Sat Oct 8 17:03:46 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 Sat Oct 8 2011 at 17:03:47 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: 295 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3591 !!! WARNING: ASL 227 has a net charge of -0.1000 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: 0.5131236 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): -5.141000 64.23800 ymin,ymax (A): 14.02600 76.45800 zmin,zma (A): -13.01200 34.29000 x,y,z range (A): 69.37900 62.43200 47.30200 scale (grids/A): 0.5131236 object centre (A): 29.54850 45.24200 10.63900 number of atom coordinates read : 3591 total number of charged atoms : 3444 net assigned charge : -8.099986 assigned positive charge : 550.4739 centred at (gu) : 89.99097 87.65700 89.47526 assigned negative charge : -558.5759 centred at (gu) : 89.96892 87.70274 89.50576 start vw surface at 0.1400000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 5948 nv = 96 ne = 84 npr = 72849 no. pairs analyzed = 72849 no. exposed pairs = 4468 no. arc points = 30765 no. surface atoms = 1502 nbur = 2089 mkacc time = 0.1900000 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 = 1.652000 m= 209 mr = 3099 m= 0 mr = 3 time to grow re-entrant surface = 0.2300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3900000 number of dielectric boundary points 3055 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3056 ## 479 charges are in solution ## iepsmp to db, and charging done at 0.5000000 number of grid points assigned charge 8019 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -7.1126750E-11 -1.7417957E-10 midg,1,midg; midg,igrid,midg -4.7554658E-11 -1.2828354E-10 1,midg,midg; igrid,midg,midg -1.8078343E-10 -8.1235761E-11 gauss-seidel spectral radius is 0.9804862 estimated iterations to convergence 59 setup time was (sec) 0.7000000 now iterating at: 17:03:48 rms-change max change #iterations 6.2429570E-02 12.72914 at 10iterations 3.6384962E-03 0.6106567 at 20iterations 2.2138565E-04 4.3251038E-02 at 30iterations 2.8582712E-05 4.8637390E-03 at 40iterations 7.2954667E-06 1.3718605E-03 at 50iterations finished qdiffx linear iterations at : 17:03:52 total time elapsed so far: 5.350000 # loops : 50 mean,max change (kT/e) : 7.2954667E-06 1.3718605E-03 energy calculations done at 5.350000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 5.530000 DelPhi exited at 17:03:53 5.531u 0.460s 0:06.26 95.6% 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 Sat Oct 8 2011 at 17:03:53 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: 295 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3591 !!! WARNING: ASL 227 has a net charge of -0.1000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 1.539371 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): -5.141000 64.23800 ymin,ymax (A): 14.02600 76.45800 zmin,zma (A): -13.01200 34.29000 x,y,z range (A): 69.37900 62.43200 47.30200 scale (grids/A): 1.539371 object centre (A): 29.54850 45.24200 10.63900 number of atom coordinates read : 3591 total number of charged atoms : 3444 net assigned charge : -8.099986 assigned positive charge : 550.4739 centred at (gu) : 89.97214 82.97010 88.42471 assigned negative charge : -558.5759 centred at (gu) : 89.90640 83.10787 88.51688 start vw surface at 0.1400000 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 67226 reading accessible surface arcs data from file ARCDAT no. of arc points read = 30765 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.568000 m= 19746 mr = 46243 m= 1702 mr = 13271 m= 32 mr = 731 m= 0 mr = 0 time to grow re-entrant surface = 0.2900000 no. cavity mid-points inaccessible to solvent = 401 time to turn everything in is 0.5800000 number of dielectric boundary points 28461 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 458 ## 7 charges are in solution ## iepsmp to db, and charging done at 0.7100000 number of grid points assigned charge 26034 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) : 0.5131236 object centre at (A) : 29.54850 45.24200 10.63900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.2448683E-03 -1.5630927E-03 midg,1,midg; midg,igrid,midg -1.4386061E-02 -1.4001676E-02 1,midg,midg; igrid,midg,midg 7.8741955E-03 -2.4043149E-03 gauss-seidel spectral radius is 0.9979970 estimated iterations to convergence 178 setup time was (sec) 0.9400000 now iterating at: 17:03:54 rms-change max change #iterations 3.307586 171.7227 at 10iterations 1.312308 45.37577 at 20iterations 0.5273482 18.84496 at 30iterations 0.2103475 7.553413 at 40iterations 8.4239095E-02 3.017654 at 50iterations 3.3482928E-02 1.187851 at 60iterations 1.3439573E-02 0.4720554 at 70iterations 5.3715738E-03 0.1879120 at 80iterations 2.1598339E-03 7.5271130E-02 at 90iterations 8.6385559E-04 3.1719923E-02 at 100iterations 3.5142610E-04 1.2390137E-02 at 110iterations 1.4573942E-04 6.1864853E-03 at 120iterations finished qdiffx linear iterations at : 17:04:06 total time elapsed so far: 12.44000 # loops : 120 mean,max change (kT/e) : 1.4573942E-04 6.1864853E-03 energy calculations done at 12.44000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.62000 DelPhi exited at 17:04:06 12.621u 0.513s 0:13.40 97.9% 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 Sat Oct 8 2011 at 17:04:06 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: 295 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3591 !!! WARNING: ASL 227 has a net charge of -0.1000 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: 2.309056 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): -5.141000 64.23800 ymin,ymax (A): 14.02600 76.45800 zmin,zma (A): -13.01200 34.29000 x,y,z range (A): 69.37900 62.43200 47.30200 scale (grids/A): 2.309056 object centre (A): 29.54850 45.24200 10.63900 number of atom coordinates read : 3591 total number of charged atoms : 3444 net assigned charge : -8.099986 assigned positive charge : 550.4739 centred at (gu) : 89.95792 79.45492 87.63680 assigned negative charge : -558.5759 centred at (gu) : 89.85958 79.66159 87.77528 start vw surface at 0.1500000 fill in re-entrant regions at 0.4600000 boundary points on vw surface= 156857 reading accessible surface arcs data from file ARCDAT no. of arc points read = 30765 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.540000 m= 70457 mr = 113659 m= 18003 mr = 55363 m= 2578 mr = 13019 m= 131 mr = 1613 m= 2 mr = 31 m= 0 mr = 0 time to grow re-entrant surface = 0.8600000 no. cavity mid-points inaccessible to solvent = 1377 time to turn everything in is 1.430000 number of dielectric boundary points 64343 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 53 iepsmp to db, and charging done at 1.580000 number of grid points assigned charge 27490 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) : 1.539371 object centre at (A) : 29.54850 45.24200 10.63900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.4178193E-03 -1.4130094E-02 midg,1,midg; midg,igrid,midg -0.3019826 -0.2709838 1,midg,midg; igrid,midg,midg 0.4088744 -4.9272418E-02 gauss-seidel spectral radius is 0.9990839 estimated iterations to convergence 261 setup time was (sec) 1.810000 now iterating at: 17:04:09 rms-change max change #iterations 8.880198 271.2857 at 10iterations 4.927300 127.2371 at 20iterations 2.707533 69.64931 at 30iterations 1.480592 34.75028 at 40iterations 0.8089691 18.91282 at 50iterations 0.4403934 9.084867 at 60iterations 0.2391702 5.280211 at 70iterations 0.1296148 2.921029 at 80iterations 7.0089206E-02 1.513011 at 90iterations 3.8019158E-02 0.8511543 at 100iterations 2.0557603E-02 0.4153559 at 110iterations 1.1124475E-02 0.2417755 at 120iterations 5.9926296E-03 0.1181755 at 130iterations 3.2535349E-03 6.8350434E-02 at 140iterations 1.7611283E-03 3.8681030E-02 at 150iterations 9.5246744E-04 2.0133972E-02 at 160iterations 5.1808933E-04 1.0803223E-02 at 170iterations 2.8420042E-04 6.4830780E-03 at 180iterations finished qdiffx linear iterations at : 17:04:27 total time elapsed so far: 20.68000 # loops : 180 mean,max change (kT/e) : 2.8420042E-04 6.4830780E-03 energy calculations done at 20.68000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 20.84000 DelPhi exited at 17:04:28 20.849u 0.545s 0:21.71 98.4% 0+0k 0+0io 0pf+0w