Tue Oct 11 01:37:26 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 01:37:26 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 = 2610 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: 0.5954770 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): 18.21400 77.99800 ymin,ymax (A): -10.74900 43.89800 zmin,zma (A): -7.558000 35.11900 x,y,z range (A): 59.78400 54.64700 42.67700 scale (grids/A): 0.5954770 object centre (A): 48.10600 16.57450 13.78050 number of atom coordinates read : 2610 total number of charged atoms : 2469 net assigned charge : 7.000024 assigned positive charge : 392.7107 centred at (gu) : 88.08412 89.64644 89.61182 assigned negative charge : -385.7115 centred at (gu) : 88.32993 89.80726 89.75468 start vw surface at 0.1200000 fill in re-entrant regions at 0.1300000 boundary points on vw surface= 6162 nv = 96 ne = 84 npr = 52980 no. pairs analyzed = 52980 no. exposed pairs = 3072 no. arc points = 21850 no. surface atoms = 1041 nbur = 1569 mkacc time = 0.1400000 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 = 1.456000 m= 268 mr = 3450 m= 4 mr = 30 m= 0 mr = 0 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 22 time to turn everything in is 0.3100000 number of dielectric boundary points 2954 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2156 ## 245 charges are in solution ## iepsmp to db, and charging done at 0.4000000 number of grid points assigned charge 7621 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 7.4307827E-09 -1.9753694E-09 midg,1,midg; midg,igrid,midg 7.9630675E-09 -2.5303812E-09 1,midg,midg; igrid,midg,midg 1.5432471E-08 -3.5345915E-09 gauss-seidel spectral radius is 0.9854049 estimated iterations to convergence 68 setup time was (sec) 0.5700000 now iterating at: 01:37:27 rms-change max change #iterations 0.1079520 20.30072 at 10iterations 9.8767905E-03 1.793182 at 20iterations 1.4680800E-03 0.3398438 at 30iterations 3.7795879E-04 9.2426300E-02 at 40iterations 1.0369613E-04 2.6031494E-02 at 50iterations finished qdiffx linear iterations at : 01:37:31 total time elapsed so far: 4.830000 # loops : 50 mean,max change (kT/e) : 1.0369613E-04 2.6031494E-02 energy calculations done at 4.830000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 5.000000 DelPhi exited at 01:37:32 5.007u 0.477s 0:06.43 85.0% 0+0k 0+0io 3pf+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 01:37:32 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 = 2610 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: 1.786431 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): 18.21400 77.99800 ymin,ymax (A): -10.74900 43.89800 zmin,zma (A): -7.558000 35.11900 x,y,z range (A): 59.78400 54.64700 42.67700 scale (grids/A): 1.786431 object centre (A): 48.10600 16.57450 13.78050 number of atom coordinates read : 2610 total number of charged atoms : 2469 net assigned charge : 7.000024 assigned positive charge : 392.7107 centred at (gu) : 84.25177 88.93867 88.83473 assigned negative charge : -385.7115 centred at (gu) : 84.98964 89.42159 89.26399 start vw surface at 0.1300000 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 67025 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21850 grid for indexing accessible points = 1.400000 m= 22798 mr = 46896 m= 3058 mr = 16924 m= 137 mr = 1831 m= 3 mr = 50 m= 0 mr = 0 time to grow re-entrant surface = 0.2900000 no. cavity mid-points inaccessible to solvent = 2272 time to turn everything in is 0.5700000 number of dielectric boundary points 27320 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 213 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.7100000 number of grid points assigned charge 19235 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) : 0.5954770 object centre at (A) : 48.10600 16.57450 13.78050 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.0968057E-02 4.5029977E-03 midg,1,midg; midg,igrid,midg 