Tue Oct 11 00:29:36 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 Tue Oct 11 2011 at 00:29:36 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2141 !!! WARNING: ASP 298 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= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 0.5808736 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): 20.02000 81.30700 ymin,ymax (A): -0.6960000 43.29400 zmin,zma (A): -6.799000 42.36400 x,y,z range (A): 61.28700 43.99000 49.16300 scale (grids/A): 0.5808736 object centre (A): 50.66350 21.29900 17.78250 number of atom coordinates read : 2141 total number of charged atoms : 1998 net assigned charge : -0.4999969 assigned positive charge : 313.0405 centred at (gu) : 89.10973 89.48566 90.05829 assigned negative charge : -313.5410 centred at (gu) : 89.14716 89.69290 90.18240 start vw surface at 0.1900000 fill in re-entrant regions at 0.2000000 boundary points on vw surface= 4774 nv = 96 ne = 84 npr = 42803 no. pairs analyzed = 42803 no. exposed pairs = 2860 no. arc points = 20338 no. surface atoms = 954 nbur = 1187 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 = 1.484000 m= 217 mr = 2396 m= 1 mr = 10 m= 0 mr = 0 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 30 time to turn everything in is 0.3400000 number of dielectric boundary points 2586 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2000 ## 243 charges are in solution ## iepsmp to db, and charging done at 0.4700000 number of grid points assigned charge 6005 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.7980699E-09 -2.1740723E-09 midg,1,midg; midg,igrid,midg 3.5062355E-09 -3.1211775E-09 1,midg,midg; igrid,midg,midg 5.7634936E-10 -5.9384508E-10 gauss-seidel spectral radius is 0.9846389 estimated iterations to convergence 66 setup time was (sec) 0.6200000 now iterating at: 00:29:36 rms-change max change #iterations 8.2058236E-02 13.89773 at 10iterations 6.3033970E-03 1.069467 at 20iterations 4.8708753E-04 7.9685211E-02 at 30iterations 3.8339236E-05 7.5187683E-03 at 40iterations 2.9351083E-06 5.3024292E-04 at 50iterations finished qdiffx linear iterations at : 00:29:39 total time elapsed so far: 3.740000 # loops : 50 mean,max change (kT/e) : 2.9351083E-06 5.3024292E-04 energy calculations done at 3.740000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.970000 DelPhi exited at 00:29:40 3.973u 0.159s 0:04.48 91.9% 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 Tue Oct 11 2011 at 00:29:40 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 = 2141 !!! WARNING: ASP 298 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= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 1.742621 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): 20.02000 81.30700 ymin,ymax (A): -0.6960000 43.29400 zmin,zma (A): -6.799000 42.36400 x,y,z range (A): 61.28700 43.99000 49.16300 scale (grids/A): 1.742621 object centre (A): 50.66350 21.29900 17.78250 number of atom coordinates read : 2141 total number of charged atoms : 1998 net assigned charge : -0.4999969 assigned positive charge : 313.0405 centred at (gu) : 87.32891 88.45653 90.17455 assigned negative charge : -313.5410 centred at (gu) : 87.44142 89.07869 90.54732 start vw surface at 0.1800000 fill in re-entrant regions at 0.2700000 boundary points on vw surface= 52426 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20338 grid for indexing accessible points = 1.400000 m= 16921 mr = 34499 m= 2184 mr = 11765 m= 80 mr = 1275 m= 0 mr = 11 time to grow re-entrant surface = 0.2100000 no. cavity mid-points inaccessible to solvent = 891 time to turn everything in is 0.5300000 number of dielectric boundary points 24061 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 204 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.6800000 number of grid points assigned charge 15540 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) : 0.5808736 object centre at (A) : 50.66350 21.29900 17.78250 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 8.6994348E-03 -1.3104207E-02 midg,1,midg; midg,igrid,midg 7.1367272E-03 -3.0835359E-03 1,midg,midg; igrid,midg,midg -1.2454779E-02 5.3749974E-03 gauss-seidel spectral radius is 0.9983316 estimated iterations to convergence 194 setup time was (sec) 0.8900000 now iterating at: 00:29:41 rms-change max change #iterations 3.142401 176.2294 at 10iterations 1.350163 56.14382 at 20iterations 0.5800947 22.57547 at 30iterations 0.2510496 10.29832 at 40iterations 0.1084631 4.138421 at 50iterations 4.6710949E-02 1.823549 at 60iterations 2.0167904E-02 0.8642731 at 70iterations 8.6921640E-03 0.3724060 at 80iterations 3.7506130E-03 0.1463718 at 90iterations 1.6246790E-03 5.8219910E-02 at 100iterations 7.0033257E-04 2.8185844E-02 at 110iterations 3.0231930E-04 1.2363434E-02 at 120iterations finished qdiffx linear iterations at : 00:29:50 total time elapsed so far: 9.260000 # loops : 120 mean,max change (kT/e) : 3.0231930E-04 1.2363434E-02 energy calculations done at 9.260000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.500000 DelPhi exited at 00:29:50 9.505u 0.262s 0:10.30 94.7% 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 00:29:50 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 = 2141 !!! WARNING: ASP 298 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= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 2.613931 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): 20.02000 81.30700 ymin,ymax (A): -0.6960000 43.29400 zmin,zma (A): -6.799000 42.36400 x,y,z range (A): 61.28700 43.99000 49.16300 scale (grids/A): 2.613931 object centre (A): 50.66350 21.29900 17.78250 number of atom coordinates read : 2141 total number of charged atoms : 1998 net assigned charge : -0.4999969 assigned positive charge : 313.0405 centred at (gu) : 85.99320 87.68481 90.26185 assigned negative charge : -313.5410 centred at (gu) : 86.16222 88.61812 90.82095 start vw surface at 0.1900000 fill in re-entrant regions at 0.4500000 boundary points on vw surface= 121350 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20338 grid for indexing accessible points = 1.400000 m= 56301 mr = 84150 m= 18305 mr = 44489 m= 3664 mr = 14358 m= 332 mr = 2548 m= 12 mr = 192 m= 0 mr = 0 time to grow re-entrant surface = 0.6800001 no. cavity mid-points inaccessible to solvent = 3053 time to turn everything in is 1.230000 number of dielectric boundary points 54227 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 5 iepsmp to db, and charging done at 1.390000 number of grid points assigned charge 15976 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) : 1.742621 object centre at (A) : 50.66350 21.29900 17.78250 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1475661 -0.1926808 midg,1,midg; midg,igrid,midg 8.5696720E-02 -9.8299468E-03 1,midg,midg; igrid,midg,midg -0.2545970 0.1506864 gauss-seidel spectral radius is 0.9991665 estimated iterations to convergence 274 setup time was (sec) 1.610000 now iterating at: 00:29:52 rms-change max change #iterations 7.772942 398.7959 at 10iterations 4.360907 115.7824 at 20iterations 2.426972 61.85641 at 30iterations 1.354663 37.50024 at 40iterations 0.7529390 17.35226 at 50iterations 0.4179732 9.712332 at 60iterations 0.2313221 5.135503 at 70iterations 0.1285388 2.992661 at 80iterations 7.1158901E-02 1.660526 at 90iterations 3.9437801E-02 0.8056011 at 100iterations 2.1795971E-02 0.4614258 at 110iterations 1.2126833E-02 0.2717587 at 120iterations 6.7148181E-03 0.1609650 at 130iterations 3.7039958E-03 8.3538055E-02 at 140iterations 2.0547954E-03 4.4572830E-02 at 150iterations 1.1383066E-03 2.6443481E-02 at 160iterations 6.3087989E-04 1.5975952E-02 at 170iterations 3.4985555E-04 7.6751709E-03 at 180iterations finished qdiffx linear iterations at : 00:30:07 total time elapsed so far: 15.80000 # loops : 180 mean,max change (kT/e) : 3.4985555E-04 7.6751709E-03 energy calculations done at 15.80000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 16.03000 DelPhi exited at 00:30:07 16.035u 0.266s 0:16.68 97.6% 0+0k 0+0io 0pf+0w