Sun Oct 9 13:11:42 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+sph2.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 = amb2.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 Sun Oct 9 2011 at 13:11:42 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: 319 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2375 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: 0.6938489 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): -6.716000 44.59200 ymin,ymax (A): -14.08600 36.90000 zmin,zma (A): 2.244000 44.94600 x,y,z range (A): 51.30800 50.98600 42.70200 scale (grids/A): 0.6938489 object centre (A): 18.93800 11.40700 23.59500 number of atom coordinates read : 2375 total number of charged atoms : 2234 net assigned charge : 3.500020 assigned positive charge : 364.6371 centred at (gu) : 89.60138 91.26630 90.73238 assigned negative charge : -361.1376 centred at (gu) : 89.63802 91.42744 90.76652 start vw surface at 0.1300000 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 7775 nv = 96 ne = 84 npr = 47366 no. pairs analyzed = 47366 no. exposed pairs = 3010 no. arc points = 21123 no. surface atoms = 1012 nbur = 1363 mkacc time = 9.9999994E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 487 mr = 4248 m= 3 mr = 89 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 3928 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1984 ## 188 charges are in solution ## iepsmp to db, and charging done at 0.3700000 number of grid points assigned charge 8719 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 3.1697418E-08 9.0244763E-09 midg,1,midg; midg,igrid,midg 6.9014959E-08 -6.0498564E-08 1,midg,midg; igrid,midg,midg 4.0687489E-08 6.4578809E-09 gauss-seidel spectral radius is 0.9892092 estimated iterations to convergence 78 setup time was (sec) 0.4800000 now iterating at: 13:11:42 rms-change max change #iterations 0.1996941 28.49743 at 10iterations 2.4430202E-02 2.955724 at 20iterations 3.2643103E-03 0.5550003 at 30iterations 6.1912969E-04 9.1876984E-02 at 40iterations 1.6706996E-04 2.6214600E-02 at 50iterations finished qdiffx linear iterations at : 13:11:45 total time elapsed so far: 2.870000 # loops : 50 mean,max change (kT/e) : 1.6706996E-04 2.6214600E-02 energy calculations done at 2.870000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.050000 DelPhi exited at 13:11:45 3.053u 0.145s 0:03.46 92.1% 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 Sun Oct 9 2011 at 13:11:45 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: 319 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2375 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: 2.081547 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): -6.716000 44.59200 ymin,ymax (A): -14.08600 36.90000 zmin,zma (A): 2.244000 44.94600 x,y,z range (A): 51.30800 50.98600 42.70200 scale (grids/A): 2.081547 object centre (A): 18.93800 11.40700 23.59500 number of atom coordinates read : 2375 total number of charged atoms : 2234 net assigned charge : 3.500020 assigned positive charge : 364.6371 centred at (gu) : 88.80376 93.79850 92.19681 assigned negative charge : -361.1376 centred at (gu) : 88.91381 94.28224 92.29926 start vw surface at 0.1300000 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 82808 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21123 grid for indexing accessible points = 1.400000 m= 31394 mr = 57391 m= 5434 mr = 23224 m= 496 mr = 3391 m= 14 mr = 251 m= 0 mr = 0 time to grow re-entrant surface = 0.2700000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5600000 number of dielectric boundary points 35889 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 120 iepsmp to db, and charging done at 0.6700000 number of grid points assigned charge 17714 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) : 0.6938489 object centre at (A) : 18.93800 11.40700 23.59500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.4239771E-02 1.0729178E-02 midg,1,midg; midg,igrid,midg 1.3289173E-02 -4.3039083E-02 1,midg,midg; igrid,midg,midg 5.6252282E-02 -1.4202693E-02 gauss-seidel spectral radius is 0.9988295 estimated iterations to convergence 231 setup time was (sec) 0.8200000 now iterating at: 13:11:46 rms-change max change #iterations 4.925687 224.9860 at 10iterations 2.419867 79.88571 at 20iterations 1.195284 37.29846 at 30iterations 0.5928140 18.58708 at 40iterations 0.2935532 9.959866 at 50iterations 0.1455680 4.799920 at 60iterations 7.2751753E-02 2.077042 at 70iterations 3.6202662E-02 1.044700 at 80iterations 1.8020023E-02 0.5559692 at 90iterations 9.1281449E-03 0.2692680 at 100iterations 4.6789837E-03 0.1413040 at 110iterations 2.4821234E-03 7.7650070E-02 at 120iterations finished qdiffx linear iterations at : 13:11:52 total time elapsed so far: 6.730000 # loops : 120 mean,max change (kT/e) : 2.4821234E-03 7.7650070E-02 energy calculations done at 6.730000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 6.900000 DelPhi exited at 13:11:53 6.901u 0.161s 0:07.44 94.8% 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 Sun Oct 9 2011 at 13:11:53 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: 319 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2375 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: 3.122320 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): -6.716000 44.59200 ymin,ymax (A): -14.08600 36.90000 zmin,zma (A): 2.244000 44.94600 x,y,z range (A): 51.30800 50.98600 42.70200 scale (grids/A): 3.122320 object centre (A): 18.93800 11.40700 23.59500 number of atom coordinates read : 2375 total number of charged atoms : 2234 net assigned charge : 3.500020 assigned positive charge : 364.6371 centred at (gu) : 88.20570 95.69753 93.29514 assigned negative charge : -361.1376 centred at (gu) : 88.37070 96.42343 93.44892 start vw surface at 0.1500000 fill in re-entrant regions at 0.8200000 boundary points on vw surface= 190790 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21123 grid for indexing accessible points = 1.400000 m= 99850 mr = 138562 m= 37848 mr = 81637 m= 9865 mr = 30433 m= 1894 mr = 7423 m= 266 mr = 1384 m= 4 mr = 182 m= 0 mr = 2 time to grow re-entrant surface = 0.9100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.850000 number of dielectric boundary points 80894 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.000000 number of grid points assigned charge 17867 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) : 2.081547 object centre at (A) : 18.93800 11.40700 23.59500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.4110568 -6.7514763E-03 midg,1,midg; midg,igrid,midg 0.2530594 -0.4451839 1,midg,midg; igrid,midg,midg 0.6362089 -0.4289468 gauss-seidel spectral radius is 0.9993002 estimated iterations to convergence 298 setup time was (sec) 2.180000 now iterating at: 13:11:55 rms-change max change #iterations 11.01791 497.1979 at 10iterations 6.545279 134.3505 at 20iterations 3.882298 75.35383 at 30iterations 2.295882 42.60239 at 40iterations 1.358863 23.40949 at 50iterations 0.7986940 14.16913 at 60iterations 0.4699031 7.911285 at 70iterations 0.2761118 4.615692 at 80iterations 0.1622767 2.686943 at 90iterations 9.5433161E-02 1.658577 at 100iterations 5.6016702E-02 0.9826736 at 110iterations 3.3188250E-02 0.5571914 at 120iterations 1.9720867E-02 0.3771973 at 130iterations 1.1934164E-02 0.2161884 at 140iterations 7.3939753E-03 0.1616440 at 150iterations 4.7934395E-03 0.1030502 at 160iterations 3.2859368E-03 6.8794250E-02 at 170iterations 2.3961088E-03 5.1094055E-02 at 180iterations finished qdiffx linear iterations at : 13:12:06 total time elapsed so far: 13.27000 # loops : 180 mean,max change (kT/e) : 2.3961088E-03 5.1094055E-02 energy calculations done at 13.27000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.45000 DelPhi exited at 13:12:07 13.447u 0.185s 0:13.91 97.9% 0+0k 0+0io 0pf+0w