Tue Oct 11 07:36:14 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 07:36:14 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: 255 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2599 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: 0.6960330 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): -13.25700 37.89000 ymin,ymax (A): -21.70800 26.56500 zmin,zma (A): -5.713000 40.19000 x,y,z range (A): 51.14700 48.27300 45.90300 scale (grids/A): 0.6960330 object centre (A): 12.31650 2.428500 17.23850 number of atom coordinates read : 2599 total number of charged atoms : 2277 net assigned charge : 6.500006 assigned positive charge : 362.8112 centred at (gu) : 90.96085 88.02896 89.49677 assigned negative charge : -356.3117 centred at (gu) : 91.04388 88.00926 89.67168 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 7897 nv = 96 ne = 84 npr = 47662 no. pairs analyzed = 47662 no. exposed pairs = 2832 no. arc points = 19640 no. surface atoms = 964 nbur = 1635 mkacc time = 0.1600000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 551 mr = 4630 m= 4 mr = 104 m= 0 mr = 0 time to grow re-entrant surface = 0.2000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3700000 number of dielectric boundary points 3718 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1735 ## 155 charges are in solution ## iepsmp to db, and charging done at 0.5400000 number of grid points assigned charge 8850 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.2849578E-07 -3.1830456E-08 midg,1,midg; midg,igrid,midg 4.8225591E-08 3.4521346E-08 1,midg,midg; igrid,midg,midg 6.4208542E-08 5.9943543E-09 gauss-seidel spectral radius is 0.9892738 estimated iterations to convergence 79 setup time was (sec) 0.7200000 now iterating at: 07:36:15 rms-change max change #iterations 0.2010895 27.46079 at 10iterations 2.4269713E-02 3.172579 at 20iterations 3.1907151E-03 0.4373283 at 30iterations 5.1126507E-04 6.5319061E-02 at 40iterations 1.0771345E-04 1.6395569E-02 at 50iterations finished qdiffx linear iterations at : 07:36:19 total time elapsed so far: 4.550000 # loops : 50 mean,max change (kT/e) : 1.0771345E-04 1.6395569E-02 energy calculations done at 4.550000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.770000 DelPhi exited at 07:36:20 4.771u 0.437s 0:06.00 86.6% 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 Tue Oct 11 2011 at 07:36:20 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: 255 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2599 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: 2.088099 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): -13.25700 37.89000 ymin,ymax (A): -21.70800 26.56500 zmin,zma (A): -5.713000 40.19000 x,y,z range (A): 51.14700 48.27300 45.90300 scale (grids/A): 2.088099 object centre (A): 12.31650 2.428500 17.23850 number of atom coordinates read : 2599 total number of charged atoms : 2277 net assigned charge : 6.500006 assigned positive charge : 362.8112 centred at (gu) : 92.88220 84.08649 88.48989 assigned negative charge : -356.3117 centred at (gu) : 93.13139 84.02770 89.01488 start vw surface at 0.1500000 fill in re-entrant regions at 0.3400000 boundary points on vw surface= 83500 reading accessible surface arcs data from file ARCDAT no. of arc points read = 19640 grid for indexing accessible points = 1.400000 m= 34451 mr = 59566 m= 6820 mr = 26720 m= 553 mr = 4616 m= 11 mr = 286 m= 0 mr = 0 time to grow re-entrant surface = 0.4700000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.8800000 number of dielectric boundary points 34147 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 85 iepsmp to db, and charging done at 1.030000 number of grid points assigned charge 18079 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) : 0.6960330 object centre at (A) : 12.31650 2.428500 17.23850 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 7.4561894E-02 -1.0617052E-02 