2.2825032E-02 -2.1422178E-02 1,midg,midg; igrid,midg,midg 8.5456995E-03 1.4375543E-03 gauss-seidel spectral radius is 0.9984485 estimated iterations to convergence 201 setup time was (sec) 0.9100000 now iterating at: 01:37:34 rms-change max change #iterations 3.722041 155.3334 at 10iterations 1.657022 70.01216 at 20iterations 0.7366327 25.49940 at 30iterations 0.3282306 11.35943 at 40iterations 0.1462744 5.153076 at 50iterations 6.5412320E-02 2.438992 at 60iterations 2.9417269E-02 1.033506 at 70iterations 1.3324858E-02 0.4515266 at 80iterations 6.1434880E-03 0.2178345 at 90iterations 2.9098126E-03 0.1109161 at 100iterations 1.4836638E-03 6.4384460E-02 at 110iterations 8.1369834E-04 4.1393280E-02 at 120iterations finished qdiffx linear iterations at : 01:37:45 total time elapsed so far: 11.97000 # loops : 120 mean,max change (kT/e) : 8.1369834E-04 4.1393280E-02 energy calculations done at 11.97000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.14000 DelPhi exited at 01:37:46 12.145u 0.520s 0:13.68 92.5% 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 Tue Oct 11 2011 at 01:37:46 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 = 2610 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: 2.679647 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): 18.21400 77.99800 ymin,ymax (A): -10.74900 43.89800 zmin,zma (A): -7.558000 35.11900 x,y,z range (A): 59.78400 54.64700 42.67700 scale (grids/A): 2.679647 object centre (A): 48.10600 16.57450 13.78050 number of atom coordinates read : 2610 total number of charged atoms : 2469 net assigned charge : 7.000024 assigned positive charge : 392.7107 centred at (gu) : 81.37766 88.40793 88.25190 assigned negative charge : -385.7115 centred at (gu) : 82.48434 89.13241 88.89583 start vw surface at 0.1200000 fill in re-entrant regions at 0.4600000 boundary points on vw surface= 155584 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21850 grid for indexing accessible points = 1.400000 m= 76207 mr = 114036 m= 25120 mr = 62569 m= 5199 mr = 20217 m= 581 mr = 3869 m= 10 mr = 375 m= 1 mr = 1 m= 0 mr = 0 time to grow re-entrant surface = 0.8400000 no. cavity mid-points inaccessible to solvent = 7449 time to turn everything in is 1.420000 number of dielectric boundary points 61635 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4 iepsmp to db, and charging done at 1.590000 number of grid points assigned charge 19750 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) : 1.786431 object centre at (A) : 48.10600 16.57450 13.78050 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2160266 6.0096692E-02 midg,1,midg; midg,igrid,midg 0.2023100 -0.4125946 1,midg,midg; igrid,midg,midg 4.6858139E-02 0.3879073 gauss-seidel spectral radius is 0.9992021 estimated iterations to convergence 280 setup time was (sec) 1.810000 now iterating at: 01:37:48 rms-change max change #iterations 8.978988 292.0912 at 10iterations 5.127716 125.7327 at 20iterations 2.892530 65.14304 at 30iterations 1.636432 39.40508 at 40iterations 0.9227893 18.80995 at 50iterations 0.5204508 10.27461 at 60iterations 0.2931492 5.861899 at 70iterations 0.1648505 3.413114 at 80iterations 9.2838258E-02 2.002931 at 90iterations 5.2348178E-02 1.060161 at 100iterations 2.9563211E-02 0.5981293 at 110iterations 1.6721999E-02 0.3194656 at 120iterations 9.5403800E-03 0.1974030 at 130iterations 5.5052522E-03 0.1319122 at 140iterations 3.2436573E-03 7.4489594E-02 at 150iterations 1.9850121E-03 5.0407410E-02 at 160iterations 1.2827506E-03 3.5133362E-02 at 170iterations 8.7477849E-04 2.3849487E-02 at 180iterations finished qdiffx linear iterations at : 01:38:06 total time elapsed so far: 19.37000 # loops : 180 mean,max change (kT/e) : 8.7477849E-04 2.3849487E-02 energy calculations done at 19.37000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 19.53000 DelPhi exited at 01:38:07 19.535u 0.503s 0:20.88 95.9% 0+0k 0+0io 0pf+0w