Mon Oct 10 17:07:46 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 Mon Oct 10 2011 at 17:07:46 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: 285 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2737 !!! WARNING: HIT 107 has a net charge of 0.5140 !!! WARNING: GLN 355 has a net charge of -0.2720 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: 0.6209772 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): -25.68600 31.64300 ymin,ymax (A): -10.75100 39.33900 zmin,zma (A): 4.805000 60.87400 x,y,z range (A): 57.32900 50.09000 56.06900 scale (grids/A): 0.6209772 object centre (A): 2.978500 14.29400 32.83950 number of atom coordinates read : 2737 total number of charged atoms : 2596 net assigned charge : -1.757969 assigned positive charge : 414.4553 centred at (gu) : 91.26846 90.43710 91.53372 assigned negative charge : -416.2144 centred at (gu) : 91.42244 90.28310 91.58618 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 7236 nv = 96 ne = 84 npr = 53325 no. pairs analyzed = 53325 no. exposed pairs = 3833 no. arc points = 27152 no. surface atoms = 1285 nbur = 1452 mkacc time = 0.1200000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 382 mr = 3594 m= 4 mr = 28 m= 0 mr = 0 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3000000 number of dielectric boundary points 4000 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2797 ## 295 charges are in solution ## iepsmp to db, and charging done at 0.4100000 number of grid points assigned charge 8823 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.7916539E-09 -7.1967472E-09 midg,1,midg; midg,igrid,midg -1.1517807E-08 1.0801416E-08 1,midg,midg; igrid,midg,midg 7.3631310E-09 -1.6882717E-08 gauss-seidel spectral radius is 0.9865958 estimated iterations to convergence 71 setup time was (sec) 0.5200000 now iterating at: 17:07:47 rms-change max change #iterations 0.1267100 19.44221 at 10iterations 1.1867101E-02 1.746519 at 20iterations 1.0955146E-03 0.1561371 at 30iterations 1.0235999E-04 1.7630577E-02 at 40iterations 1.0546076E-05 1.5335083E-03 at 50iterations finished qdiffx linear iterations at : 17:07:50 total time elapsed so far: 3.220000 # loops : 50 mean,max change (kT/e) : 1.0546076E-05 1.5335083E-03 energy calculations done at 3.220000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.400000 DelPhi exited at 17:07:51 3.405u 0.227s 0:04.06 89.1% 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 Mon Oct 10 2011 at 17:07:51 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: 285 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2737 !!! WARNING: HIT 107 has a net charge of 0.5140 !!! WARNING: GLN 355 has a net charge of -0.2720 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: 1.862931 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): -25.68600 31.64300 ymin,ymax (A): -10.75100 39.33900 zmin,zma (A): 4.805000 60.87400 x,y,z range (A): 57.32900 50.09000 56.06900 scale (grids/A): 1.862931 object centre (A): 2.978500 14.29400 32.83950 number of atom coordinates read : 2737 total number of charged atoms : 2596 net assigned charge : -1.757969 assigned positive charge : 414.4553 centred at (gu) : 93.80489 91.31058 94.60051 assigned negative charge : -416.2144 centred at (gu) : 94.26706 90.84914 94.75809 start vw surface at 0.1600000 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 78296 reading accessible surface arcs data from file ARCDAT no. of arc points read = 27152 grid for indexing accessible points = 1.400000 m= 26467 mr = 51616 m= 3835 mr = 18247 m= 203 mr = 2081 m= 3 mr = 58 m= 0 mr = 0 time to grow re-entrant surface = 0.2500000 no. cavity mid-points inaccessible to solvent = 401 time to turn everything in is 0.5400000 number of dielectric boundary points 36802 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 227 iepsmp to db, and charging done at 0.6600000 number of grid points assigned charge 20374 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) : 0.6209772 object centre at (A) : 2.978500 14.29400 32.83950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.7253095E-02 