Wed Dec 28 11:01:59 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+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 Wed Dec 28 2011 at 11:01:59 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: 259 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1948 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: 0.5736662 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): -7.179000 34.15500 ymin,ymax (A): 6.536000 51.63100 zmin,zma (A): 5.053000 67.11000 x,y,z range (A): 41.33400 45.09500 62.05700 scale (grids/A): 0.5736662 object centre (A): 13.48800 29.08350 36.08150 number of atom coordinates read : 1948 total number of charged atoms : 1816 net assigned charge : 2.000005 assigned positive charge : 290.4340 centred at (gu) : 90.04222 90.66649 90.70493 assigned negative charge : -288.4343 centred at (gu) : 90.05151 90.88229 90.71208 start vw surface at 0.1400000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 4244 nv = 96 ne = 84 npr = 39908 no. pairs analyzed = 39908 no. exposed pairs = 2485 no. arc points = 17456 no. surface atoms = 844 nbur = 1104 mkacc time = 0.1200000 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 = 1.484000 m= 188 mr = 2246 m= 0 mr = 10 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 26 time to turn everything in is 0.2900000 number of dielectric boundary points 2176 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1782 ## 230 charges are in solution ## iepsmp to db, and charging done at 0.4200000 number of grid points assigned charge 5382 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 3.8626041E-10 3.3959410E-10 midg,1,midg; midg,igrid,midg 2.3887954E-09 -2.5713995E-09 1,midg,midg; igrid,midg,midg 4.7442333E-10 2.6708560E-10 gauss-seidel spectral radius is 0.9842343 estimated iterations to convergence 65 setup time was (sec) 0.6200000 now iterating at: 11:02:00 rms-change max change #iterations 7.8458622E-02 12.90079 at 10iterations 5.8375350E-03 1.145876 at 20iterations 4.3881507E-04 8.3663940E-02 at 30iterations 3.3178261E-05 6.2489510E-03 at 40iterations 2.4704407E-06 4.5394897E-04 at 50iterations finished qdiffx linear iterations at : 11:02:04 total time elapsed so far: 4.180000 # loops : 50 mean,max change (kT/e) : 2.4704407E-06 4.5394897E-04 energy calculations done at 4.180000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.350000 DelPhi exited at 11:02:05 4.354u 0.418s 0:05.96 79.8% 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 28 2011 at 11:02:05 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: 259 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1948 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: 1.720998 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): -7.179000 34.15500 ymin,ymax (A): 6.536000 51.63100 zmin,zma (A): 5.053000 67.11000 x,y,z range (A): 41.33400 45.09500 62.05700 scale (grids/A): 1.720998 object centre (A): 13.48800 29.08350 36.08150 number of atom coordinates read : 1948 total number of charged atoms : 1816 net assigned charge : 2.000005 assigned positive charge : 290.4340 centred at (gu) : 90.12671 91.99943 92.11465 assigned negative charge : -288.4343 centred at (gu) : 90.15472 92.64694 92.13622 start vw surface at 0.1500000 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 46588 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17456 grid for indexing accessible points = 1.400000 m= 15014 mr = 31329 m= 1693 mr = 10910 m= 43 mr = 914 m= 0 mr = 0 time to grow re-entrant surface = 0.2000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4700000 number of dielectric boundary points 20185 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 206 iepsmp to db, and charging done at 0.6300000 number of grid points assigned charge 14110 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) : 0.5736662 object centre at (A) : 13.48800 29.08350 36.08150 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.9372119E-02 2.3912366E-02 