 start vw surface at 0.1000000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 82707 reading accessible surface arcs data from file ARCDAT no. of arc points read = 36145 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 24303 mr = 53484 m= 2463 mr = 15944 m= 48 mr = 1120 m= 1 mr = 8 m= 0 mr = 0 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 419 time to turn everything in is 0.3900000 number of dielectric boundary points 38966 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 394 ## 4 charges are in solution ## iepsmp to db, and charging done at 0.4700000 number of grid points assigned charge 27080 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) : 0.5559025 object centre at (A) : 18.01900 -2.953501 -4.672998 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 9.3352897E-03 -5.3817820E-02 midg,1,midg; midg,igrid,midg -7.4482872E-03 1.7735061E-03 1,midg,midg; igrid,midg,midg -1.0389430E-02 -1.8978469E-02 gauss-seidel spectral radius is 0.9983504 estimated iterations to convergence 195 setup time was (sec) 0.6100000 now iterating at: 17:02:27 rms-change max change #iterations 3.956948 154.2773 at 10iterations 1.714500 56.32418 at 20iterations 0.7423637 25.16213 at 30iterations 0.3209573 9.810474 at 40iterations 0.1399462 4.341263 at 50iterations 6.0606636E-02 2.246235 at 60iterations 2.6298918E-02 0.8317165 at 70iterations 1.1422056E-02 0.4119987 at 80iterations 4.9566142E-03 0.1746109 at 90iterations 2.1582909E-03 7.5167179E-02 at 100iterations 9.3957066E-04 3.1646729E-02 at 110iterations 4.1089539E-04 1.4393330E-02 at 120iterations finished qdiffx linear iterations at : 17:02:34 total time elapsed so far: 7.680000 # loops : 120 mean,max change (kT/e) : 4.1089539E-04 1.4393330E-02 energy calculations done at 7.680000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.820000 DelPhi exited at 17:02:35 7.819u 0.203s 0:08.50 94.2% 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 17:02:35 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3666 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: 2.501561 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): -14.00100 50.03900 ymin,ymax (A): -27.32200 21.41500 zmin,zma (A): -36.65800 27.31200 x,y,z range (A): 64.04000 48.73700 63.97000 scale (grids/A): 2.501561 object centre (A): 18.01900 -2.953501 -4.672998 number of atom coordinates read : 3666 total number of charged atoms : 3521 net assigned charge : -5.499963 assigned positive charge : 554.8162 centred at (gu) : 89.02193 87.85872 93.12582 assigned negative charge : -560.3185 centred at (gu) : 88.93555 87.48462 93.81683 start vw surface at 0.1100000 fill in re-entrant regions at 0.3600000 boundary points on vw surface= 191920 reading accessible surface arcs data from file ARCDAT no. of arc points read = 36145 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 84081 mr = 131768 m= 23520 mr = 64254 m= 3678 mr = 17171 m= 227 mr = 2344 m= 1 mr = 87 m= 0 mr = 0 time to grow re-entrant surface = 0.5600001 no. cavity mid-points inaccessible to solvent = 1412 time to turn everything in is 1.010000 number of dielectric boundary points 87803 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 21 iepsmp to db, and charging done at 1.120000 number of grid points assigned charge 28136 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) : 1.667708 object centre at (A) : 18.01900 -2.953501 -4.672998 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -4.5547295E-02 -0.7731725 midg,1,midg; midg,igrid,midg -5.6177054E-02 2.1161679E-02 1,midg,midg; igrid,midg,midg -2.9814269E-02 -0.4229034 gauss-seidel spectral radius is 0.9992195 estimated iterations to convergence 283 setup time was (sec) 1.290000 now iterating at: 17:02:37 rms-change max change #iterations 10.28639 304.3458 at 10iterations 6.018589 153.6510 at 20iterations 3.480489 87.10591 at 30iterations 2.008330 42.94429 at 40iterations 1.154132 27.10354 at 50iterations 0.6591524 12.99025 at 60iterations 0.3773942 8.180744 at 70iterations 0.2149480 4.226440 at 80iterations 0.1222087 2.202770 at 90iterations 6.9407858E-02 1.324669 at 100iterations 3.9381485E-02 0.7737865 at 110iterations 2.2362949E-02 0.4282510 at 120iterations 1.2686578E-02 0.2375488 at 130iterations 7.1911477E-03 0.1295300 at 140iterations 4.0744659E-03 7.9132006E-02 at 150iterations 2.3090809E-03 4.3243408E-02 at 160iterations 1.3115868E-03 2.5670052E-02 at 170iterations 7.4630155E-04 1.4565706E-02 at 180iterations finished qdiffx linear iterations at : 17:02:50 total time elapsed so far: 14.10000 # loops : 180 mean,max change (kT/e) : 7.4630155E-04 1.4565706E-02 energy calculations done at 14.10000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 14.22000 DelPhi exited at 17:02:51 14.226u 0.307s 0:15.76 92.1% 0+0k 0+0io 0pf+0w