Sun Oct 9 07:17:46 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+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 Sun Oct 9 2011 at 07:17:46 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 = 2512 !!! WARNING: PRO 130 has a net charge of 0.5000 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: 0.5459872 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): -4.495000 42.18900 ymin,ymax (A): 36.86000 87.36600 zmin,zma (A): -3.179000 62.02400 x,y,z range (A): 46.68400 50.50600 65.20300 scale (grids/A): 0.5459872 object centre (A): 18.84700 62.11300 29.42250 number of atom coordinates read : 2512 total number of charged atoms : 2367 net assigned charge : -7.999978 assigned positive charge : 374.8410 centred at (gu) : 90.56120 88.93463 89.52943 assigned negative charge : -382.8414 centred at (gu) : 90.70889 88.57581 89.43004 start vw surface at 0.1200000 fill in re-entrant regions at 0.1300000 boundary points on vw surface= 4972 nv = 96 ne = 84 npr = 49972 no. pairs analyzed = 49972 no. exposed pairs = 3550 no. arc points = 25281 no. surface atoms = 1190 nbur = 1322 mkacc time = 0.1300000 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 = 1.568000 m= 206 mr = 2346 m= 2 mr = 4 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 2830 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2470 ## 315 charges are in solution ## iepsmp to db, and charging done at 0.4100000 number of grid points assigned charge 6388 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.1614382E-09 8.7014763E-11 midg,1,midg; midg,igrid,midg -3.4036878E-09 1.1441076E-09 1,midg,midg; igrid,midg,midg 3.1680131E-10 -1.5156143E-09 gauss-seidel spectral radius is 0.9826764 estimated iterations to convergence 63 setup time was (sec) 0.5800000 now iterating at: 07:17:47 rms-change max change #iterations 6.5804593E-02 12.31097 at 10iterations 4.2980504E-03 0.7400513 at 20iterations 2.8484795E-04 4.9032211E-02 at 30iterations 2.1901162E-05 3.9253235E-03 at 40iterations 2.6326315E-06 4.8494339E-04 at 50iterations finished qdiffx linear iterations at : 07:17:51 total time elapsed so far: 4.480000 # loops : 50 mean,max change (kT/e) : 2.6326315E-06 4.8494339E-04 energy calculations done at 4.480000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.660000 DelPhi exited at 07:17:51 4.665u 0.392s 0:05.32 94.9% 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 Sun Oct 9 2011 at 07:17:52 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 = 2512 !!! WARNING: PRO 130 has a net charge of 0.5000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 1.637962 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): -4.495000 42.18900 ymin,ymax (A): 36.86000 87.36600 zmin,zma (A): -3.179000 62.02400 x,y,z range (A): 46.68400 50.50600 65.20300 scale (grids/A): 1.637962 object centre (A): 18.84700 62.11300 29.42250 number of atom coordinates read : 2512 total number of charged atoms : 2367 net assigned charge : -7.999978 assigned positive charge : 374.8410 centred at (gu) : 91.68319 86.80334 88.58824 assigned negative charge : -382.8414 centred at (gu) : 92.12636 85.72701 88.28998 start vw surface at 0.1100000 fill in re-entrant regions at 0.1900000 boundary points on vw surface= 54677 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25281 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 16134 mr = 34731 m= 1398 mr = 10573 m= 35 mr = 593 m= 0 mr = 2 time to grow re-entrant surface = 0.2200000 no. cavity mid-points inaccessible to solvent = 298 time to turn everything in is 0.4600000 number of dielectric boundary points 26345 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 267 iepsmp to db, and charging done at 0.6000000 number of grid points assigned charge 18176 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) : 0.5459872 object centre at (A) : 18.84700 62.11300 29.42250 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -3.4782633E-02 3.5221567E-03 midg,1,midg; midg,igrid,midg -2.2616481E-02 7.8427065E-03 1,midg,midg; igrid,midg,midg -2.0693911E-03 -1.3010477E-02 gauss-seidel spectral radius is 0.9981496 estimated iterations to convergence 185 setup time was (sec) 0.7900000 now iterating at: 07:17:53 rms-change max change #iterations 3.036852 162.3800 at 10iterations 1.252414 56.02098 at 20iterations 0.5138879 20.83550 at 30iterations 0.2128807 9.222036 at 40iterations 8.7978400E-02 3.569389 at 50iterations 3.6237732E-02 1.492138 at 60iterations 1.4925287E-02 0.6521177 at 70iterations 6.1601615E-03 0.2436604 at 80iterations 2.5447926E-03 0.1108179 at 90iterations 1.0548100E-03 4.5369148E-02 at 100iterations 4.3444740E-04 1.6002655E-02 at 110iterations 1.7995863E-04 6.7479610E-03 at 120iterations finished qdiffx linear iterations at : 07:18:02 total time elapsed so far: 10.43000 # loops : 120 mean,max change (kT/e) : 1.7995863E-04 6.7479610E-03 energy calculations done at 10.43000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.59000 DelPhi exited at 07:18:03 10.598u 0.450s 0:11.30 97.6% 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 Sun Oct 9 2011 at 07:18:03 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 = 2512 !!! WARNING: PRO 130 has a net charge of 0.5000 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: 2.456942 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): -4.495000 42.18900 ymin,ymax (A): 36.86000 87.36600 zmin,zma (A): -3.179000 62.02400 x,y,z range (A): 46.68400 50.50600 65.20300 scale (grids/A): 2.456942 object centre (A): 18.84700 62.11300 29.42250 number of atom coordinates read : 2512 total number of charged atoms : 2367 net assigned charge : -7.999978 assigned positive charge : 374.8410 centred at (gu) : 92.52470 85.20478 87.88219 assigned negative charge : -382.8414 centred at (gu) : 93.18952 83.59044 87.43487 start vw surface at 0.1100000 fill in re-entrant regions at 0.3800000 boundary points on vw surface= 126548 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25281 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 56416 mr = 85212 m= 14828 mr = 43469 m= 2021 mr = 10558 m= 113 mr = 1187 m= 3 mr = 37 m= 0 mr = 0 time to grow re-entrant surface = 0.6500000 no. cavity mid-points inaccessible to solvent = 1064 time to turn everything in is 1.120000 number of dielectric boundary points 59466 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 11 iepsmp to db, and charging done at 1.240000 number of grid points assigned charge 18911 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) : 1.637962 object centre at (A) : 18.84700 62.11300 29.42250 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.9526845 2.7749825E-02 midg,1,midg; midg,igrid,midg -0.3027566 0.1085654 1,midg,midg; igrid,midg,midg -3.4210175E-02 -0.1741811 gauss-seidel spectral radius is 0.9991206 estimated iterations to convergence 266 setup time was (sec) 1.430000 now iterating at: 07:18:05 rms-change max change #iterations 7.999526 338.6702 at 10iterations 4.463395 140.1592 at 20iterations 2.495403 64.77272 at 30iterations 1.378025 36.33652 at 40iterations 0.7635499 20.75243 at 50iterations 0.4207744 11.35777 at 60iterations 0.2317497 5.554051 at 70iterations 0.1269478 3.129642 at 80iterations 6.9793865E-02 1.884734 at 90iterations 3.8253915E-02 0.8581636 at 100iterations 2.0925296E-02 0.5232439 at 110iterations 1.1469024E-02 0.2499399 at 120iterations 6.2650032E-03 0.1524582 at 130iterations 3.4264796E-03 8.9076996E-02 at 140iterations 1.8706386E-03 4.0800095E-02 at 150iterations 1.0212023E-03 2.2443771E-02 at 160iterations 5.5791961E-04 1.2527466E-02 at 170iterations 3.0486984E-04 6.7825317E-03 at 180iterations finished qdiffx linear iterations at : 07:18:21 total time elapsed so far: 17.61000 # loops : 180 mean,max change (kT/e) : 3.0486984E-04 6.7825317E-03 energy calculations done at 17.61000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 17.77000 DelPhi exited at 07:18:22 17.779u 0.477s 0:18.62 97.9% 0+0k 0+0io 0pf+0w