Wed Dec 21 14:21:09 PST 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 Wed Dec 21 2011 at 14:21:09 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: 247 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2010 !!! WARNING: ASH 25 has a net charge of -0.3190 !!! WARNING: ASH 127 has a net charge of -0.3190 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.5781285 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): -34.96900 10.34900 ymin,ymax (A): 0.2410001 41.80500 zmin,zma (A): -2.949000 58.62900 x,y,z range (A): 45.31800 41.56400 61.57800 scale (grids/A): 0.5781285 object centre (A): -12.31000 21.02300 27.84000 number of atom coordinates read : 2010 total number of charged atoms : 1876 net assigned charge : 3.362005 assigned positive charge : 296.5459 centred at (gu) : 90.35767 89.55315 90.00001 assigned negative charge : -293.1842 centred at (gu) : 90.26687 89.71006 89.99989 start vw surface at 0.1100000 fill in re-entrant regions at 0.1200000 boundary points on vw surface= 4400 nv = 96 ne = 84 npr = 41123 no. pairs analyzed = 41123 no. exposed pairs = 2586 no. arc points = 18303 no. surface atoms = 871 nbur = 1139 mkacc time = 0.1100000 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 = 1.512000 m= 191 mr = 2312 m= 0 mr = 13 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2600000 number of dielectric boundary points 2266 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1791 ## 238 charges are in solution ## iepsmp to db, and charging done at 0.3600000 number of grid points assigned charge 5560 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 6.7356765E-10 6.7671657E-10 midg,1,midg; midg,igrid,midg 3.0879379E-09 -1.3521749E-09 1,midg,midg; igrid,midg,midg -5.2821664E-10 2.0685957E-09 gauss-seidel spectral radius is 0.9844773 estimated iterations to convergence 66 setup time was (sec) 0.5200000 now iterating at: 14:21:10 rms-change max change #iterations 7.6203242E-02 16.37178 at 10iterations 5.7474882E-03 1.149006 at 20iterations 4.4811581E-04 8.7962151E-02 at 30iterations 3.3731223E-05 7.4844360E-03 at 40iterations 2.6586529E-06 5.0735474E-04 at 50iterations finished qdiffx linear iterations at : 14:21:14 total time elapsed so far: 4.480000 # loops : 50 mean,max change (kT/e) : 2.6586529E-06 5.0735474E-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 14:21:15 4.661u 0.366s 0:05.70 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 Wed Dec 21 2011 at 14:21:15 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: 247 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2010 !!! WARNING: ASH 25 has a net charge of -0.3190 !!! WARNING: ASH 127 has a net charge of -0.3190 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.734386 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): -34.96900 10.34900 ymin,ymax (A): 0.2410001 41.80500 zmin,zma (A): -2.949000 58.62900 x,y,z range (A): 45.31800 41.56400 61.57800 scale (grids/A): 1.734386 object centre (A): -12.31000 21.02300 27.84000 number of atom coordinates read : 2010 total number of charged atoms : 1876 net assigned charge : 3.362005 assigned positive charge : 296.5459 centred at (gu) : 91.07301 88.65946 90.00002 assigned negative charge : -293.1842 centred at (gu) : 90.80076 89.13073 89.99986 start vw surface at 0.1100000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 47994 reading accessible surface arcs data from file ARCDAT no. of arc points read = 18303 grid for indexing accessible points = 1.400000 m= 15947 mr = 32309 m= 1882 mr = 11499 m= 60 mr = 1053 m= 1 mr = 3 m= 0 mr = 0 time to grow re-entrant surface = 0.2000000 no. cavity mid-points inaccessible to solvent = 743 time to turn everything in is 0.4200000 number of dielectric boundary points 21020 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 202 iepsmp to db, and charging done at 0.6100000 number of grid points assigned charge 14505 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) : 0.5781285 object centre at (A) : -12.31000 21.02300 27.84000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.5101192E-02 2.5347775E-02 midg,1,midg; midg,igrid,midg 