midg,1,midg; midg,igrid,midg 1.9079436E-02 2.6620446E-02 1,midg,midg; igrid,midg,midg 1.9100690E-02 1.8365666E-02 gauss-seidel spectral radius is 0.9988273 estimated iterations to convergence 231 setup time was (sec) 1.240000 now iterating at: 07:36:21 rms-change max change #iterations 4.815135 215.4763 at 10iterations 2.394539 75.39856 at 20iterations 1.183599 33.71480 at 30iterations 0.5877835 19.32193 at 40iterations 0.2918975 8.422829 at 50iterations 0.1451432 4.135338 at 60iterations 7.2043560E-02 2.251953 at 70iterations 3.5780247E-02 1.004692 at 80iterations 1.7862979E-02 0.5141296 at 90iterations 8.8759391E-03 0.2813034 at 100iterations 4.4414592E-03 0.1426620 at 110iterations 2.2478180E-03 6.8996429E-02 at 120iterations finished qdiffx linear iterations at : 07:36:31 total time elapsed so far: 11.22000 # loops : 120 mean,max change (kT/e) : 2.2478180E-03 6.8996429E-02 energy calculations done at 11.22000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.43000 DelPhi exited at 07:36:32 11.434u 0.507s 0:12.28 97.1% 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 Tue Oct 11 2011 at 07:36:32 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: 255 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2599 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: 3.132149 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): -13.25700 37.89000 ymin,ymax (A): -21.70800 26.56500 zmin,zma (A): -5.713000 40.19000 x,y,z range (A): 51.14700 48.27300 45.90300 scale (grids/A): 3.132149 object centre (A): 12.31650 2.428500 17.23850 number of atom coordinates read : 2599 total number of charged atoms : 2277 net assigned charge : 6.500006 assigned positive charge : 362.8112 centred at (gu) : 94.32320 81.12957 87.73463 assigned negative charge : -356.3117 centred at (gu) : 94.69699 81.04144 88.52235 start vw surface at 0.1600000 fill in re-entrant regions at 1.100000 boundary points on vw surface= 192170 reading accessible surface arcs data from file ARCDAT no. of arc points read = 19640 grid for indexing accessible points = 1.400000 m= 106285 mr = 142847 m= 44685 mr = 89464 m= 12989 mr = 37258 m= 2491 mr = 10228 m= 215 mr = 1837 m= 3 mr = 117 m= 0 mr = 0 time to grow re-entrant surface = 1.480000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 2.740000 number of dielectric boundary points 77087 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.900000 number of grid points assigned charge 18216 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) : 2.088099 object centre at (A) : 12.31650 2.428500 17.23850 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.5383678 -0.1259518 midg,1,midg; midg,igrid,midg 0.1329674 0.1867062 1,midg,midg; igrid,midg,midg 1.7721066E-02 1.6478650E-02 gauss-seidel spectral radius is 0.9993034 estimated iterations to convergence 299 setup time was (sec) 3.110000 now iterating at: 07:36:36 rms-change max change #iterations 10.76012 452.4477 at 10iterations 6.330263 124.0486 at 20iterations 3.735592 69.23363 at 30iterations 2.191672 40.51199 at 40iterations 1.289008 22.21621 at 50iterations 0.7537159 13.51374 at 60iterations 0.4422263 7.120263 at 70iterations 0.2586941 4.233619 at 80iterations 0.1515053 2.587554 at 90iterations 8.8732280E-02 1.408680 at 100iterations 5.2108254E-02 0.8719959 at 110iterations 3.0573094E-02 0.5087547 at 120iterations 1.8076105E-02 0.2856884 at 130iterations 1.0750060E-02 0.1902542 at 140iterations 6.4753368E-03 0.1180935 at 150iterations 3.9970181E-03 6.9969177E-02 at 160iterations 2.5523144E-03 4.5120239E-02 at 170iterations 1.7002147E-03 3.2341003E-02 at 180iterations finished qdiffx linear iterations at : 07:36:53 total time elapsed so far: 20.11000 # loops : 180 mean,max change (kT/e) : 1.7002147E-03 3.2341003E-02 energy calculations done at 20.11000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 20.33000 DelPhi exited at 07:36:53 20.332u 0.550s 0:21.28 98.1% 0+0k 0+0io 0pf+0w