Tue Oct 11 06:16:06 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 06:16:06 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 = 2057 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 0.7152185 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): 3.506000 46.57000 ymin,ymax (A): 0.6100000 39.10200 zmin,zma (A): -2.453000 47.32200 x,y,z range (A): 43.06400 38.49200 49.77500 scale (grids/A): 0.7152185 object centre (A): 25.03800 19.85600 22.43450 number of atom coordinates read : 2057 total number of charged atoms : 1929 net assigned charge : 7.500009 assigned positive charge : 311.2470 centred at (gu) : 90.28160 91.10479 90.39479 assigned negative charge : -303.7472 centred at (gu) : 90.45818 91.10200 90.43484 start vw surface at 0.1400000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 7214 nv = 96 ne = 84 npr = 41447 no. pairs analyzed = 41447 no. exposed pairs = 2507 no. arc points = 17178 no. surface atoms = 847 nbur = 1210 mkacc time = 8.9999989E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 494 mr = 4226 m= 5 mr = 96 m= 0 mr = 0 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2600000 number of dielectric boundary points 3391 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1633 ## 172 charges are in solution ## iepsmp to db, and charging done at 0.3600000 number of grid points assigned charge 7891 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 9.1992064E-08 5.7327494E-08 midg,1,midg; midg,igrid,midg 6.0941545E-08 9.5849202E-08 1,midg,midg; igrid,midg,midg 1.6613797E-07 -2.8046497E-08 gauss-seidel spectral radius is 0.9898048 estimated iterations to convergence 81 setup time was (sec) 0.4800000 now iterating at: 06:16:06 rms-change max change #iterations 0.2031112 29.45384 at 10iterations 2.5863690E-02 3.389977 at 20iterations 3.4406700E-03 0.5761566 at 30iterations 5.2201026E-04 7.4853897E-02 at 40iterations 1.1801924E-04 1.6185760E-02 at 50iterations finished qdiffx linear iterations at : 06:16:09 total time elapsed so far: 3.100000 # loops : 50 mean,max change (kT/e) : 1.1801924E-04 1.6185760E-02 energy calculations done at 3.100000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.270000 DelPhi exited at 06:16:10 3.274u 0.185s 0:04.32 79.8% 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 Tue Oct 11 2011 at 06:16:10 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 = 2057 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: 2.145655 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): 3.506000 46.57000 ymin,ymax (A): 0.6100000 39.10200 zmin,zma (A): -2.453000 47.32200 x,y,z range (A): 43.06400 38.49200 49.77500 scale (grids/A): 2.145655 object centre (A): 25.03800 19.85600 22.43450 number of atom coordinates read : 2057 total number of charged atoms : 1929 net assigned charge : 7.500009 assigned positive charge : 311.2470 centred at (gu) : 90.84464 93.31443 91.18456 assigned negative charge : -303.7472 centred at (gu) : 91.37466 93.30597 91.30453 start vw surface at 0.1300000 fill in re-entrant regions at 0.2300000 boundary points on vw surface= 76186 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17178 grid for indexing accessible points = 1.400000 m= 31677 mr = 54577 m= 6313 mr = 24336 m= 602 mr = 4309 m= 14 mr = 292 m= 0 mr = 2 time to grow re-entrant surface = 0.2700000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5300000 number of dielectric boundary points 31276 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 53 iepsmp to db, and charging done at 0.6500000 number of grid points assigned charge 15325 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) : 0.7152185 object centre at (A) : 25.03800 19.85600 22.43450 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.8936546E-02 7.4499026E-02 midg,1,midg; midg,igrid,midg 5.2880789E-03 3.6537763E-02 