6.1513809E-03 -7.3475325E-03 1,midg,midg; igrid,midg,midg -2.4245710E-03 1.1679614E-03 gauss-seidel spectral radius is 0.9982826 estimated iterations to convergence 192 setup time was (sec) 0.8300000 now iterating at: 14:21:16 rms-change max change #iterations 2.971870 156.5019 at 10iterations 1.261834 57.65034 at 20iterations 0.5381981 21.67256 at 30iterations 0.2295601 10.25858 at 40iterations 9.8454371E-02 4.806484 at 50iterations 4.1916203E-02 1.653410 at 60iterations 1.7843569E-02 0.7179794 at 70iterations 7.6220701E-03 0.3314995 at 80iterations 3.2636900E-03 0.1359863 at 90iterations 1.3954752E-03 5.2539825E-02 at 100iterations 5.9525005E-04 2.3986816E-02 at 110iterations 2.5290190E-04 1.0543823E-02 at 120iterations finished qdiffx linear iterations at : 14:21:29 total time elapsed so far: 13.08000 # loops : 120 mean,max change (kT/e) : 2.5290190E-04 1.0543823E-02 energy calculations done at 13.08000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.24000 DelPhi exited at 14:21:34 13.244u 0.562s 0:18.67 73.9% 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 Wed Dec 21 2011 at 14:21:34 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: 247 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2010 !!! WARNING: ASH 25 has a net charge of -0.3190 !!! WARNING: ASH 127 has a net charge of -0.3190 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: 2.601578 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): -34.96900 10.34900 ymin,ymax (A): 0.2410001 41.80500 zmin,zma (A): -2.949000 58.62900 x,y,z range (A): 45.31800 41.56400 61.57800 scale (grids/A): 2.601578 object centre (A): -12.31000 21.02300 27.84000 number of atom coordinates read : 2010 total number of charged atoms : 1876 net assigned charge : 3.362005 assigned positive charge : 296.5459 centred at (gu) : 91.60945 87.98917 89.99995 assigned negative charge : -293.1842 centred at (gu) : 91.20113 88.69609 89.99998 start vw surface at 0.1400000 fill in re-entrant regions at 0.4300000 boundary points on vw surface= 111183 reading accessible surface arcs data from file ARCDAT no. of arc points read = 18303 grid for indexing accessible points = 1.400000 m= 53216 mr = 78661 m= 17037 mr = 42965 m= 3161 mr = 13618 m= 296 mr = 2168 m= 13 mr = 167 m= 1 mr = 2 m= 0 mr = 0 time to grow re-entrant surface = 0.6600000 no. cavity mid-points inaccessible to solvent = 2510 time to turn everything in is 1.220000 number of dielectric boundary points 47326 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 7 iepsmp to db, and charging done at 1.440000 number of grid points assigned charge 14998 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) : 1.734386 object centre at (A) : -12.31000 21.02300 27.84000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.3433180 0.3353887 midg,1,midg; midg,igrid,midg 4.8243444E-02 -9.9361211E-02 1,midg,midg; igrid,midg,midg -4.9084552E-02 -1.3239691E-02 gauss-seidel spectral radius is 0.9991369 estimated iterations to convergence 269 setup time was (sec) 1.800000 now iterating at: 14:21:38 rms-change max change #iterations 7.285540 309.6394 at 10iterations 4.016258 119.7982 at 20iterations 2.213586 53.29474 at 30iterations 1.215788 28.32748 at 40iterations 0.6659371 15.57878 at 50iterations 0.3641001 8.024471 at 60iterations 0.1993172 4.449710 at 70iterations 0.1092895 2.417171 at 80iterations 5.9771758E-02 1.404066 at 90iterations 3.2725785E-02 0.8035765 at 100iterations 1.7948821E-02 0.4339285 at 110iterations 9.8597100E-03 0.2295346 at 120iterations 5.3985463E-03 0.1216087 at 130iterations 2.9396752E-03 6.8807602E-02 at 140iterations 1.6135850E-03 3.8866043E-02 at 150iterations 8.8486727E-04 1.9752502E-02 at 160iterations 4.8495203E-04 1.0639191E-02 at 170iterations 2.6637394E-04 6.2294006E-03 at 180iterations finished qdiffx linear iterations at : 14:22:04 total time elapsed so far: 27.71000 # loops : 180 mean,max change (kT/e) : 2.6637394E-04 6.2294006E-03 energy calculations done at 27.71000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 27.88000 DelPhi exited at 14:22:10 27.885u 0.994s 0:35.43 81.4% 0+0k 0+0io 0pf+0w