1.8606859E-04 midg,1,midg; midg,igrid,midg -2.4366938E-02 1.8020531E-02 1,midg,midg; igrid,midg,midg 3.1112542E-02 -6.6372678E-02 gauss-seidel spectral radius is 0.9986067 estimated iterations to convergence 212 setup time was (sec) 0.8200000 now iterating at: 17:07:52 rms-change max change #iterations 4.250587 186.8850 at 10iterations 1.967736 68.16303 at 20iterations 0.9101335 35.02380 at 30iterations 0.4213471 13.31935 at 40iterations 0.1958978 7.530746 at 50iterations 9.0494119E-02 2.591379 at 60iterations 4.2019770E-02 1.408035 at 70iterations 1.9434106E-02 0.6237221 at 80iterations 9.0252087E-03 0.2837245 at 90iterations 4.1916599E-03 0.1293344 at 100iterations 1.9440525E-03 6.2995911E-02 at 110iterations 9.0287457E-04 3.0776978E-02 at 120iterations finished qdiffx linear iterations at : 17:07:58 total time elapsed so far: 7.200000 # loops : 120 mean,max change (kT/e) : 9.0287457E-04 3.0776978E-02 energy calculations done at 7.200000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.380000 DelPhi exited at 17:07:59 7.383u 0.201s 0:08.00 94.7% 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 Mon Oct 10 2011 at 17:07:59 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: 285 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2737 !!! WARNING: HIT 107 has a net charge of 0.5140 !!! WARNING: GLN 355 has a net charge of -0.2720 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: 2.794397 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): -25.68600 31.64300 ymin,ymax (A): -10.75100 39.33900 zmin,zma (A): 4.805000 60.87400 x,y,z range (A): 57.32900 50.09000 56.06900 scale (grids/A): 2.794397 object centre (A): 2.978500 14.29400 32.83950 number of atom coordinates read : 2737 total number of charged atoms : 2596 net assigned charge : -1.757969 assigned positive charge : 414.4553 centred at (gu) : 95.70709 91.96581 96.90054 assigned negative charge : -416.2144 centred at (gu) : 96.40057 91.27364 97.13705 start vw surface at 0.1500000 fill in re-entrant regions at 0.4700000 boundary points on vw surface= 181087 reading accessible surface arcs data from file ARCDAT no. of arc points read = 27152 grid for indexing accessible points = 1.400000 m= 87008 mr = 126040 m= 29380 mr = 68408 m= 6591 mr = 22411 m= 885 mr = 4543 m= 38 mr = 554 m= 0 mr = 13 time to grow re-entrant surface = 0.8300000 no. cavity mid-points inaccessible to solvent = 1368 time to turn everything in is 1.420000 number of dielectric boundary points 83020 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2 iepsmp to db, and charging done at 1.570000 number of grid points assigned charge 20768 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) : 1.862931 object centre at (A) : 2.978500 14.29400 32.83950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2508053 0.1337611 midg,1,midg; midg,igrid,midg -0.2259238 0.1710231 1,midg,midg; igrid,midg,midg 0.3274365 -0.7782502 gauss-seidel spectral radius is 0.9992744 estimated iterations to convergence 293 setup time was (sec) 1.740000 now iterating at: 17:08:01 rms-change max change #iterations 10.36864 323.6595 at 10iterations 6.218232 151.6528 at 20iterations 3.683765 75.64856 at 30iterations 2.163831 52.97950 at 40iterations 1.269314 26.13276 at 50iterations 0.7398569 14.68720 at 60iterations 0.4310690 8.574059 at 70iterations 0.2506608 5.084362 at 80iterations 0.1454867 2.684231 at 90iterations 8.4168568E-02 1.687180 at 100iterations 4.8709694E-02 0.9529095 at 110iterations 2.8191222E-02 0.4962349 at 120iterations 1.6316002E-02 0.3140516 at 130iterations 9.4278110E-03 0.1727514 at 140iterations 5.4517081E-03 0.1030283 at 150iterations 3.1536154E-03 5.7632446E-02 at 160iterations 1.8201268E-03 3.5309792E-02 at 170iterations 1.0532342E-03 1.9533157E-02 at 180iterations finished qdiffx linear iterations at : 17:08:11 total time elapsed so far: 12.48000 # loops : 180 mean,max change (kT/e) : 1.0532342E-03 1.9533157E-02 energy calculations done at 12.48000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.64000 DelPhi exited at 17:08:12 12.648u 0.262s 0:13.25 97.3% 0+0k 0+0io 0pf+0w