midg,1,midg; midg,igrid,midg 7.7028489E-03 -1.3919360E-02 1,midg,midg; igrid,midg,midg -1.8778774E-03 -3.0829471E-03 gauss-seidel spectral radius is 0.9982488 estimated iterations to convergence 190 setup time was (sec) 0.8500000 now iterating at: 11:02:06 rms-change max change #iterations 2.931485 148.3438 at 10iterations 1.238600 57.60300 at 20iterations 0.5259010 22.27131 at 30iterations 0.2221308 10.20610 at 40iterations 9.3926571E-02 3.984266 at 50iterations 3.9826747E-02 1.711076 at 60iterations 1.6784517E-02 0.7706375 at 70iterations 7.1266261E-03 0.3348035 at 80iterations 3.0099638E-03 0.1200233 at 90iterations 1.2724116E-03 5.6779861E-02 at 100iterations 5.3866598E-04 2.3578644E-02 at 110iterations 2.2821262E-04 9.7855926E-03 at 120iterations finished qdiffx linear iterations at : 11:02:17 total time elapsed so far: 11.33000 # loops : 120 mean,max change (kT/e) : 2.2821262E-04 9.7855926E-03 energy calculations done at 11.33000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.51000 DelPhi exited at 11:02:19 11.509u 0.453s 0:14.21 84.0% 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 28 2011 at 11:02:20 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: 259 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1948 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: 2.581498 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): -7.179000 34.15500 ymin,ymax (A): 6.536000 51.63100 zmin,zma (A): 5.053000 67.11000 x,y,z range (A): 41.33400 45.09500 62.05700 scale (grids/A): 2.581498 object centre (A): 13.48800 29.08350 36.08150 number of atom coordinates read : 1948 total number of charged atoms : 1816 net assigned charge : 2.000005 assigned positive charge : 290.4340 centred at (gu) : 90.19010 92.99914 93.17196 assigned negative charge : -288.4343 centred at (gu) : 90.23225 93.97045 93.20441 start vw surface at 0.1500000 fill in re-entrant regions at 0.4000000 boundary points on vw surface= 107761 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17456 grid for indexing accessible points = 1.400000 m= 50957 mr = 76199 m= 15625 mr = 41128 m= 2780 mr = 12443 m= 173 mr = 1953 m= 1 mr = 66 m= 0 mr = 0 time to grow re-entrant surface = 0.5999999 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.100000 number of dielectric boundary points 45508 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4 iepsmp to db, and charging done at 1.270000 number of grid points assigned charge 14524 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) : 1.720998 object centre at (A) : 13.48800 29.08350 36.08150 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1793520 0.3480067 midg,1,midg; midg,igrid,midg 8.2368970E-02 -0.1968597 1,midg,midg; igrid,midg,midg -4.2338114E-02 -5.3224701E-02 gauss-seidel spectral radius is 0.9991245 estimated iterations to convergence 267 setup time was (sec) 1.510000 now iterating at: 11:02:21 rms-change max change #iterations 7.322473 284.9568 at 10iterations 4.042914 114.2403 at 20iterations 2.217691 60.43491 at 30iterations 1.216493 30.55379 at 40iterations 0.6651967 15.87640 at 50iterations 0.3632686 8.737609 at 60iterations 0.1981071 4.700924 at 70iterations 0.1080924 2.654382 at 80iterations 5.9004288E-02 1.382561 at 90iterations 3.2210413E-02 0.8195038 at 100iterations 1.7530322E-02 0.4322352 at 110iterations 9.5749740E-03 0.2203957 at 120iterations 5.2212556E-03 0.1176529 at 130iterations 2.8485523E-03 7.0350647E-02 at 140iterations 1.5524653E-03 3.5992622E-02 at 150iterations 8.4902026E-04 2.0458221E-02 at 160iterations 4.6248842E-04 1.1846066E-02 at 170iterations 2.5207113E-04 5.6419373E-03 at 180iterations finished qdiffx linear iterations at : 11:02:39 total time elapsed so far: 18.85000 # loops : 180 mean,max change (kT/e) : 2.5207113E-04 5.6419373E-03 energy calculations done at 18.85000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 19.03000 DelPhi exited at 11:02:40 19.032u 0.448s 0:20.23 96.2% 0+0k 0+0io 0pf+0w