Tue Oct 11 06:16:10 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 06:16:10 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 = 1929 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: 0.7231216 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): 20.11600 64.36900 ymin,ymax (A): -3.492000 33.39000 zmin,zma (A): 23.42200 72.65300 x,y,z range (A): 44.25300 36.88200 49.23100 scale (grids/A): 0.7231216 object centre (A): 42.24250 14.94900 48.03750 number of atom coordinates read : 1929 total number of charged atoms : 1881 net assigned charge : 6.500005 assigned positive charge : 302.9431 centred at (gu) : 89.80526 89.72031 88.40429 assigned negative charge : -296.4432 centred at (gu) : 89.96876 89.77694 88.34087 start vw surface at 0.1300000 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 7110 nv = 96 ne = 84 npr = 36316 no. pairs analyzed = 36316 no. exposed pairs = 2569 no. arc points = 17365 no. surface atoms = 868 nbur = 1061 mkacc time = 0.1200000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 558 mr = 3992 m= 7 mr = 108 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 0.3000000 number of dielectric boundary points 3575 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1554 ## 132 charges are in solution ## iepsmp to db, and charging done at 0.4200000 number of grid points assigned charge 7749 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 4.8740681E-08 8.9695888E-08 midg,1,midg; midg,igrid,midg 1.2261400E-07 3.9621820E-08 1,midg,midg; igrid,midg,midg 1.9237922E-07 -2.9161638E-08 gauss-seidel spectral radius is 0.9900190 estimated iterations to convergence 81 setup time was (sec) 0.6000000 now iterating at: 06:16:11 rms-change max change #iterations 0.2121989 35.42644 at 10iterations 2.7092330E-02 4.048210 at 20iterations 3.5210133E-03 0.4457932 at 30iterations 4.8519310E-04 6.5589905E-02 at 40iterations 8.1479484E-05 1.1562347E-02 at 50iterations finished qdiffx linear iterations at : 06:16:15 total time elapsed so far: 4.150000 # loops : 50 mean,max change (kT/e) : 8.1479484E-05 1.1562347E-02 energy calculations done at 4.150000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.370000 DelPhi exited at 06:16:16 4.377u 0.417s 0:05.43 88.0% 0+0k 0+0io 6pf+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 06:16:16 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 = 1929 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: 2.169365 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): 20.11600 64.36900 ymin,ymax (A): -3.492000 33.39000 zmin,zma (A): 23.42200 72.65300 x,y,z range (A): 44.25300 36.88200 49.23100 scale (grids/A): 2.169365 object centre (A): 42.24250 14.94900 48.03750 number of atom coordinates read : 1929 total number of charged atoms : 1881 net assigned charge : 6.500005 assigned positive charge : 302.9431 centred at (gu) : 89.41566 89.16130 85.21316 assigned negative charge : -296.4432 centred at (gu) : 89.90639 89.33112 85.02271 start vw surface at 0.1300000 fill in re-entrant regions at 0.3000000 boundary points on vw surface= 74642 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17365 grid for indexing accessible points = 1.400000 m= 31703 mr = 52064 m= 6999 mr = 24041 m= 744 mr = 4747 m= 21 mr = 384 m= 0 mr = 2 time to grow re-entrant surface = 0.4400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.8000000 number of dielectric boundary points 32871 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 50 iepsmp to db, and charging done at 0.9400000 number of grid points assigned charge 14951 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) : 0.7231216 object centre at (A) : 42.24250 14.94900 48.03750 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 6.0271374E-03 3.6334164E-02 midg,1,midg; midg,igrid,midg 3.4994245E-02 6.1551300E-03 1,midg,midg; igrid,midg,midg 5.4530125E-02 3.4201261E-02 gauss-seidel spectral radius is 0.9988698 estimated iterations to convergence 235 setup time was (sec) 1.130000 now iterating at: 06:16:17 rms-change max change #iterations 4.652099 226.3433 at 10iterations 2.328318 73.77459 at 20iterations 1.170880 37.00343 at 30iterations 0.5872623 16.97389 at 40iterations 0.2956215 10.04174 at 50iterations 0.1486355 4.445261 at 60iterations 7.4475147E-02 2.551843 at 70iterations 3.7413217E-02 1.241364 at 80iterations 1.8802200E-02 0.5469375 at 90iterations 9.4858864E-03 0.2738667 at 100iterations 4.7541466E-03 0.1426945 at 110iterations 2.4084705E-03 6.9153309E-02 at 120iterations finished qdiffx linear iterations at : 06:16:27 total time elapsed so far: 10.16000 # loops : 120 mean,max change (kT/e) : 2.4084705E-03 6.9153309E-02 energy calculations done at 10.16000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.38000 DelPhi exited at 06:16:27 10.384u 0.461s 0:11.16 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 06:16:27 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 = 1929 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: 3.254047 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): 20.11600 64.36900 ymin,ymax (A): -3.492000 33.39000 zmin,zma (A): 23.42200 72.65300 x,y,z range (A): 44.25300 36.88200 49.23100 scale (grids/A): 3.254047 object centre (A): 42.24250 14.94900 48.03750 number of atom coordinates read : 1929 total number of charged atoms : 1881 net assigned charge : 6.500005 assigned positive charge : 302.9431 centred at (gu) : 89.12350 88.74200 82.81960 assigned negative charge : -296.4432 centred at (gu) : 89.85965 88.99659 82.53410 start vw surface at 4.520000 fill in re-entrant regions at 5.350000 boundary points on vw surface= 171650 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17365 grid for indexing accessible points = 1.400000 m= 95926 mr = 125246 m= 42261 mr = 79541 m= 13540 mr = 34849 m= 2933 mr = 10550 m= 392 mr = 2122 m= 11 mr = 231 m= 0 mr = 2 time to grow re-entrant surface = 1.370000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 6.860000 number of dielectric boundary points 74172 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 7.040000 number of grid points assigned charge 15039 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) : 2.169365 object centre at (A) : 42.24250 14.94900 48.03750 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.1623870E-02 -4.6212538E-03 midg,1,midg; midg,igrid,midg 0.2822238 3.1893369E-02 1,midg,midg; igrid,midg,midg 0.4363389 0.5236160 gauss-seidel spectral radius is 0.9993174 estimated iterations to convergence 302 setup time was (sec) 7.240000 now iterating at: 06:16:35 rms-change max change #iterations 10.40710 330.6639 at 10iterations 6.253720 142.0965 at 20iterations 3.752579 77.13683 at 30iterations 2.241585 45.33071 at 40iterations 1.335729 23.99761 at 50iterations 0.7927336 15.54158 at 60iterations 0.4708270 9.376937 at 70iterations 0.2788088 5.311660 at 80iterations 0.1648189 2.962959 at 90iterations 9.7490832E-02 1.778992 at 100iterations 5.7595406E-02 1.009912 at 110iterations 3.4141626E-02 0.7215214 at 120iterations 2.0225143E-02 0.3612046 at 130iterations 1.2022704E-02 0.2309237 at 140iterations 7.2138682E-03 0.1326065 at 150iterations 4.3974333E-03 8.0774307E-02 at 160iterations 2.7518133E-03 4.9331188E-02 at 170iterations 1.7948552E-03 3.3830643E-02 at 180iterations finished qdiffx linear iterations at : 06:16:50 total time elapsed so far: 22.32000 # loops : 180 mean,max change (kT/e) : 1.7948552E-03 3.3830643E-02 energy calculations done at 22.32000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 22.54000 DelPhi exited at 06:16:51 22.542u 0.472s 0:23.67 97.2% 0+0k 0+0io 0pf+0w