Mon Oct 10 10:18:56 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 10:18:56 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 = 2778 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: 0.5771632 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): -21.98000 39.70100 ymin,ymax (A): -12.21400 43.86000 zmin,zma (A): -1.161000 51.43800 x,y,z range (A): 61.68100 56.07400 52.59900 scale (grids/A): 0.5771632 object centre (A): 8.860500 15.82300 25.13850 number of atom coordinates read : 2778 total number of charged atoms : 2632 net assigned charge : 11.00002 assigned positive charge : 408.2211 centred at (gu) : 91.99790 91.78522 86.92411 assigned negative charge : -397.2215 centred at (gu) : 92.09285 91.81624 86.70135 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1000000 boundary points on vw surface= 6341 nv = 96 ne = 84 npr = 53153 no. pairs analyzed = 53153 no. exposed pairs = 4009 no. arc points = 29578 no. surface atoms = 1338 nbur = 1440 mkacc time = 8.9999996E-02 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= 318 mr = 2911 m= 1 mr = 10 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 0.2100000 number of dielectric boundary points 3739 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2971 ## 325 charges are in solution ## iepsmp to db, and charging done at 0.2700000 number of grid points assigned charge 7970 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -3.7268322E-09 3.0062104E-09 midg,1,midg; midg,igrid,midg 1.9041593E-09 2.6676350E-09 1,midg,midg; igrid,midg,midg 2.5015849E-09 9.6042641E-10 gauss-seidel spectral radius is 0.9845086 estimated iterations to convergence 66 setup time was (sec) 0.4000000 now iterating at: 10:18:57 rms-change max change #iterations 9.1135114E-02 15.23332 at 10iterations 6.8955147E-03 1.045425 at 20iterations 5.4086122E-04 8.4449768E-02 at 30iterations 4.6223540E-05 8.0094337E-03 at 40iterations 5.3686913E-06 6.6280365E-04 at 50iterations finished qdiffx linear iterations at : 10:18:59 total time elapsed so far: 3.310000 # loops : 50 mean,max change (kT/e) : 5.3686913E-06 6.6280365E-04 energy calculations done at 3.310000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.450000 DelPhi exited at 10:19:00 3.458u 0.161s 0:03.95 91.3% 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 10:19:00 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 = 2778 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: 1.731489 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): -21.98000 39.70100 ymin,ymax (A): -12.21400 43.86000 zmin,zma (A): -1.161000 51.43800 x,y,z range (A): 61.68100 56.07400 52.59900 scale (grids/A): 1.731489 object centre (A): 8.860500 15.82300 25.13850 number of atom coordinates read : 2778 total number of charged atoms : 2632 net assigned charge : 11.00002 assigned positive charge : 408.2211 centred at (gu) : 95.99334 95.35526 80.77184 assigned negative charge : -397.2215 centred at (gu) : 96.27822 95.44868 80.10385 start vw surface at 0.1000000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 68286 reading accessible surface arcs data from file ARCDAT no. of arc points read = 29578 grid for indexing accessible points = 1.400000 m= 22096 mr = 42784 m= 2862 mr = 14438 m= 114 mr = 1342 m= 2 mr = 14 m= 0 mr = 0 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3500000 number of dielectric boundary points 34782 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 238 ## 2 charges are in solution ## iepsmp to db, and charging done at 0.4200000 number of grid points assigned charge 20375 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) : 0.5771632 object centre at (A) : 8.860500 15.82300 25.13850 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -7.4195825E-03 1.3509479E-02 midg,1,midg; midg,igrid,midg 1.8267492E-02 2.7927691E-02 1,midg,midg; igrid,midg,midg -4.7736368E-03 1.1893881E-02 gauss-seidel spectral radius is 0.9983814 estimated iterations to convergence 197 setup time was (sec) 0.5600000 now iterating at: 10:19:01 rms-change max change #iterations 3.525748 170.0110 at 10iterations 1.524070 54.96265 at 20iterations 0.6650507 25.11635 at 30iterations 0.2900430 9.769763 at 40iterations 0.1261866 4.638004 at 50iterations 5.5326503E-02 2.045113 at 60iterations 2.4004593E-02 0.8968248 at 70iterations 1.0481699E-02 0.3884430 at 80iterations 4.5881937E-03 0.1538382 at 90iterations 2.0025624E-03 7.5262070E-02 at 100iterations 8.7244465E-04 2.9985428E-02 at 110iterations 3.8173501E-04 1.3238668E-02 at 120iterations finished qdiffx linear iterations at : 10:19:08 total time elapsed so far: 7.710000 # loops : 120 mean,max change (kT/e) : 3.8173501E-04 1.3238668E-02 energy calculations done at 7.710000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.840000 DelPhi exited at 10:19:08 7.840u 0.207s 0:08.32 96.6% 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 10:19:08 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 = 2778 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: 2.597234 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): -21.98000 39.70100 ymin,ymax (A): -12.21400 43.86000 zmin,zma (A): -1.161000 51.43800 x,y,z range (A): 61.68100 56.07400 52.59900 scale (grids/A): 2.597234 object centre (A): 8.860500 15.82300 25.13850 number of atom coordinates read : 2778 total number of charged atoms : 2632 net assigned charge : 11.00002 assigned positive charge : 408.2211 centred at (gu) : 98.98984 98.03304 76.15768 assigned negative charge : -397.2215 centred at (gu) : 99.41737 98.17304 75.15586 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.2900000 boundary points on vw surface= 157928 reading accessible surface arcs data from file ARCDAT no. of arc points read = 29578 grid for indexing accessible points = 1.400000 m= 72362 mr = 105232 m= 23833 mr = 55023 m= 4738 mr = 17303 m= 411 mr = 2989 m= 18 mr = 177 m= 0 mr = 0 time to grow re-entrant surface = 0.4800000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.8600000 number of dielectric boundary points 78566 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 5 iepsmp to db, and charging done at 0.9500000 number of grid points assigned charge 21048 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) : 1.731489 object centre at (A) : 8.860500 15.82300 25.13850 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1198664 0.1438459 midg,1,midg; midg,igrid,midg 0.2929356 0.3379160 1,midg,midg; igrid,midg,midg -0.3524749 0.2225048 gauss-seidel spectral radius is 0.9992005 estimated iterations to convergence 279 setup time was (sec) 1.090000 now iterating at: 10:19:10 rms-change max change #iterations 9.106998 362.8527 at 10iterations 5.322290 158.6116 at 20iterations 3.072449 97.76534 at 30iterations 1.762553 46.36038 at 40iterations 1.005571 25.03286 at 50iterations 0.5711740 15.16273 at 60iterations 0.3239502 7.501465 at 70iterations 0.1834121 4.190659 at 80iterations 0.1035786 2.848660 at 90iterations 5.8384247E-02 1.639565 at 100iterations 3.2943107E-02 0.7835960 at 110iterations 1.8520083E-02 0.4123774 at 120iterations 1.0420452E-02 0.1991277 at 130iterations 5.8773593E-03 0.1212463 at 140iterations 3.3053805E-03 6.8038940E-02 at 150iterations 1.8550107E-03 3.8286209E-02 at 160iterations 1.0461040E-03 2.3478270E-02 at 170iterations 5.8788358E-04 1.1526108E-02 at 180iterations finished qdiffx linear iterations at : 10:19:21 total time elapsed so far: 12.64000 # loops : 180 mean,max change (kT/e) : 5.8788358E-04 1.1526108E-02 energy calculations done at 12.64000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.79000 DelPhi exited at 10:19:22 12.788u 0.206s 0:13.31 97.5% 0+0k 0+0io 0pf+0w