1,midg,midg; igrid,midg,midg 4.9266651E-02 1.2371705E-02 gauss-seidel spectral radius is 0.9988508 estimated iterations to convergence 233 setup time was (sec) 0.8000000 now iterating at: 06:16:11 rms-change max change #iterations 4.658559 191.3693 at 10iterations 2.324319 81.48616 at 20iterations 1.166937 35.51884 at 30iterations 0.5799864 17.15208 at 40iterations 0.2915157 9.042306 at 50iterations 0.1458941 4.393669 at 60iterations 7.3007576E-02 2.123489 at 70iterations 3.6512855E-02 1.166393 at 80iterations 1.8261479E-02 0.5403347 at 90iterations 9.1724638E-03 0.2614384 at 100iterations 4.5986492E-03 0.1407871 at 110iterations 2.3430204E-03 6.9568634E-02 at 120iterations finished qdiffx linear iterations at : 06:16:17 total time elapsed so far: 6.770000 # loops : 120 mean,max change (kT/e) : 2.3430204E-03 6.9568634E-02 energy calculations done at 6.770000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 6.940000 DelPhi exited at 06:16:17 6.944u 0.164s 0:07.47 95.0% 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 Tue Oct 11 2011 at 06:16:18 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 = 2057 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1000000 grid size : 179 scale,in grids/A, set to be: 3.218483 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): 3.506000 46.57000 ymin,ymax (A): 0.6100000 39.10200 zmin,zma (A): -2.453000 47.32200 x,y,z range (A): 43.06400 38.49200 49.77500 scale (grids/A): 3.218483 object centre (A): 25.03800 19.85600 22.43450 number of atom coordinates read : 2057 total number of charged atoms : 1929 net assigned charge : 7.500009 assigned positive charge : 311.2470 centred at (gu) : 91.26691 94.97178 91.77670 assigned negative charge : -303.7472 centred at (gu) : 92.06196 94.95891 91.95688 start vw surface at 0.1900000 fill in re-entrant regions at 0.8100000 boundary points on vw surface= 175816 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17178 grid for indexing accessible points = 1.400000 m= 97600 mr = 131299 m= 40795 mr = 81934 m= 12077 mr = 33906 m= 2449 mr = 9418 m= 267 mr = 1789 m= 12 mr = 166 m= 0 mr = 5 time to grow re-entrant surface = 0.8500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.770000 number of dielectric boundary points 70499 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.900000 number of grid points assigned charge 15432 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) : 2.145655 object centre at (A) : 25.03800 19.85600 22.43450 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.3416801 0.9229393 midg,1,midg; midg,igrid,midg 3.8848395E-04 0.2793486 1,midg,midg; igrid,midg,midg 0.3875215 0.1834787 gauss-seidel spectral radius is 0.9992996 estimated iterations to convergence 298 setup time was (sec) 2.050000 now iterating at: 06:16:20 rms-change max change #iterations 10.31908 364.8278 at 10iterations 6.132343 145.6631 at 20iterations 3.638075 79.23048 at 30iterations 2.155803 46.21712 at 40iterations 1.271959 27.57065 at 50iterations 0.7491966 15.54598 at 60iterations 0.4412161 8.459702 at 70iterations 0.2596166 4.914673 at 80iterations 0.1523423 2.774343 at 90iterations 8.9547187E-02 1.608423 at 100iterations 5.2713636E-02 0.8806667 at 110iterations 3.0989651E-02 0.5423498 at 120iterations 1.8317763E-02 0.3300018 at 130iterations 1.0906884E-02 0.1837978 at 140iterations 6.5852134E-03 0.1265135 at 150iterations 4.0617283E-03 7.1731567E-02 at 160iterations 2.6022824E-03 4.8736572E-02 at 170iterations 1.7568531E-03 3.1864166E-02 at 180iterations finished qdiffx linear iterations at : 06:16:29 total time elapsed so far: 11.44000 # loops : 180 mean,max change (kT/e) : 1.7568531E-03 3.1864166E-02 energy calculations done at 11.44000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.61000 DelPhi exited at 06:16:30 11.611u 0.175s 0:12.31 95.6% 0+0k 0+0io 0pf+0w