Tue Nov 22 14:11:10 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 Tue Nov 22 2011 at 14:11:14 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1962 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: 0.6433657 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): -4.024000 35.07900 ymin,ymax (A): -4.657000 48.54400 zmin,zma (A): -24.05300 31.28100 x,y,z range (A): 39.10300 53.20100 55.33400 scale (grids/A): 0.6433657 object centre (A): 15.52750 21.94350 3.614000 number of atom coordinates read : 1962 total number of charged atoms : 1830 net assigned charge : 5.000007 assigned positive charge : 287.8260 centred at (gu) : 90.22990 93.00298 90.01986 assigned negative charge : -282.8263 centred at (gu) : 90.26810 93.08160 89.96649 start vw surface at 0.1200000 fill in re-entrant regions at 0.1300000 boundary points on vw surface= 5613 nv = 96 ne = 84 npr = 40250 no. pairs analyzed = 40250 no. exposed pairs = 2371 no. arc points = 17063 no. surface atoms = 803 nbur = 1159 mkacc time = 7.9999998E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 295 mr = 3172 m= 0 mr = 43 time to grow re-entrant surface = 9.0000004E-02 no. cavity mid-points inaccessible to solvent = 10 time to turn everything in is 0.2300000 number of dielectric boundary points 2693 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1678 ## 167 charges are in solution ## iepsmp to db, and charging done at 0.3300000 number of grid points assigned charge 6489 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 3.2354768E-09 1.3134246E-08 midg,1,midg; midg,igrid,midg 8.2494118E-09 1.1637526E-09 1,midg,midg; igrid,midg,midg 1.1147874E-08 4.8746749E-09 gauss-seidel spectral radius is 0.9874267 estimated iterations to convergence 73 setup time was (sec) 0.4600000 now iterating at: 14:11:16 rms-change max change #iterations 0.1249072 17.81975 at 10iterations 1.2519323E-02 2.299803 at 20iterations 1.2590076E-03 0.1925964 at 30iterations 1.2638028E-04 2.0042419E-02 at 40iterations 1.2569031E-05 1.9512177E-03 at 50iterations finished qdiffx linear iterations at : 14:11:21 total time elapsed so far: 3.040000 # loops : 50 mean,max change (kT/e) : 1.2569031E-05 1.9512177E-03 energy calculations done at 3.040000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.200000 DelPhi exited at 14:11:23 3.206u 0.182s 0:08.64 39.1% 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 Nov 22 2011 at 14:11:23 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 = 1962 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: 1.930097 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): -4.024000 35.07900 ymin,ymax (A): -4.657000 48.54400 zmin,zma (A): -24.05300 31.28100 x,y,z range (A): 39.10300 53.20100 55.33400 scale (grids/A): 1.930097 object centre (A): 15.52750 21.94350 3.614000 number of atom coordinates read : 1962 total number of charged atoms : 1830 net assigned charge : 5.000007 assigned positive charge : 287.8260 centred at (gu) : 90.68967 99.00880 90.05968 assigned negative charge : -282.8263 centred at (gu) : 90.80447 99.24500 89.89957 start vw surface at 0.1100000 fill in re-entrant regions at 0.1900000 boundary points on vw surface= 59767 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17063 grid for indexing accessible points = 1.400000 m= 22831 mr = 41515 m= 3542 mr = 17674 m= 172 mr = 2345 m= 1 mr = 82 m= 0 mr = 0 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 2019 time to turn everything in is 0.4200000 number of dielectric boundary points 24697 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 140 iepsmp to db, and charging done at 0.5300000 number of grid points assigned charge 14422 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) : 0.6433657 object centre at (A) : 15.52750 21.94350 3.614000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.9209032E-02 2.5396196E-02 midg,1,midg; midg,igrid,midg 3.3843089E-02 8.6579211E-03 1,midg,midg; igrid,midg,midg 3.8695431E-03 4.9289330E-05 gauss-seidel spectral radius is 0.9985912 estimated iterations to convergence 211 setup time was (sec) 0.6900000 now iterating at: 14:11:27 rms-change max change #iterations 3.614223 200.2666 at 10iterations 1.672063 60.17533 at 20iterations 0.7772182 28.94951 at 30iterations 0.3601932 12.46490 at 40iterations 0.1657460 5.751619 at 50iterations 7.6554373E-02 2.700115 at 60iterations 3.5452764E-02 1.206554 at 70iterations 1.6418006E-02 0.5554698 at 80iterations 7.5642667E-03 0.2471924 at 90iterations 3.5181304E-03 0.1363969 at 100iterations 1.6238111E-03 5.5786133E-02 at 110iterations 7.5262052E-04 2.6872993E-02 at 120iterations finished qdiffx linear iterations at : 14:11:46 total time elapsed so far: 6.970000 # loops : 120 mean,max change (kT/e) : 7.5262052E-04 2.6872993E-02 energy calculations done at 6.970000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.150000 DelPhi exited at 14:11:48 7.152u 0.195s 0:25.17 29.1% 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 Nov 22 2011 at 14:11:49 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 = 1962 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: 2.895146 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): -4.024000 35.07900 ymin,ymax (A): -4.657000 48.54400 zmin,zma (A): -24.05300 31.28100 x,y,z range (A): 39.10300 53.20100 55.33400 scale (grids/A): 2.895146 object centre (A): 15.52750 21.94350 3.614000 number of atom coordinates read : 1962 total number of charged atoms : 1830 net assigned charge : 5.000007 assigned positive charge : 287.8260 centred at (gu) : 91.03442 103.5132 90.08957 assigned negative charge : -282.8263 centred at (gu) : 91.20692 103.8675 89.84933 start vw surface at 0.1100000 fill in re-entrant regions at 0.3500000 boundary points on vw surface= 138236 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17063 grid for indexing accessible points = 1.400000 m= 72311 mr = 100389 m= 27773 mr = 60472 m= 6296 mr = 23407 m= 776 mr = 4971 m= 50 mr = 548 m= 0 mr = 24 time to grow re-entrant surface = 0.6199999 no. cavity mid-points inaccessible to solvent = 6732 time to turn everything in is 1.080000 number of dielectric boundary points 55631 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.210000 number of grid points assigned charge 14640 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) : 1.930097 object centre at (A) : 15.52750 21.94350 3.614000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.110229 9.3196079E-02 midg,1,midg; midg,igrid,midg 0.3322292 -1.4601747E-02 1,midg,midg; igrid,midg,midg 2.1533195E-02 2.3660739E-03 gauss-seidel spectral radius is 0.9992340 estimated iterations to convergence 285 setup time was (sec) 1.370000 now iterating at: 14:11:53 rms-change max change #iterations 8.434063 366.8237 at 10iterations 4.842348 136.9869 at 20iterations 2.753273 65.15784 at 30iterations 1.559532 32.71651 at 40iterations 0.8903148 18.40361 at 50iterations 0.5056217 10.41033 at 60iterations 0.2863826 5.856864 at 70iterations 0.1628191 3.107203 at 80iterations 9.2281938E-02 1.803754 at 90iterations 5.2438851E-02 1.036258 at 100iterations 2.9790685E-02 0.5761701 at 110iterations 1.6843468E-02 0.3097439 at 120iterations 9.5711024E-03 0.1912503 at 130iterations 5.4223859E-03 9.8459244E-02 at 140iterations 3.0879050E-03 6.3095093E-02 at 150iterations 1.7519550E-03 3.3481598E-02 at 160iterations 9.9332526E-04 2.2640228E-02 at 170iterations 5.6545151E-04 1.0939837E-02 at 180iterations finished qdiffx linear iterations at : 14:12:27 total time elapsed so far: 13.25000 # loops : 180 mean,max change (kT/e) : 5.6545151E-04 1.0939837E-02 energy calculations done at 13.25000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.42000 DelPhi exited at 14:12:32 13.421u 0.230s 0:42.61 32.0% 0+0k 0+0io 0pf+0w